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Fields O, Hammond MJ, Xu X, O'Neill EC. Advances in euglenoid genomics: unravelling the fascinating biology of a complex clade. Trends Genet 2024:S0168-9525(24)00173-2. [PMID: 39147613 DOI: 10.1016/j.tig.2024.07.007] [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: 06/27/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024]
Abstract
Euglenids have long been studied due to their unique physiology and versatile metabolism, providing underpinnings for much of our understanding of photosynthesis and biochemistry, and a growing opportunity in biotechnology. Until recently there has been a lack of genetic studies due to their large and complex genomes, but recently new technologies have begun to unveil their genetic capabilities. Whilst much research has focused on the model organism Euglena gracilis, other members of the euglenids have now started to receive due attention. Currently only poor nuclear genome assemblies of E. gracilis and Rhabdomonas costata are available, but there are many more plastid genome sequences and an increasing number of transcriptomes. As more assemblies become available, there are great opportunities to understand the fundamental biology of these organisms and to exploit them for biotechnology.
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Affiliation(s)
- Oskar Fields
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; These authors contributed equally
| | - Michael J Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic; These authors contributed equally
| | - Xiao Xu
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; These authors contributed equally
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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2
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Nagamine S, Oishi R, Ueda M, Sakamoto T, Nakazawa M. Genome editing-based mutagenesis stably modifies composition of wax esters synthesized by Euglena gracilis under anaerobic conditions. BIORESOURCE TECHNOLOGY 2024:131255. [PMID: 39127356 DOI: 10.1016/j.biortech.2024.131255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Microalgal oil production represents a promising renewable biofuel source. Metabolic engineering can enhance its utility, transforming it into an improved biofuel and expanding its applications as a feedstock for commodity chemicals, thereby increasing their value in biorefineries. This study focused on anaerobic wax ester production by the microalga Euglena gracilis, aiming to develop stable mutant strains with altered wax ester profiles through genome editing. Two enzymes in the fatty acid beta-oxidation pathway involved in wax ester production were targeted-3-ketoacyl-CoA thiolase and acyl-CoA dehydrogenase-using clustered regularly interspaced short palindromic repeats/Cas9. The results revealed one genetic mutation that lengthened and three that shortened the distribution of wax ester compositions compared to the wild-type (WT). The triple-KO mutant, combining mutations that shorten wax ester chains, produced wax esters with acyl chains two carbons shorter than WT. This study established a methodology to stably modify wax ester composition in E. gracilis.
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Affiliation(s)
- Sakura Nagamine
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Japan
| | - Rikuto Oishi
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Japan
| | - Mitsuhiro Ueda
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Japan
| | - Tatsuji Sakamoto
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Japan
| | - Masami Nakazawa
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Japan.
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Raihan MT, Ishikawa T. Biochemical and Functional Profiling of Thioredoxin-Dependent Cytosolic GPX-like Proteins in Euglena gracilis. Biomolecules 2024; 14:765. [PMID: 39062479 PMCID: PMC11275057 DOI: 10.3390/biom14070765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/28/2024] Open
Abstract
Unlike plants and animals, the phytoflagellate Euglena gracilis lacks catalase and contains a non-selenocysteine glutathione peroxidase-like protein (EgGPXL), two peroxiredoxins (EgPrx1 and EgPrx4), and one ascorbate peroxidase in the cytosol to maintain reactive oxygen species (ROS) homeostasis. In the present study, the full-length cDNA of three cytosolic EgGPXLs was obtained and further characterized biochemically and functionally. These EgGPXLs used thioredoxin instead of glutathione as an electron donor to reduce the levels of H2O2 and t-BOOH. The specific peroxidase activities of these enzymes for H2O2 and t-BOOH were 1.3 to 4.9 and 0.79 to 3.5 µmol/min/mg protein, respectively. Cytosolic EgGPXLs and EgPrx1/EgPrx4 were silenced simultaneously to investigate the synergistic effects of these genes on the physiological function of E. gracilis. The suppression of cytosolic EgGPXL genes was unable to induce any critical phenomena in Euglena under normal (100 μmol photons m-2 s-1) and high-light conditions (350 μmol photons m-2 s-1) at both autotrophic and heterotrophic states. Unexpectedly, the suppression of EgGPXL genes was able to rescue the EgPrx1/EgPrx4-silenced cell line from a critical situation. This study explored the potential resilience of Euglena to ROS, even with restriction of the cytosolic antioxidant system, indicating the involvement of some compensatory mechanisms.
