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Novák Vanclová AM, Nef C, Füssy Z, Vancl A, Liu F, Bowler C, Dorrell RG. New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates. EMBO Rep 2024; 25:1859-1885. [PMID: 38499810 PMCID: PMC11014865 DOI: 10.1038/s44319-024-00103-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024] Open
Abstract
Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.
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Affiliation(s)
- Anna Mg Novák Vanclová
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- Institute Jacques Monod, Paris, France.
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Zoltán Füssy
- Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Adél Vancl
- Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Fuhai Liu
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Centre de Recherches Interdisciplinaires, Paris, France
- Tsinghua-UC Berkeley Shenzhen Institute, Shenzhen, China
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Richard G Dorrell
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, Sorbonne Université, Paris, France.
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Pan Y, Zhang W, Wang X, Jouhet J, Maréchal E, Liu J, Xia XQ, Hu H. Allele-dependent expression and functionality of lipid enzyme phospholipid:diacylglycerol acyltransferase affect diatom carbon storage and growth. PLANT PHYSIOLOGY 2024; 194:1024-1040. [PMID: 37930282 DOI: 10.1093/plphys/kiad581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/06/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
In the acyl-CoA-independent pathway of triacylglycerol (TAG) synthesis unique to plants, fungi, and algae, TAG formation is catalyzed by the enzyme phospholipid:diacylglycerol acyltransferase (PDAT). The unique PDAT gene of the model diatom Phaeodactylum tricornutum strain CCMP2561 boasts 47 single nucleotide variants within protein coding regions of the alleles. To deepen our understanding of TAG synthesis, we observed the allele-specific expression of PDAT by the analysis of 87 published RNA-sequencing (RNA-seq) data and experimental validation. The transcription of one of the two PDAT alleles, Allele 2, could be specifically induced by decreasing nitrogen concentrations. Overexpression of Allele 2 in P. tricornutum substantially enhanced the accumulation of TAG by 44% to 74% under nutrient stress; however, overexpression of Allele 1 resulted in little increase of TAG accumulation. Interestingly, a more serious growth inhibition was observed in the PDAT Allele 1 overexpression strains compared with Allele 2 counterparts. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that enzymes encoded by PDAT Allele 2 but not Allele 1 had TAG biosynthetic activity, and 7 N-terminal and 3 C-terminal amino acid variants between the 2 allele-encoded proteins substantially affected enzymatic activity. P. tricornutum PDAT, localized in the innermost chloroplast membrane, used monogalactosyldiacylglycerol and phosphatidylcholine as acyl donors as demonstrated by the increase of the 2 lipids in PDAT knockout lines, which indicated a common origin in evolution with green algal PDATs. Our study reveals unequal roles among allele-encoded PDATs in mediating carbon storage and growth in response to nitrogen stress and suggests an unsuspected strategy toward lipid and biomass improvement for biotechnological purposes.
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Affiliation(s)
- Yufang Pan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaofei Wang
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, Grenoble Cedex 9 38054, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, Grenoble Cedex 9 38054, France
| | - Jin Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanhua Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Huang T, Pan Y, Maréchal E, Hu H. Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:385-403. [PMID: 37733835 DOI: 10.1111/tpj.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid-enriched fraction was obtained and 2850 proteins were identified, including 92 plastid-encoded proteins, through label-free quantitative proteomic technology. Among them, 839 nuclear-encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria-encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long-chain acyl-CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four-layered-membrane plastid based on the proteomic and GFP-fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis.
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Affiliation(s)
- Teng 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
| | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, 38054, Grenoble Cedex 9, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Füssy Z, Oborník M. Complex Endosymbioses I: From Primary to Complex Plastids, Serial Endosymbiotic Events. Methods Mol Biol 2024; 2776:21-41. [PMID: 38502496 DOI: 10.1007/978-1-0716-3726-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
A considerable part of the diversity of eukaryotic phototrophs consists of algae with plastids that evolved from endosymbioses between two eukaryotes. These complex plastids are characterized by a high number of envelope membranes (more than two) and some of them contain a residual nucleus of the endosymbiotic alga called a nucleomorph. Complex plastid-bearing algae are thus chimeric cell assemblies, eukaryotic symbionts living in a eukaryotic host. In contrast, the primary plastids of the Archaeplastida (plants, green algae, red algae, and glaucophytes) possibly evolved from a single endosymbiosis with a cyanobacterium and are surrounded by two membranes. Complex plastids have been acquired several times by unrelated groups of eukaryotic heterotrophic hosts, suggesting that complex plastids are somewhat easier to obtain than primary plastids. Evidence suggests that complex plastids arose twice independently in the green lineage (euglenophytes and chlorarachniophytes) through secondary endosymbiosis, and four times in the red lineage, first through secondary endosymbiosis in cryptophytes, then by higher-order events in stramenopiles, alveolates, and haptophytes. Engulfment of primary and complex plastid-containing algae by eukaryotic hosts (secondary, tertiary, and higher-order endosymbioses) is also responsible for numerous plastid replacements in dinoflagellates. Plastid endosymbiosis is accompanied by massive gene transfer from the endosymbiont to the host nucleus and cell adaptation of both endosymbiotic partners, which is related to the trophic switch to phototrophy and loss of autonomy of the endosymbiont. Such a process is essential for the metabolic integration and division control of the endosymbiont in the host. Although photosynthesis is the main advantage of acquiring plastids, loss of photosynthesis often occurs in algae with complex plastids. This chapter summarizes the essential knowledge of the acquisition, evolution, and function of complex plastids.
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Affiliation(s)
- Zoltán Füssy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
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Richtová J, Bazalová O, Horák A, Tomčala A, Gonepogu VG, Oborník M, Doležel D. Circadian rhythms and circadian clock gene homologs of complex alga Chromera velia. FRONTIERS IN PLANT SCIENCE 2023; 14:1226027. [PMID: 38143581 PMCID: PMC10739334 DOI: 10.3389/fpls.2023.1226027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Most organisms on Earth are affected by periodic changes in their environment. The circadian clock is an endogenous device that synchronizes behavior, physiology, or biochemical processes to an approximately 24-hour cycle, allowing organisms to anticipate the periodic changes of day and night. Although circadian clocks are widespread in organisms, the actual molecular components differ remarkably among the clocks of plants, animals, fungi, and prokaryotes. Chromera velia is the closest known photosynthetic relative of apicomplexan parasites. Formation of its motile stage, zoospores, has been described as associated with the light part of the day. We examined the effects on the periodic release of the zoospores under different light conditions and investigated the influence of the spectral composition on zoosporogenesis. We performed a genomic search for homologs of known circadian clock genes. Our results demonstrate the presence of an almost 24-hour free-running cycle of zoosporogenesis. We also identified the blue light spectra as the essential compound for zoosporogenesis. Further, we developed a new and effective method for zoospore separation from the culture and estimated the average motility speed and lifespan of the C. velia zoospores. Our genomic search identified six cryptochrome-like genes, two genes possibly related to Arabidopsis thaliana CCA/LHY, whereas no homolog of an animal, cyanobacterial, or fungal circadian clock gene was found. Our results suggest that C. velia has a functional circadian clock, probably based mainly on a yet undefined mechanism.
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Affiliation(s)
- Jitka Richtová
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Parasitology, České Budějovice, Czechia
| | - Olga Bazalová
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Entomology, České Budějovice, Czechia
| | - Aleš Horák
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Parasitology, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Aleš Tomčala
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, Vodňany, Czechia
| | - Vijaya Geetha Gonepogu
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Parasitology, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Miroslav Oborník
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Parasitology, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - David Doležel
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Entomology, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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Russo MT, Rogato A, Jaubert M, Karas BJ, Falciatore A. Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology. JOURNAL OF PHYCOLOGY 2023; 59:1114-1122. [PMID: 37975560 DOI: 10.1111/jpy.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Abstract
Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.
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Affiliation(s)
- Monia T Russo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Alessandra Rogato
- Institute of Biosciences and Bioresources, National Research Council, IBBR-CNR, Naples, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marianne Jaubert
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Angela Falciatore
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
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Jiang Y, Cao T, Yang Y, Zhang H, Zhang J, Li X. A chlorophyll c synthase widely co-opted by phytoplankton. Science 2023; 382:92-98. [PMID: 37797009 DOI: 10.1126/science.adg7921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Marine and terrestrial photosynthesis exhibit a schism in the accessory chlorophyll (Chl) that complements the function of Chl a: Chl b for green plants versus Chl c for most eukaryotic phytoplankton. The enzymes that mediate Chl c biosynthesis have long remained elusive. In this work, we identified the CHLC dioxygenase (Phatr3_J43737) from the marine diatom Phaeodactylum tricornutum as the Chl c synthase. The chlc mutants lacked Chl c, instead accumulating its precursors, and exhibited growth defects. In vitro, recombinant CHLC protein converted these precursors into Chl c, thereby confirming its identity. Phylogenetic evidence demonstrates conserved use of CHLC across phyla but also the existence of distinct Chl c synthases in different algal groups. Our study addresses a long-outstanding question with implications for both contemporary and ancient marine photosynthesis.
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Affiliation(s)
- Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jingyu Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
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Gomes KM, Nunn BL, Chappell PD, Jenkins BD. Subcellular proteomics for determining iron-limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta). JOURNAL OF PHYCOLOGY 2023; 59:1085-1099. [PMID: 37615442 DOI: 10.1111/jpy.13379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Diatoms are important primary producers in the world's oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low-Fe stress-induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under low-Fe stress, diatoms alter plastid-specific processes, including components of electron transport. These physiological changes suggest changes of protein content and in protein abundances within the diatom plastid. While in silico predictions provide putative information on plastid-localized proteins, knowledge of diatom plastid proteins remains limited in comparison to well-studied model photosynthetic organisms. To address this, we employed shotgun proteomics to investigate the proteome of subcellular plastid-enriched fractions from Thalassiosira pseudonana to gain a better understanding of how the plastid proteome is remodeled in response to Fe limitation. Using mass spectrometry-based peptide identification and quantification, we analyzed T. pseudonana grown under Fe-replete and -limiting conditions. Through these analyses, we inferred the relative quantities of each protein, revealing that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle. Additionally, we observed changes in the expression of light-harvesting proteins. In silico localization predictions of proteins identified in this plastid-enriched proteome allowed for an in-depth comparison of theoretical versus observed plastid-localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.
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Affiliation(s)
- Kristofer M Gomes
- Department of Biological Sciences, University of Rhode Island, Rhode Island, Kingston, USA
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Washington, Seattle, USA
| | - P Dreux Chappell
- College of Marine Science, University of South Florida, Florida, St. Petersburg, USA
| | - Bethany D Jenkins
- Department of Cell and Molecular Biology, University of Rhode Island, Rhode Island, Kingston, USA
- Graduate School of Oceanography, University of Rhode Island, Rhode Island, Narragansett, USA
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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Kaha M, Noda M, Maeda Y, Kaneko Y, Yoshino T, Tanaka T. Characterization of oil body-associated proteins obtained from oil bodies with different sizes in oleaginous diatom Fistulifera solaris. J Biosci Bioeng 2023; 135:359-368. [PMID: 36935336 DOI: 10.1016/j.jbiosc.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 03/19/2023]
Abstract
Oil body-associated proteins from the oleaginous diatom Fistulifera solaris were identified by proteomic analysis of oil bodies of various sizes (small, middle, and large) by time-dependent culturing upon nutrient-starvation at 36, 96 and 168 h. This diatom strain has the capability to accumulate neutral lipids and triacylglycerol. Liquid chromatography-tandem mass spectrometry analysis revealed 662 proteins in all oil body sizes. Among these, 132 proteins were predicted to be localized to the endoplasmic reticulum. Seventeen proteins that exhibited a positive correlation with gene expression and the oil body size were selected as novel candidates for oil body-associated proteins. Among the 17 protein candidates, two proteins encoded by fso:g8246 and fso:g10200 were confirmed to be localized on the surface of the oil body and endoplasmic reticulum. A protein encoded by fso:g2514, which is involved in sterol biosynthesis, was also identified. This protein was likely to localize to mitochondria; however, inhibitor assays suggested that it might play a role in lipid degradation. Our work provides new insights into the proteomics of microalgae and provides a valuable strategy for boosting lipid productivity in microalgae.
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Affiliation(s)
- Marshila Kaha
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masayoshi Noda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yumika Kaneko
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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11
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Murison V, Hérault J, Schoefs B, Marchand J, Ulmann L. Bioinformatics-Based Screening Approach for the Identification and Characterization of Lipolytic Enzymes from the Marine Diatom Phaeodactylum tricornutum. Mar Drugs 2023; 21:md21020125. [PMID: 36827166 PMCID: PMC9964374 DOI: 10.3390/md21020125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Oleaginous diatoms accumulate lipids of biotechnological interest when exposed to nutrient stress conditions such as nitrogen starvation. While accumulation mechanisms are well-known and have been engineered to improve lipid production, degradation mechanisms remain poorly investigated in diatoms. Identifying lipid-degrading enzymes is the initial step to understanding the catabolic processes. In this study, an in silico screening of the genome of Phaeodactylum tricornutum led to the identification of 57 putative triacylglycerol lipases (EC 3.1.1.3) grouped in 4 families. Further analysis revealed the presence of conserved domains and catalytic residues of lipases. Physico-chemical characteristics and subcellular localization predictions highlighted that a majority of these putative proteins are hydrophilic and cytosolic, suggesting they could be recruited to lipid droplets directly from the cytosol. Among the 57 identified putative proteins, three lipases were identified as possibly involved in lipophagy due to a potential vacuolar localization. The expression of the mRNA corresponding to the 57 proteins was then searched in 3 transcriptomic datasets obtained under nitrogen starvation. Nine genes were highly regulated and were considered as encoding enzymes with a probable important function in lipid catabolism. A tertiary structure prediction of these nine candidates yielded eight functional 3D models. Among those, two downregulated enzymes, Phatr3_J54974 and Phatr3_EG00720, were highlighted as good targets for future functional genomics and purification studies to investigate their role in lipid degradation.
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Affiliation(s)
- Victor Murison
- BiOSSE, Biology of Organisms: Stress, Health, Environment, Département Génie Biologique, Institut Universitaire de Technologie, Le Mans Université, F-53020 Laval, France
| | - Josiane Hérault
- BiOSSE, Biology of Organisms: Stress, Health, Environment, Département Génie Biologique, Institut Universitaire de Technologie, Le Mans Université, F-53020 Laval, France
| | - Benoît Schoefs
- BiOSSE, Biology of Organisms: Stress, Health, Environment, UFR Sciences et Techniques, Le Mans Université, F-72085 Le Mans, France
| | - Justine Marchand
- BiOSSE, Biology of Organisms: Stress, Health, Environment, UFR Sciences et Techniques, Le Mans Université, F-72085 Le Mans, France
| | - Lionel Ulmann
- BiOSSE, Biology of Organisms: Stress, Health, Environment, Département Génie Biologique, Institut Universitaire de Technologie, Le Mans Université, F-53020 Laval, France
- Correspondence:
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12
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Cock JM. The model system Ectocarpus: Integrating functional genomics into brown algal research. JOURNAL OF PHYCOLOGY 2023; 59:4-8. [PMID: 36477437 DOI: 10.1111/jpy.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Affiliation(s)
- J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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13
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Kazamia E, Mach J, McQuaid JB, Gao X, Coale TH, Malych R, Camadro J, Lesuisse E, Allen AE, Bowler C, Sutak R. In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum. PLANT DIRECT 2022; 6:e472. [PMID: 36582220 PMCID: PMC9792268 DOI: 10.1002/pld3.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/03/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
UNLABELLED The model pennate diatom Phaeodactylum tricornutum is able to assimilate a range of iron sources. It therefore provides a platform to study different mechanisms of iron processing concomitantly in the same cell. In this study, we follow the localization of three iron starvation induced proteins (ISIPs) in vivo, driven by their native promoters and tagged by fluorophores in an engineered line of P. tricornutum. We find that the localization patterns of ISIPs are dynamic and variable depending on the overall iron status of the cell and the source of iron it is exposed to. Notwithstanding, a shared destination of the three ISIPs both under ferric iron and siderophore-bound iron supplementation is a globular compartment in the vicinity of the chloroplast. In a proteomic analysis, we identify that the cell engages endocytosis machinery involved in the vesicular trafficking as a response to siderophore molecules, even when these are not bound to iron. Our results suggest that there may be a direct vesicle traffic connection between the diatom cell membrane and the periplastidial compartment (PPC) that co-opts clathrin-mediated endocytosis and the "cytoplasm to vacuole" (Cvt) pathway, for proteins involved in iron assimilation. Proteomics data are available via ProteomeXchange with identifier PXD021172. HIGHLIGHT The marine diatom P. tricornutum engages a vesicular network to traffic siderophores and phytotransferrin from the cell membrane directly to a putative iron processing site in the vicinity of the chloroplast.