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Affiliation(s)
- Md Topu Raihan
- The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori 680-8550, Japan;
| | - Takahiro Ishikawa
- The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori 680-8550, Japan;
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Japan
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Field MC. Ras superfamily GTPases and signal transduction in Euglena gracilis. Protist 2024; 175:126017. [PMID: 38295671 DOI: 10.1016/j.protis.2024.126017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024]
Abstract
Biological complexity is challenging to define, but can be considered through one or more features, including overall genome size, number of genes, morphological features, multicellularity, number of life cycle stages and the ability to adapt to different environments. Euglena gracilis meets several of these criteria, with a large genome of ∼38,000 protein coding genes and a considerable ability to survive under many different conditions, some of which can be described as challenging or harsh. Potential molecular exemplars of complexity tying these aspects together are signalling pathways, including GTPases, kinases and ubiquitylation, which increase the functionality of the gene-encoded proteome manyfold. Each of these examples can modulate both protein activity and gene expression. To address the connection between genome size and complexity I have undertaken a brief, and somewhat qualitative, survey of the small ras-like GTPase superfamily of E. gracilis. Unexpectedly, apart from Rab-GTPases which control intracellular transport and organelle identify, the size of the GTPase cohort is modest, and, for example, has not scaled with gene number when compared to the close relatives, trypanosomatids. I suggest that understanding the functions of this protein family will be vital to uncovering the complexity of E. gracilis biology.
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Affiliation(s)
- Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK; Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
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5
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Shen A, Qian A, Ma S, Xiang S, Ouyang L, Shao L. Transcriptome analysis of the bloom-forming dinoflagellate Prorocentrum donghaiense exposed to Ginkgo biloba leaf extract, with an emphasis on photosynthesis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:18579-18592. [PMID: 38351353 DOI: 10.1007/s11356-024-32409-8] [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: 08/03/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Ginkgo biloba leaf extract (GBE) can effectively treat bloom-forming freshwater algae. However, there is limited information about the underlying suppression mechanism of the marine bloom-forming Prorocentrum donghaiense-the most dominant algal bloom species in the East China Sea. We investigated the effect of GBE on P. donghaiense in terms of its response to photosynthesis at the molecular/omic level. In total, 93,743 unigenes were annotated using six functional databases. Furthermore, 67,203 differentially expressed genes (DEGs) were identified in algae treated with 1.8 g∙L-1 GBE. Among these DEGs, we identified the genes involved in photosynthesis. PsbA, PsbB and PsbD in photosystem II, PsaA in photosystem I, and PetB and PetD in the cytochrome b6/f complex were downregulated. Other related genes, such as PsaC, PsaE, and PsaF in photosystem I; PetA in the cytochrome b6/f complex; and atpA, atpD, atpH, atpG, and atpE in the F-type H+-ATPase were upregulated. These results suggest that the structure and activity of the complexes were destroyed by GBE, thereby inhibiting the electron flow between the primary and secondary quinone electron acceptors, primary quinone electron acceptor, and oxygen-evolving complex in the PSII complex, and interrupting the electron flow between PSII and PSI, ultimately leading to a decline in algal cell photosynthesis. These findings provide a basis for understanding the molecular mechanisms underlying P. donghaiense exposure to GBE and a theoretical basis for the prevention and control of harmful algal blooms.
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Affiliation(s)
- Anglu Shen
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
| | - Aixue Qian
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Shengwei Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, People's Republic of China
| | - Shu Xiang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Longling Ouyang
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Beijing, People's Republic of China
- East China Sea Fisheries Research Institute, Shanghai, 200090, China
| | - Liu Shao
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
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Nakazawa M, Inui H. Understanding wax ester synthesis in Euglena gracilis: Insights into mitochondrial anaerobic respiration. Protist 2023; 174:125996. [PMID: 38041972 DOI: 10.1016/j.protis.2023.125996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/31/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
Euglena gracilis, photosynthetic protist, has a unique ability to generate wax esters in the absence of oxygen, employing a distinctive fatty acid synthesis mechanism. Through comprehensive inhibitor assays and gene-silencing techniques, our research clearly emphasized the indispensable role of the mitochondrial anaerobic respiratory chain in this biosynthesis. We identified acyl-CoA dehydrogenase, electron transfer flavoprotein (ETF), and rhodoquinone (RQ) as central molecular components in the pathway. These findings strongly indicated a potential reversal of beta-oxidation occurring within mitochondria for fatty acid production in anaerobic conditions. Furthermore, our analysis revealed the pivotal function of nicotinamide nucleotide transhydrogenase (NNT) in efficiently managing the NADPH/NAD+ conversion essential for sustaining anaerobic metabolism. This review outlines our key findings and provides a comprehensive understanding of the molecular mechanisms that enable E. gracilis to produce wax ester anaerobically.