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Affiliation(s)
- Elena Kazamia
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Jan Mach
- Department of Parasitology, Faculty of ScienceCharles UniversityVestecCzech Republic
| | - Jeffrey B. McQuaid
- Microbial and Environmental GenomicsJ. Craig Venter InstituteLa JollaCaliforniaUSA
- The Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
| | - Xia Gao
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Tyler H. Coale
- Scripps Institution of Oceanography, Integrative Oceanography DivisionUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Ronald Malych
- Department of Parasitology, Faculty of ScienceCharles UniversityVestecCzech Republic
| | | | | | - Andrew E. Allen
- Microbial and Environmental GenomicsJ. Craig Venter InstituteLa JollaCaliforniaUSA
- Scripps Institution of Oceanography, Integrative Oceanography DivisionUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Robert Sutak
- Department of Parasitology, Faculty of ScienceCharles UniversityVestecCzech Republic
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14
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Tilney CL, Hubbard KA. Expression of nuclear-encoded, haptophyte-derived ftsH genes support extremely rapid PSII repair and high-light photoacclimation in Karenia brevis (Dinophyceae). HARMFUL ALGAE 2022; 118:102295. [PMID: 36195421 DOI: 10.1016/j.hal.2022.102295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
Karenia brevis, a neurotoxic dinoflagellate that produces brevetoxins, is endemic to the Gulf of Mexico and can grow at high irradiances typical of surface waters found there. To build upon a growing number of studies addressing high-light tolerance in K. brevis, specific photobiology and molecular mechanisms underlying this capacity were evaluated in culture. Since photosystem II (PSII) repair cycle activity can be crucial to high light tolerance in plants and algae, the present study assessed this capacity in K. brevis and characterized the ftsH-like genes which are fundamental to this process. Compared with cultures grown in low-light, cultures grown in high-light showed a 65-fold increase in PSII photoinactivation, a ∼50-fold increase in PSII repair, enhanced nonphotochemical quenching (NPQ), and depressed Fv/Fm. Repair rates were among the fastest reported in phytoplankton. Publicly available K. brevis transcriptomes (MMETSP) were queried for ftsH-like sequences and refined with additional sequencing from two K. brevis strains. The genes were phylogenetically related to haptophyte orthologs, implicating acquisition during tertiary endosymbiosis. RT-qPCR of three of the four ftsH-like homologs revealed that poly-A tails predominated in all homologs, and that the most highly expressed homolog had a 5' splice leader and amino-acid motifs characteristic of chloroplast targeting, indicating nuclear encoding for this plastid-targeted gene. High-light cultures showed a ∼1.5-fold upregulation in mRNA expression of the thylakoid-associated genes. Overall, in conjunction with NPQ mechanisms, rapid PSII repair mediated by a haptophyte-derived ftsH prevents chronic photoinhibition in K. brevis. Our findings continue to build the case that high-light photobiology-supported by the acquisition and maintenance of tertiary endosymbiotic genes-is critical to the success of K. brevis in the Gulf of Mexico.
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Affiliation(s)
- Charles L Tilney
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA; Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, Québec, G5M 1L7, Canada.
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA
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15
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Liu S, Storti M, Finazzi G, Bowler C, Dorrell RG. A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum. FRONTIERS IN PLANT SCIENCE 2022; 13:950467. [PMID: 36212359 PMCID: PMC9546453 DOI: 10.3389/fpls.2022.950467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.
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Affiliation(s)
- Shun Liu
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Mattia Storti
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
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16
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You Y, Sun X, Ma M, He J, Li L, Porto FW, Lin S. Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton. Nat Commun 2022; 13:4022. [PMID: 35821503 PMCID: PMC9276738 DOI: 10.1038/s41467-022-31802-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/05/2022] [Indexed: 11/30/2022] Open
Abstract
Trypsin is best known as a digestive enzyme in animals, but remains unexplored in phytoplankton, the major primary producers in the ocean. Here we report the prevalence of trypsin genes in global ocean phytoplankton and significant influences of environmental nitrogen (N) and phosphorus (P) on their expression. Using CRISPR/Cas9 mediated-knockout and overexpression analyses, we further reveal that a trypsin in Phaeodactylum tricornutum (PtTryp2) functions to repress N acquisition, but its expression decreases under N-deficiency to promote N acquisition. On the contrary, PtTryp2 promotes phosphate uptake per se, and its expression increases under P-deficiency to further reinforce P acquisition. Furthermore, PtTryp2 knockout led to amplitude magnification of the nitrate and phosphate uptake ‘seesaw’, whereas PtTryp2 overexpression dampened it, linking PtTryp2 to stabilizing N:P stoichiometry. Our data demonstrate that PtTryp2 is a coordinate regulator of N:P stoichiometric homeostasis. The study opens a window for deciphering how phytoplankton adapt to nutrient-variable marine environments. Using CRISPR-Cas9 mediated-knockout and overexpression analyses, this study shows that a trypsin in the diatom Phaeodactylum tricornutum promotes phosphorus uptake and inhibits nitrogen uptake but its expression is downregulated under nitrogen stress and upregulated under phosphorus stress. Together, the findings suggest this trypsin is a coordinate regulator of nutrient homeostasis.
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Affiliation(s)
- Yanchun You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiamin He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Felipe Wendt Porto
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China. .,Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA.
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17
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Pinseel E, Nakov T, Van den Berge K, Downey KM, Judy KJ, Kourtchenko O, Kremp A, Ruck EC, Sjöqvist C, Töpel M, Godhe A, Alverson AJ. Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. THE ISME JOURNAL 2022; 16:1776-1787. [PMID: 35383290 PMCID: PMC9213524 DOI: 10.1038/s41396-022-01230-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 05/01/2023]
Abstract
The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.
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Affiliation(s)
- Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA, USA
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anke Kremp
- Leibniz-Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Conny Sjöqvist
- Environmental and Marine Biology, Åbo Akademi University, Åbo, Finland
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
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18
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Maeda Y, Tanaka T. Molecular Insights into Lipoxygenases in Diatoms Based on Structure Prediction: a Pioneering Study on Lipoxygenases Found in Pseudo-nitzschia arenysensis and Fragilariopsis cylindrus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:468-479. [PMID: 35397048 DOI: 10.1007/s10126-022-10120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Diatoms produce a variety of oxylipins which are oxygenated polyunsaturated fatty acids and are involved in chemical defense and intercellular communication, among other roles. Although the chemistry of diatom oxylipins has long been studied, the enzymes involved in their production, in particular lipoxygenase (LOX), which catalyzes the initial reaction of the synthesis, have not been discovered in diatom genomes. Recently, diatom LOXs were found in two species, Pseudo-nitzschia arenysensis (PaLOX) and Fragilariopsis cylindrus (FcLOX); however, the enzymology of these LOXs is largely unknown. In this review article, we discuss the potential functions of the diatom LOXs based on previously reported structures of LOXs derived from various organisms other than diatoms. Since the structures of PaLOX and FcLOX have not yet been solved, we discussed their functions, such as regio- and stereospecificities, on the basis of their structures predicted using a computational tool based on deep learning technology. Both diatom LOXs were predicted to conserve common core domains with relatively wide substrate-binding pockets. The stereo-determinant residues in PaLOX and FcLOX suggest S specificity. We assume that the highly conserved common core domain can be a clue to reveal unidentified lox genes from the accumulated diatom genome information with the aid of high-throughput structure prediction tools and structure-based alignment tools in the near future.
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Affiliation(s)
- Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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19
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Rozenberg A, Kaczmarczyk I, Matzov D, Vierock J, Nagata T, Sugiura M, Katayama K, Kawasaki Y, Konno M, Nagasaka Y, Aoyama M, Das I, Pahima E, Church J, Adam S, Borin VA, Chazan A, Augustin S, Wietek J, Dine J, Peleg Y, Kawanabe A, Fujiwara Y, Yizhar O, Sheves M, Schapiro I, Furutani Y, Kandori H, Inoue K, Hegemann P, Béjà O, Shalev-Benami M. Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels. Nat Struct Mol Biol 2022; 29:592-603. [PMID: 35710843 DOI: 10.1038/s41594-022-00783-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/27/2022] [Indexed: 11/09/2022]
Abstract
Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel.
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Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Igor Kaczmarczyk
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Yuma Kawasaki
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yujiro Nagasaka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Mako Aoyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Efrat Pahima
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Church
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariel Chazan
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Sandra Augustin
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Wietek
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Julien Dine
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Akira Kawanabe
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, Miki-cho, Japan
| | - Yuichiro Fujiwara
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, Miki-cho, Japan
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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20
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Skeffington AW, Gentzel M, Ohara A, Milentyev A, Heintze C, Böttcher L, Görlich S, Shevchenko A, Poulsen N, Kröger N. Shedding light on silica biomineralization by comparative analysis of the silica-associated proteomes from three diatom species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1700-1716. [PMID: 35403318 DOI: 10.1111/tpj.15765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/17/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica biomineralization proteins have been identified. Therefore, it is currently unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species-specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica, and Cyclotella cryptica) by complete demineralization of the cell walls. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis of the extracts identified 92 proteins that we name 'soluble silicome proteins' (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In-depth bioinformatics analyses revealed that SSPs could be grouped into distinct classes based on short unconventional sequence motifs whose functions are yet unknown. The results from the in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall.
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Affiliation(s)
- Alastair W Skeffington
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Marc Gentzel
- Center for Cellular and Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Andre Ohara
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Alexander Milentyev
- Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Christoph Heintze
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Lorenz Böttcher
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Stefan Görlich
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Nils Kröger
- B CUBE Center for Molecular Bioengineering, TU Dresden, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, TU Dresden, 01062, Dresden, Germany
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21
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. SCIENCE ADVANCES 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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22
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Seydoux C, Storti M, Giovagnetti V, Matuszyńska A, Guglielmino E, Zhao X, Giustini C, Pan Y, Blommaert L, Angulo J, Ruban AV, Hu H, Bailleul B, Courtois F, Allorent G, Finazzi G. Impaired photoprotection in Phaeodactylum tricornutum KEA3 mutants reveals the proton regulatory circuit of diatoms light acclimation. THE NEW PHYTOLOGIST 2022; 234:578-591. [PMID: 35092009 PMCID: PMC9306478 DOI: 10.1111/nph.18003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Diatoms are successful phytoplankton clades able to acclimate to changing environmental conditions, including e.g. variable light intensity. Diatoms are outstanding at dissipating light energy exceeding the maximum photosynthetic electron transfer (PET) capacity via the nonphotochemical quenching (NPQ) process. While the molecular effectors of NPQ as well as the involvement of the proton motive force (PMF) in its regulation are known, the regulators of the PET/PMF relationship remain unidentified in diatoms. We generated mutants of the H+ /K+ antiporter KEA3 in the model diatom Phaeodactylum tricornutum. Loss of KEA3 activity affects the PET/PMF coupling and NPQ responses at the onset of illumination, during transients and in steady-state conditions. Thus, this antiporter is a main regulator of the PET/PMF coupling. Consistent with this conclusion, a parsimonious model including only two free components, KEA3 and the diadinoxanthin de-epoxidase, describes most of the feedback loops between PET and NPQ. This simple regulatory system allows for efficient responses to fast (minutes) or slow (e.g. diel) changes in light environment, thanks to the presence of a regulatory calcium ion (Ca2+ )-binding domain in KEA3 modulating its activity. This circuit is likely tuned by the NPQ-effector proteins, LHCXs, providing diatoms with the required flexibility to thrive in different ocean provinces.
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Affiliation(s)
- Claire Seydoux
- CNRSCEAINRAEIRIGLPCVUniversité Grenoble AlpesGrenoble38000France
| | - Mattia Storti
- CNRSCEAINRAEIRIGLPCVUniversité Grenoble AlpesGrenoble38000France
| | - Vasco Giovagnetti
- Departement of BiochemistryQueen Mary University of LondonMile End RoadLondonE14NSUK
| | - Anna Matuszyńska
- Computational Life ScienceDepartment of BiologyRWTH Aachen UniversityWorringer Weg 1Aachen52074Germany
| | | | - Xue Zhao
- CNRSCEAINRAEIRIGLPCVUniversité Grenoble AlpesGrenoble38000France
| | - Cécile Giustini
- CNRSCEAINRAEIRIGLPCVUniversité Grenoble AlpesGrenoble38000France
| | - Yufang Pan
- Key Laboratory of Algal BiologyInstitute of HydrobiologyChinese Academy of SciencesWuhan430072China
| | - Lander Blommaert
- Laboratory of Chloroplast Biology and Light Sensing in MicroalgaeInstitut de Biologie Physico ChimiqueCNRSSorbonne UniversitéParis75005France
| | - Jhoanell Angulo
- CNRSCEAINRAEIRIGLPCVUniversité Grenoble AlpesGrenoble38000France
| | - Alexander V. Ruban
- Departement of BiochemistryQueen Mary University of LondonMile End RoadLondonE14NSUK
| | - Hanhua Hu
- Key Laboratory of Algal BiologyInstitute of HydrobiologyChinese Academy of SciencesWuhan430072China
| | - Benjamin Bailleul
- Laboratory of Chloroplast Biology and Light Sensing in MicroalgaeInstitut de Biologie Physico ChimiqueCNRSSorbonne UniversitéParis75005France
| | | | | | - Giovanni Finazzi
- CNRSCEAINRAEIRIGLPCVUniversité Grenoble AlpesGrenoble38000France
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23
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Azuma T, Pánek T, Tice AK, Kayama M, Kobayashi M, Miyashita H, Suzaki T, Yabuki A, Brown MW, Kamikawa R. An enigmatic stramenopile sheds light on early evolution in Ochrophyta plastid organellogenesis. Mol Biol Evol 2022; 39:6555011. [PMID: 35348760 PMCID: PMC9004409 DOI: 10.1093/molbev/msac065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host–plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.
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Affiliation(s)
- Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | | | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | | | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology, Japan
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa oiwake cho, Sakyo ku, Kyoto, Kyoto, Japan
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24
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Cho A, Tikhonenkov DV, Hehenberger E, Karnkowska A, Mylnikov AP, Keeling PJ. Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles. Mol Phylogenet Evol 2022; 171:107468. [DOI: 10.1016/j.ympev.2022.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
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25
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Sabatino V, Orefice I, Marotta P, Ambrosino L, Chiusano ML, d'Ippolito G, Romano G, Fontana A, Ferrante MI. Silencing of a Pseudo-nitzschia arenysensis lipoxygenase transcript leads to reduced oxylipin production and impaired growth. THE NEW PHYTOLOGIST 2022; 233:809-822. [PMID: 34533849 DOI: 10.1111/nph.17739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Because of their importance as chemical mediators, the presence of a rich and varied family of lipoxygenase (LOX) products, collectively named oxylipins, has been investigated thoroughly in diatoms, and the involvement of these products in important processes such as bloom regulation has been postulated. Nevertheless, little information is available on the enzymes and pathways operating in these protists. Exploiting transcriptome data, we identified and characterized a LOX gene, PaLOX, in Pseudo-nitzschia arenysensis, a marine diatom known to produce different species of oxylipins by stereo- and regio-selective oxidation of eicosapentaenoic acid (EPA) at C12 and C15. PaLOX RNA interference correlated with a decrease of the lipid-peroxidizing activity and oxylipin synthesis, as well as with a reduction of growth of P. arenysensis. In addition, sequence analysis and structure models of the C-terminal part of the predicted protein closely fitted with the data for established LOXs from other organisms. The presence in the genome of a single LOX gene, whose downregulation impairs both 12- and 15-oxylipins synthesis, together with the in silico 3D protein modelling suggest that PaLOX encodes for a 12/15S-LOX with a dual specificity, and provides additional support to the correlation between cell growth and oxylipin biosynthesis in diatoms.