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Affiliation(s)
- Masami Nakazawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan.
| | - Hiroshi Inui
- Department of Applied Biological Chemistry, Faculty of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan; Department of Health and Nutrition, Otemae University, Osaka, Japan
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Gao P, Zhong Y, Sun C. Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1740-1748. [PMID: 37705346 PMCID: PMC10679874 DOI: 10.3724/abbs.2023143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/28/2023] [Indexed: 09/15/2023] Open
Abstract
Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5' terminal outron and spliced leader (SL) RNA, remains elusive. Here, we identify 166 spliceosomal protein genes and two snRNA genes from E. gracilis by performing bioinformatics analysis from a combination of next-generation and full-length transcriptomic RNA sequencing (RNAseq) data as well as draft genomic data. With the spliceosomal proteins we identified in hand, the insensitivity of E. gracilis to some splicing modulators is revealed at the sequence level. The prevalence of SL RNA-mediated trans-splicing is estimated to be more than 70% from our full-length RNAseq data. Finally, the splicing proteomes between E. gracilis and its three evolutionary cousins within the same Excavata group are compared. In conclusion, our study characterizes the spliceosomal components in E. gracilis and provides the molecular basis for further exploration of underlying splicing mechanisms.
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Affiliation(s)
- Pingwei Gao
- />Scientific Research CenterChengdu Medical CollegeChengdu610500China
| | - Yujie Zhong
- />Scientific Research CenterChengdu Medical CollegeChengdu610500China
| | - Chengfu Sun
- />Scientific Research CenterChengdu Medical CollegeChengdu610500China
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Kim S, Im H, Yu J, Kim K, Kim M, Lee T. Biofuel production from Euglena: Current status and techno-economic perspectives. BIORESOURCE TECHNOLOGY 2023; 371:128582. [PMID: 36610485 DOI: 10.1016/j.biortech.2023.128582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Sustainable aviation fuels (SAFs) can contribute reduce greenhouse gas emissions compared to conventional fuel. With the increasing SAFs demand, various generations of resources have been shifted from the 1st generation (oil crops), the 2nd generation (agricultural waste), to the 3rd generation (microalgae). Microalgae are the most suitable feedstock for jet biofuel production than other resources because of their productivity and capability to capture carbon dioxide. However, microalgae-based biofuel has a limitation of high freezing point. Recently, a jet biofuel derived from Euglena wax ester has been paying attention due to its low freezing point. Challenges still remain to enhance production yields in both upstream and downstream processes. Studies on downstream processes as well as techno-economic analysis on biofuel production using Euglena are highly limited to date. Economic aspects for the biofuel production will be ensured via valorization of industrial byproducts such as food wastes.
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Affiliation(s)
- Sunah Kim
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Hyungjoon Im
- Institute for Environment and Energy, Pusan National University, Busan 46241, Republic of Korea
| | - Jaecheul Yu
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea; Institute for Environment and Energy, Pusan National University, Busan 46241, Republic of Korea
| | - Keunho Kim
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Minjeong Kim
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Taeho Lee
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
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Inwongwan S, Pekkoh J, Pumas C, Sattayawat P. Metabolic network reconstruction of Euglena gracilis: Current state, challenges, and applications. Front Microbiol 2023; 14:1143770. [PMID: 36937274 PMCID: PMC10018167 DOI: 10.3389/fmicb.2023.1143770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
A metabolic model, representing all biochemical reactions in a cell, is a prerequisite for several approaches in systems biology used to explore the metabolic phenotype of an organism. Despite the use of Euglena in diverse industrial applications and as a biological model, there is limited understanding of its metabolic network capacity. The unavailability of the completed genome data and the highly complex evolution of Euglena are significant obstacles to the reconstruction and analysis of its genome-scale metabolic model. In this mini-review, we discuss the current state and challenges of metabolic network reconstruction in Euglena gracilis. We have collated and present the available relevant data for the metabolic network reconstruction of E. gracilis, which could be used to improve the quality of the metabolic model of E. gracilis. Furthermore, we deliver the potential applications of the model in metabolic engineering. Altogether, it is supposed that this mini-review would facilitate the investigation of metabolic networks in Euglena and further lay out a direction for model-assisted metabolic engineering.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jeeraporn Pekkoh
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Chayakorn Pumas
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pachara Sattayawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- *Correspondence: Pachara Sattayawat,