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Affiliation(s)
- Valeria Sabatino
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Ida Orefice
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Pina Marotta
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Luca Ambrosino
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Maria Luisa Chiusano
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
- Department of Agriculture, Università degli Studi di Napoli Federico II, Portici, 80055, Italy
| | - Giuliana d'Ippolito
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli - Naples, I-80078, Italy
| | - Giovanna Romano
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Angelo Fontana
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli - Naples, I-80078, Italy
- Laboratory of Bio-Organic Chemistry and Chemical Biology, Dipartimento di Biologia, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, Napoli, 80126, Italy
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26
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Hippmann AA, Schuback N, Moon K, McCrow JP, Allen AE, Foster LF, Green BR, Maldonado MT. Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom. PLANT DIRECT 2022; 6:e376. [PMID: 35079683 PMCID: PMC8777261 DOI: 10.1002/pld3.376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 05/19/2023]
Abstract
Diatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earth's photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria, and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood. We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light harvesting in the oceanic diatom Thalassiosira oceanica (Hippmann et al., 2017, 10.1371/journal.pone.0181753). In order to gain a better understanding of the overall metabolic changes that help alleviate the stress of Cu limitation, we have further analyzed the comprehensive proteomic datasets generated in that study to identify differentially expressed proteins involved in carbon, nitrogen, and oxidative stress-related metabolic pathways. Metabolic pathway analysis showed integrated responses to Cu limitation. The upregulation of ferredoxin (Fdx) was correlated with upregulation of plastidial Fdx-dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis, thus suggesting an integration of nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential expression of glycolytic isoenzymes located in the chloroplast and mitochondria may enable them to channel both excess electrons and/or ATP between these compartments. An additional support for chloroplast-mitochondrial cross-talk is the increased expression of chloroplast and mitochondrial proteins involved in the proposed malate shunt under Cu limitation.
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Affiliation(s)
- Anna A. Hippmann
- Department of Earth Ocean and Atmospheric ScienceUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Nina Schuback
- Department of Earth Ocean and Atmospheric ScienceUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Kyung‐Mee Moon
- Biochemistry and Molecular BiologyMichael Smith LaboratoriesVancouverBritish ColumbiaCanada
| | - John P. McCrow
- Microbial and Environmental GenomicsJ. Craig Venter InstituteLa JollaCAUSA
| | - Andrew E. Allen
- Microbial and Environmental GenomicsJ. Craig Venter InstituteLa JollaCAUSA
- Scripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Leonard F. Foster
- Biochemistry and Molecular BiologyMichael Smith LaboratoriesVancouverBritish ColumbiaCanada
| | - Beverley R. Green
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Maria T. Maldonado
- Department of Earth Ocean and Atmospheric ScienceUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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27
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Passi A, Tibocha-Bonilla JD, Kumar M, Tec-Campos D, Zengler K, Zuniga C. Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data. Metabolites 2021; 12:14. [PMID: 35050136 PMCID: PMC8778254 DOI: 10.3390/metabo12010014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.
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Affiliation(s)
- Anurag Passi
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
| | - Juan D. Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA;
| | - Manish Kumar
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
| | - Diego Tec-Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán, Merida 97203, Yucatan, Mexico
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0403, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
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28
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Buck JM, Kroth PG, Lepetit B. Identification of sequence motifs in Lhcx proteins that confer qE-based photoprotection in the diatom Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1721-1734. [PMID: 34651379 DOI: 10.1111/tpj.15539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/11/2021] [Indexed: 05/08/2023]
Abstract
Photosynthetic organisms in nature often experience light fluctuations. While low light conditions limit the energy uptake by algae, light absorption exceeding the maximal rate of photosynthesis may go along with enhanced formation of potentially toxic reactive oxygen species. To preempt high light-induced photodamage, photosynthetic organisms evolved numerous photoprotective mechanisms. Among these, energy-dependent fluorescence quenching (qE) provides a rapid mechanism to dissipate thermally the excessively absorbed energy. Diatoms thrive in all aquatic environments and thus belong to the most important primary producers on earth. qE in diatoms is provided by a concerted action of Lhcx proteins and the xanthophyll cycle pigment diatoxanthin. While the exact Lhcx activation mechanism of diatom qE is unknown, two lumen-exposed acidic amino acids within Lhcx proteins were proposed to function as regulatory switches upon light-induced lumenal acidification. By introducing a modified Lhcx1 lacking these amino acids into a Phaeodactylum tricornutum Lhcx1-null qE knockout line, we demonstrate that qE is unaffected by these two amino acids. Based on sequence comparisons with Lhcx4, being incapable of providing qE, we perform domain swap experiments of Lhcx4 with Lhcx1 and identify two peptide motifs involved in conferring qE. Within one of these motifs, we identify a tryptophan residue with a major influence on qE establishment. This tryptophan residue is located in close proximity to the diadinoxanthin/diatoxanthin-binding site based on the recently revealed diatom Lhc crystal structure. Our findings provide a structural explanation for the intimate link of Lhcx and diatoxanthin in providing qE in diatoms.
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Affiliation(s)
- Jochen M Buck
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, 78457, Germany
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Onyshchenko A, Roberts WR, Ruck EC, Lewis JA, Alverson AJ. The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis. THE NEW PHYTOLOGIST 2021; 232:1750-1764. [PMID: 34379807 PMCID: PMC9292941 DOI: 10.1111/nph.17673] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/03/2021] [Indexed: 05/05/2023]
Abstract
Although most of the tens of thousands of diatom species are photoautotrophs, a small number of heterotrophic species no longer photosynthesize. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia Nitz4, to determine how carbon metabolism was altered in the wake of this trophic shift. Nitzschia Nitz4 has retained its plastid and plastid genome, but changes associated with the transition to heterotrophy were cellular-wide and included losses of photosynthesis-related genes from the nuclear and plastid genomes, elimination of isoprenoid biosynthesis in the plastid, and remodeling of mitochondrial glycolysis to maximize adenosine triphosphte (ATP) yield. The genome contains a β-ketoadipate pathway that may allow Nitzschia Nitz4 to metabolize lignin-derived compounds. Diatom plastids lack an oxidative pentose phosphate pathway (oPPP), leaving photosynthesis as the primary source of NADPH to support essential biosynthetic pathways in the plastid and, by extension, limiting available sources of NADPH in nonphotosynthetic plastids. The genome revealed similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids and highlighted the ancestral absence of a plastid oPPP as a potentially important constraint on loss of photosynthesis, a hypothesis supported by the higher frequency of transitions to parasitism or heterotrophy in lineages that have a plastid oPPP.
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Affiliation(s)
- Anastasiia Onyshchenko
- Department of Biological SciencesUniversity of Arkansas1 University of ArkansasFayettevilleAR72701USA
| | - Wade R. Roberts
- Department of Biological SciencesUniversity of Arkansas1 University of ArkansasFayettevilleAR72701USA
| | - Elizabeth C. Ruck
- Department of Biological SciencesUniversity of Arkansas1 University of ArkansasFayettevilleAR72701USA
| | - Jeffrey A. Lewis
- Department of Biological SciencesUniversity of Arkansas1 University of ArkansasFayettevilleAR72701USA
| | - Andrew J. Alverson
- Department of Biological SciencesUniversity of Arkansas1 University of ArkansasFayettevilleAR72701USA
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Oliver A, Podell S, Pinowska A, Traller JC, Smith SR, McClure R, Beliaev A, Bohutskyi P, Hill EA, Rabines A, Zheng H, Allen LZ, Kuo A, Grigoriev IV, Allen AE, Hazlebeck D, Allen EE. Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Sci Rep 2021; 11:15592. [PMID: 34341414 PMCID: PMC8329260 DOI: 10.1038/s41598-021-95106-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/14/2021] [Indexed: 01/13/2023] Open
Abstract
A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.
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Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
| | | | | | - Sarah R Smith
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alex Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Pavlo Bohutskyi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Eric A Hill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ariel Rabines
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Hong Zheng
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Andrew E Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Eric E Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. .,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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Moulin SLY, Beyly-Adriano A, Cuiné S, Blangy S, Légeret B, Floriani M, Burlacot A, Sorigué D, Samire PP, Li-Beisson Y, Peltier G, Beisson F. Fatty acid photodecarboxylase is an ancient photoenzyme that forms hydrocarbons in the thylakoids of algae. PLANT PHYSIOLOGY 2021; 186:1455-1472. [PMID: 33856460 PMCID: PMC8260138 DOI: 10.1093/plphys/kiab168] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/07/2021] [Indexed: 05/11/2023]
Abstract
Fatty acid photodecarboxylase (FAP) is one of the few enzymes that require light for their catalytic cycle (photoenzymes). FAP was first identified in the microalga Chlorella variabilis NC64A, and belongs to an algae-specific subgroup of the glucose-methanol-choline oxidoreductase family. While the FAP from C. variabilis and its Chlamydomonas reinhardtii homolog CrFAP have demonstrated in vitro activities, their activities and physiological functions have not been studied in vivo. Furthermore, the conservation of FAP activity beyond green microalgae remains hypothetical. Here, using a C. reinhardtii FAP knockout line (fap), we showed that CrFAP is responsible for the formation of 7-heptadecene, the only hydrocarbon of this alga. We further showed that CrFAP was predominantly membrane-associated and that >90% of 7-heptadecene was recovered in the thylakoid fraction. In the fap mutant, photosynthetic activity was not affected under standard growth conditions, but was reduced after cold acclimation when light intensity varied. A phylogenetic analysis that included sequences from Tara Ocean identified almost 200 putative FAPs and indicated that FAP was acquired early after primary endosymbiosis. Within Bikonta, FAP was retained in secondary photosynthetic endosymbiosis lineages but absent from those that lost the plastid. Characterization of recombinant FAPs from various algal genera (Nannochloropsis, Ectocarpus, Galdieria, Chondrus) provided experimental evidence that FAP photochemical activity was present in red and brown algae, and was not limited to unicellular species. These results thus indicate that FAP was conserved during the evolution of most algal lineages where photosynthesis was retained, and suggest that its function is linked to photosynthetic membranes.
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Affiliation(s)
- Solène L Y Moulin
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
- Present address: Stanford University, 279 Campus Dr, Stanford, CA 94305
| | - Audrey Beyly-Adriano
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Stéphan Cuiné
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Stéphanie Blangy
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Bertrand Légeret
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Magali Floriani
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV/SRTE/LECO, Cadarache, 13108 Saint-Paul-Lez-Durance, France
| | - Adrien Burlacot
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
- Present address: Howard Hughes Medical Institute, Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA
| | - Damien Sorigué
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Poutoum-Palakiyem Samire
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Yonghua Li-Beisson
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Gilles Peltier
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Fred Beisson
- CEA, CNRS, Aix-Marseille University, Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM), UMR7265, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
- Author for communication:
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Bilcke G, Osuna-Cruz CM, Santana Silva M, Poulsen N, D'hondt S, Bulankova P, Vyverman W, De Veylder L, Vandepoele K. Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:315-336. [PMID: 33901335 DOI: 10.1111/tpj.15291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23 328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24 h. Phylostratigraphic analysis found that rhythmic genes are enriched in highly conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall-associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for the study of diurnal regulation in photosynthetic eukaryotes.
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Affiliation(s)
- Gust Bilcke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, 9000, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, 9000, Belgium
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
| | - Marta Santana Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, Technical University of Dresden, Tatzberg 41, Dresden, 01307, Germany
| | - Sofie D'hondt
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, 9000, Belgium
| | - Petra Bulankova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Wim Vyverman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, 9000, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
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Using Diatom and Apicomplexan Models to Study the Heme Pathway of Chromera velia. Int J Mol Sci 2021; 22:ijms22126495. [PMID: 34204357 PMCID: PMC8233740 DOI: 10.3390/ijms22126495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 12/20/2022] Open
Abstract
Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway’s enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.
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Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. Proc Natl Acad Sci U S A 2021; 118:2009974118. [PMID: 33419955 DOI: 10.1073/pnas.2009974118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.
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35
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Smith R, Jouhet J, Gandini C, Nekrasov V, Marechal E, Napier JA, Sayanova O. Plastidial acyl carrier protein Δ9-desaturase modulates eicosapentaenoic acid biosynthesis and triacylglycerol accumulation in Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1247-1259. [PMID: 33725374 PMCID: PMC8360179 DOI: 10.1111/tpj.15231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
The unicellular marine diatom Phaeodactylum tricornutum accumulates up to 35% eicosapentaenoic acid (EPA, 20:5n3) and has been used as a model organism to study long chain polyunsaturated fatty acids (LC-PUFA) biosynthesis due to an excellent annotated genome sequence and established transformation system. In P. tricornutum, the majority of EPA accumulates in polar lipids, particularly in galactolipids such as mono- and di-galactosyldiacylglycerol. LC-PUFA biosynthesis is considered to start from oleic acid (18:1n9). EPA can be synthesized via a series of desaturation and elongation steps occurring at the endoplasmic reticulum and newly synthesized EPA is then imported into the plastids for incorporation into galactolipids via an unknown route. The basis for the flux of EPA is fundamental to understanding LC-PUFA biosynthesis in diatoms. We used P. tricornutum to study acyl modifying activities, upstream of 18:1n9, on subsequent LC-PUFA biosynthesis. We identified the gene coding for the plastidial acyl carrier protein Δ9-desaturase, a key enzyme in fatty acid modification and analyzed the impact of overexpression and knock out of this gene on glycerolipid metabolism. This revealed a previously unknown role of this soluble desaturase in EPA synthesis and production of triacylglycerol. This study provides further insight into the distinctive nature of lipid metabolism in the marine diatom P. tricornutum and suggests additional approaches for tailoring oil composition in microalgae.
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Affiliation(s)
- Richard Smith
- Department of Plant SciencesRothamsted ResearchHarpendenHertsAL5 2JQUK
- Present address:
AlgenuityEden LaboratoryBroadmead RoadStewartbyMK43 9NDUK
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale Univ. Grenoble AlpesCNRSIRAECEAIRIGGrenoble38000France
| | - Chiara Gandini
- Department of Plant SciencesRothamsted ResearchHarpendenHertsAL5 2JQUK
- Present address:
Open Bioeconomy LaboratoryDepartment of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Vladimir Nekrasov
- Department of Plant SciencesRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Eric Marechal
- Laboratoire de Physiologie Cellulaire et Végétale Univ. Grenoble AlpesCNRSIRAECEAIRIGGrenoble38000France
| | | | - Olga Sayanova
- Department of Plant SciencesRothamsted ResearchHarpendenHertsAL5 2JQUK
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36
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Kong L, Price NM. Transcriptomes of an oceanic diatom reveal the initial and final stages of acclimation to copper deficiency. Environ Microbiol 2021; 24:951-966. [PMID: 34029435 DOI: 10.1111/1462-2920.15609] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022]
Abstract
Copper (Cu) concentration is greatly reduced in the open sea so that phytoplankton must adjust their uptake systems and acclimate to sustain growth. Acclimation to low Cu involves changes to the photosynthetic apparatus and specific biochemical reactions that use Cu, but little is known how Cu affects cellular metabolic networks. Here we report results of whole transcriptome analysis of a plastocyanin-containing diatom, Thalassiosira oceanica 1005, during its initial stages of acclimation and after long-term adaptation in Cu-deficient seawater. Gene expression profiles, used to identify Cu-regulated metabolic pathways, show downregulation of anabolic and energy-yielding reactions in Cu-limited cells. These include the light reactions of photosynthesis, carbon fixation, nitrogen assimilation and glycolysis. Reduction of these pathways is consistent with reduced growth requirements for C and N caused by slower rates of photosynthetic electron transport. Upregulation of oxidative stress defence systems persists in adapted cells, suggesting cellular damage by increased reactive oxygen species (ROS) occurs even after acclimation. Copper deficiency also alters fatty acid metabolism, possibly in response to an increase in lipid peroxidation and membrane damage driven by ROS. During the initial stages of Cu-limitation the majority of differentially regulated genes are associated with photosynthetic metabolism, highlighting the chloroplast as the primary target of low Cu availability. The results provide insights into the mechanisms of acclimation and adaptation of T. oceanica to Cu deficiency.
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Affiliation(s)
- Liangliang Kong
- Department of Biology, McGill University, Montréal, QC, Canada.,College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Neil M Price
- Department of Biology, McGill University, Montréal, QC, Canada
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Avilan L, Lebrun R, Puppo C, Citerne S, Cuiné S, Li‐Beisson Y, Menand B, Field B, Gontero B. ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2021; 230:1517-1532. [PMID: 33595847 PMCID: PMC8252717 DOI: 10.1111/nph.17286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/08/2021] [Indexed: 05/08/2023]
Abstract
Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta- and tetraphosphate ((p)ppGpp). In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here, we studied the function of ppGpp in the diatom Phaeodactylum tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using nontargeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.
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Affiliation(s)
- Luisana Avilan
- CNRSBIPUMR 7281IMM FR 3479Aix Marseille Univ31 Chemin Joseph AiguierMarseille13009France
- Centre for Enzyme InnovationSchool of Biological SciencesInstitute of Biological and Biomedical SciencesUniversity of PortsmouthPortsmouthPO1 2DYUK
| | - Regine Lebrun
- Plate‐forme ProtéomiqueMarseille Protéomique (MaP)IMM FR 3479, 31 Chemin Joseph AiguierMarseille13009France
| | - Carine Puppo
- CNRSBIPUMR 7281IMM FR 3479Aix Marseille Univ31 Chemin Joseph AiguierMarseille13009France
| | - Sylvie Citerne
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Stephane Cuiné
- CEA, CNRS, UMR7265 BIAMCEA CadaracheAix‐Marseille UnivSaint‐Paul‐lez Durance13108France
| | - Yonghua Li‐Beisson
- CEA, CNRS, UMR7265 BIAMCEA CadaracheAix‐Marseille UnivSaint‐Paul‐lez Durance13108France
| | - Benoît Menand
- CEA, CNRS, UMR7265 BIAMAix‐Marseille UnivMarseille13009France
| | - Ben Field
- CEA, CNRS, UMR7265 BIAMAix‐Marseille UnivMarseille13009France
| | - Brigitte Gontero
- CNRSBIPUMR 7281IMM FR 3479Aix Marseille Univ31 Chemin Joseph AiguierMarseille13009France
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Vancaester E, Depuydt T, Osuna-Cruz CM, Vandepoele K. Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms. Mol Biol Evol 2021; 37:3243-3257. [PMID: 32918458 DOI: 10.1093/molbev/msaa182] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.
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Affiliation(s)
- Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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Teng L, Han W, Fan X, Zhang X, Xu D, Wang Y, Rahman S, Pellegrini M, Mock T, Ye N. Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica. PLANT MOLECULAR BIOLOGY 2021; 105:611-623. [PMID: 33528753 DOI: 10.1007/s11103-020-01113-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/30/2020] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the chloroplast genome because it is predicted to possess a plastid transit peptide.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Life Science, Dezhou University, Dezhou, 253023, China
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Sadequr Rahman
- Tropical Medicine and Biology Platform and School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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40
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Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance. PLoS One 2021; 16:e0241960. [PMID: 33760840 PMCID: PMC7990286 DOI: 10.1371/journal.pone.0241960] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/03/2021] [Indexed: 12/22/2022] Open
Abstract
Diatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the composition of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model of Thalassiosira pseudonana strain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5–200 μmol photons m-2 s-1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatom Thalassiosira pseudonana provides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.
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41
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Gao X, Bowler C, Kazamia E. Iron metabolism strategies in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2165-2180. [PMID: 33693565 PMCID: PMC7966952 DOI: 10.1093/jxb/eraa575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 03/03/2021] [Indexed: 05/28/2023]
Abstract
Diatoms are one of the most successful group of photosynthetic eukaryotes in the contemporary ocean. They are ubiquitously distributed and are the most abundant primary producers in polar waters. Equally remarkable is their ability to tolerate iron deprivation and respond to periodic iron fertilization. Despite their relatively large cell sizes, diatoms tolerate iron limitation and frequently dominate iron-stimulated phytoplankton blooms, both natural and artificial. Here, we review the main iron use strategies of diatoms, including their ability to assimilate and store a range of iron sources, and the adaptations of their photosynthetic machinery and architecture to iron deprivation. Our synthesis relies on published literature and is complemented by a search of 82 diatom transcriptomes, including information collected from seven representatives of the most abundant diatom genera in the world's oceans.
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Affiliation(s)
- Xia Gao
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Elena Kazamia
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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42
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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43
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Cheng H, Shao Z, Lu C, Duan D. Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. BMC PLANT BIOLOGY 2021; 21:87. [PMID: 33568068 PMCID: PMC7874618 DOI: 10.1186/s12870-021-02849-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. RESULTS Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. CONCLUSIONS Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.
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Affiliation(s)
- Haomiao Cheng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
| | - Chang Lu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co Ltd, Qingdao, 266400, P. R. China.
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44
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Grigoriev IV, Hayes RD, Calhoun S, Kamel B, Wang A, Ahrendt S, Dusheyko S, Nikitin R, Mondo SJ, Salamov A, Shabalov I, Kuo A. PhycoCosm, a comparative algal genomics resource. Nucleic Acids Res 2021; 49:D1004-D1011. [PMID: 33104790 PMCID: PMC7779022 DOI: 10.1093/nar/gkaa898] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.
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Affiliation(s)
- Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard D Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bishoy Kamel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alice Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Dusheyko
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Roman Nikitin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor Shabalov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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45
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Liu B, Sun Y, Hang W, Wang X, Xue J, Ma R, Jia X, Li R. Characterization of a Novel Acyl-ACP Δ 9 Desaturase Gene Responsible for Palmitoleic Acid Accumulation in a Diatom Phaeodactylum tricornutum. Front Microbiol 2020; 11:584589. [PMID: 33391203 PMCID: PMC7772203 DOI: 10.3389/fmicb.2020.584589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
Palmitoleic acid (16:1Δ9) possesses a double bond at the seventh carbon atom from methyl end of the acyl chain and belongs to unusual ω-7 monounsaturated fatty acids with broad applications in food, pharmaceuticals, cosmetics, biofuel, and other industries. This high-value fatty acid accumulates up to >40% of total lipid in the marine diatom Phaeodactylum tricornutum. The present study was conducted to determine the key gene responsible for 16:1Δ9 biosynthesis in this unicellular alga. A new full-length cDNA and genomic DNA encoding acyl-ACP Δ9 desaturase (PtAAD) were isolated from P. tricornutum cells. Expression levels of PtAAD gene under normal and stress culture conditions were both positively correlated with 16:1Δ9 accumulation, implying its potential role for fatty acid determination. Functional complementation assay of a yeast mutant strain BY4839 evidenced that PtAAD could restore the synthesis of unsaturated fatty acid, especially generating high levels of 16:1Δ9. Further transient expression of PtAAD gene in Nicotiana benthamiana leaves was accompanied by the accumulation of 16:1Δ9, which was absent from control groups. Three-dimensional structure modeling studies showed that functional domain of PtAAD contained three variant amino acids (F160, A223, and L156), which may narrow the space shape of substrate-binding cavity to ensure the entry of 16:0-ACP. Consistent with this prediction, the mutated version of PtAAD gene (F160L, A223T, and L156M) in N. benthamiana systems failed to accumulate 16:1Δ9, but increased levels of 18:1Δ9. Taken together, PtAAD exhibits a strong enzymatic activity and substrate preference for 16:0-ACP, acting as the key player for high biosynthesis and accumulation of 16:1Δ9 in this alga. These findings provide new insights for better understanding the palmitoleic acid and oil biosynthetic mechanism in P. tricornutum, indicating that PtAAD gene may have practical applications for enriching palmitoleic acid and oil yield in other commercial oleaginous algae and crops.
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Affiliation(s)
- Baoling Liu
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China.,College of Plant Protection, Shanxi Agricultural University, Jinzhong, China
| | - Yan Sun
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Wei Hang
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Xiaodan Wang
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Jinai Xue
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Ruiyan Ma
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyun Jia
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Runzhi Li
- College of Agriculture, Shanxi Agricultural University, Jinzhong, China
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46
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Nakov T, Judy KJ, Downey KM, Ruck EC, Alverson AJ. Transcriptional Response of Osmolyte Synthetic Pathways and Membrane Transporters in a Euryhaline Diatom During Long-term Acclimation to a Salinity Gradient. JOURNAL OF PHYCOLOGY 2020; 56:1712-1728. [PMID: 32750159 DOI: 10.1111/jpy.13061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/10/2020] [Indexed: 05/15/2023]
Abstract
How diatoms respond to fluctuations in osmotic pressure is important from both ecological and applied perspectives. It is well known that osmotic stress affects photosynthesis and can result in the accumulation of compounds desirable in pharmaceutical and alternative fuel industries. Gene expression responses to osmotic stress have been studied in short-term trials, but it is unclear whether the same mechanisms are recruited during long-term acclimation. We used RNA-seq to study the genome-wide transcription patterns in the euryhaline diatom, Cyclotella cryptica, following long-term acclimation to salinity that spanned the natural range of fresh to oceanic water. Long-term acclimated C. cryptica exhibited induced synthesis or repressed degradation of the osmolytes glycine betaine, taurine and dimethylsulfoniopropionate (DMSP). Although changes in proline concentration is one of the main responses in short-term osmotic stress, we did not detect a transcriptional change in proline biosynthetic pathways in our long-term experiment. Expression of membrane transporters showed a general tendency for increased import of potassium and export of sodium, consistent with the electrochemical gradients and dependence on co-transported molecules. Our results show substantial between-genotype differences in growth and gene expression reaction norms and suggest that the regulation of proline synthesis important in short-term osmotic stress might not be maintained in long-term acclimation. Further examination using time-course gene expression experiments, metabolomics and genetic validation of gene functions would reinforce patterns inferred from RNA-seq data.
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Affiliation(s)
- Teofil Nakov
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
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47
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Dittami SM, Corre E, Brillet-Guéguen L, Lipinska AP, Pontoizeau N, Aite M, Avia K, Caron C, Cho CH, Collén J, Cormier A, Delage L, Doubleau S, Frioux C, Gobet A, González-Navarrete I, Groisillier A, Hervé C, Jollivet D, KleinJan H, Leblanc C, Liu X, Marie D, Markov GV, Minoche AE, Monsoor M, Pericard P, Perrineau MM, Peters AF, Siegel A, Siméon A, Trottier C, Yoon HS, Himmelbauer H, Boyen C, Tonon T. The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga. Mar Genomics 2020; 52:100740. [PMID: 31937506 DOI: 10.1016/j.margen.2020.100740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/01/2020] [Indexed: 11/20/2022]
Abstract
Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France.
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Noé Pontoizeau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Meziane Aite
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Komlan Avia
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Université de Strasbourg, INRA, SVQV UMR-A 1131, F-68000 Colmar, France
| | - Christophe Caron
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Sylvie Doubleau
- IRD, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | | | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Irene González-Navarrete
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Agnès Groisillier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Cécile Hervé
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Hetty KleinJan
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Xi Liu
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - André E Minoche
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Misharl Monsoor
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Pierre Pericard
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Marie-Mathilde Perrineau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, United Kingdom
| | | | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Amandine Siméon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Camille Trottier
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France; Laboratory of Digital Sciences of Nantes (LS2N) - University of Nantes, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190 Vienna, Austria
| | - Catherine Boyen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Thierry Tonon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
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Tomčala A, Michálek J, Schneedorferová I, Füssy Z, Gruber A, Vancová M, Oborník M. Fatty Acid Biosynthesis in Chromerids. Biomolecules 2020; 10:E1102. [PMID: 32722284 PMCID: PMC7464705 DOI: 10.3390/biom10081102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Fatty acids are essential components of biological membranes, important for the maintenance of cellular structures, especially in organisms with complex life cycles like protozoan parasites. Apicomplexans are obligate parasites responsible for various deadly diseases of humans and livestock. We analyzed the fatty acids produced by the closest phototrophic relatives of parasitic apicomplexans, the chromerids Chromera velia and Vitrella brassicaformis, and investigated the genes coding for enzymes involved in fatty acids biosynthesis in chromerids, in comparison to their parasitic relatives. Based on evidence from genomic and metabolomic data, we propose a model of fatty acid synthesis in chromerids: the plastid-localized FAS-II pathway is responsible for the de novo synthesis of fatty acids reaching the maximum length of 18 carbon units. Short saturated fatty acids (C14:0-C18:0) originate from the plastid are then elongated and desaturated in the cytosol and the endoplasmic reticulum. We identified giant FAS I-like multi-modular enzymes in both chromerids, which seem to be involved in polyketide synthesis and fatty acid elongation. This full-scale description of the biosynthesis of fatty acids and their derivatives provides important insights into the reductive evolutionary transition of a phototropic algal ancestor to obligate parasites.
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Affiliation(s)
- Aleš Tomčala
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Fisheries and Protection of Waters, CENAKVA, Institute of Aquaculture and Protection of Waters, University of South Bohemia, Husova 458/102, 370 05 České Budějovice, Czech Republic
| | - Jan Michálek
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Ivana Schneedorferová
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
| | - Ansgar Gruber
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
| | - Marie Vancová
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
| | - Miroslav Oborník
- Biology Centre CAS, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (A.T.); (J.M.); (I.S.); (Z.F.); (A.G.); (M.V.)
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
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49
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Alanine to serine substitutions drive thermal adaptation in a psychrophilic diatom cytochrome c 6. J Biol Inorg Chem 2020; 25:489-500. [PMID: 32219554 DOI: 10.1007/s00775-020-01777-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
In this study, we investigate the thermodynamic mechanisms by which electron transfer proteins adapt to environmental temperature by directly comparing the redox properties and folding stability of a psychrophilic cytochrome c and a mesophilic homolog. Our model system consists of two cytochrome c6 proteins from diatoms: one adapted specifically to polar environments, the other adapted generally to surface ocean environments. Direct electrochemistry shows that the midpoint potential for the mesophilic homolog is slightly higher at all temperatures measured. Cytochrome c6 from the psychrophilic diatom unfolds with a melting temperature 10.4 °C lower than the homologous mesophilic cytochrome c6. Changes in free energy upon unfolding are identical, within error, for the psychrophilic and mesophilic protein; however, the chemical unfolding transition of the psychrophilic cytochrome c6 is more cooperative than for the mesophilic cytochrome c6. Substituting alanine residues found in the mesophile with serine found in corresponding positions of the psychrophile demonstrates that burial of the polar serine both decreases the thermal stability and decreases the midpoint potential. The mutagenesis data, combined with differences in the m-value of chemical denaturation, suggest that differences in solvent accessibility of the hydrophobic core underlie the adaptation of cytochrome c6 to differing environmental temperature.
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50
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Fabris M, George J, Kuzhiumparambil U, Lawson CA, Jaramillo-Madrid AC, Abbriano RM, Vickers CE, Ralph P. Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids. ACS Synth Biol 2020; 9:598-612. [PMID: 32032487 DOI: 10.1021/acssynbio.9b00455] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.
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Affiliation(s)
- Michele Fabris
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
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