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Calloni RD, Muchut RJ, Garay AS, Arias DG, Iglesias AA, Guerrero SA. Functional and structural characterization of an endo-β-1,3-glucanase from Euglena gracilis. Biochimie 2022; 208:117-128. [PMID: 36586565 DOI: 10.1016/j.biochi.2022.12.016] [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: 09/14/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Endo-β-1,3-glucanases from several organisms have attracted much attention in recent years because of their capability for in vitro degrading β-1,3-glucan as a critical step for both biofuels production and short-chain oligosaccharides synthesis. In this study, we biochemically characterized a putative endo-β-1,3-glucanase (EgrGH64) belonging to the family GH64 from the single-cell protist Euglena gracilis. The gene coding for the enzyme was heterologously expressed in a prokaryotic expression system supplemented with 3% (v/v) ethanol to optimize the recombinant protein right folding. Thus, the produced enzyme was highly purified by immobilized-metal affinity and gel filtration chromatography. The enzymatic study demonstrated that EgrGH64 could hydrolyze laminarin (KM 23.5 mg ml-1,kcat 1.20 s-1) and also, but with less enzymatic efficiency, paramylon (KM 20.2 mg ml-1,kcat 0.23 ml mg-1 s-1). The major product of the hydrolysis of both substrates was laminaripentaose. The enzyme could also use ramified β-glucan from the baker's yeast cell wall as a substrate (KM 2.10 mg ml-1, kcat 0.88 ml mg-1 s-1). This latter result, combined with interfacial kinetic analysis evidenced a protein's greater efficiency for the yeast polysaccharide, and a higher number of hydrolysis sites in the β-1,3/β-1,6-glucan. Concurrently, the enzyme efficiently inhibited the fungal growth when used at 1.0 mg/mL (15.4 μM). This study contributes to assigning a correct function and determining the enzymatic specificity of EgrGH64, which emerges as a relevant biotechnological tool for processing β-glucans.
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Affiliation(s)
- Rodrigo D Calloni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Robertino J Muchut
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina
| | - Alberto S Garay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Diego G Arias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
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Tanaka Y, Goto K, Jun L, Nishino K, Ogawa T, Maruta T, Ishikawa T. Identification of glucanases and phosphorylases involved in hypoxic paramylon degradation in Euglena gracilis. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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He J, Du M, Chen Y, Liu Y, Zhang J(K, Fu W, Lei A, Wang J. Fatty Acid Accumulations and Transcriptome Analyses Under Different Treatments in a Model Microalga Euglena gracilis. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.884451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With the continuous growth of the world’s population and the increasing development of industrialization, the demand for energy by human beings has been expanding, resulting in an increasingly severe energy crisis. Microalgae are considered the most potential alternatives to traditional fossil fuels due to their many advantages, like fast growth rate, strong carbon sequestration capacity, and low growth environment requirements. Euglena can use carbon sources such as glucose, ethanol, and others for heterotrophic growth. Moreover, Euglena is highly adaptable to the environment and has a high tolerance to various environmental stresses, such as salinity, heavy metals, antibiotics, etc. Different treatments of Euglena cells could affect their growth and the accumulation of bioactive substances, especially fatty acids. To expand the industrial application of Euglena as a potential biodiesel candidate, we determine the physiological responses of Euglena against environmental stresses (antibiotics, heavy metals, salinity) or carbon resources (glucose and ethanol), and evaluate the potential for higher quality and yield of fatty acid with a high growth rate. Adding glucose into the culture media increases cell biomass and fatty acid production with high-quality biodiesel characters. The transcriptome analysis helped explore the possible regulation and biosynthesis of fatty acids under different treatments and exploited in the improvement of biodiesel production. This study provides insights for further improvement and various culture treatments for Euglena-based biodiesel and jet fuels.
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Tamaki S, Sato R, Koshitsuka Y, Asahina M, Kodama Y, Ishikawa T, Shinomura T. Suppression of the Lycopene Cyclase Gene Causes Downregulation of Ascorbate Peroxidase Activity and Decreased Glutathione Pool Size, Leading to H 2O 2 Accumulation in Euglena gracilis. FRONTIERS IN PLANT SCIENCE 2021; 12:786208. [PMID: 34925426 PMCID: PMC8678482 DOI: 10.3389/fpls.2021.786208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/11/2021] [Indexed: 06/02/2023]
Abstract
Carotenoids are photosynthetic pigments and hydrophobic antioxidants that are necessary for the survival of photosynthetic organisms, including the microalga Euglena gracilis. In the present study, we identified an uncharacterized gene encoding the E. gracilis β-carotene synthetic enzyme lycopene cyclase (EgLCY) and discovered a relationship between EgLCY-mediated carotenoid synthesis and the reactive oxygen species (ROS) scavenging system ascorbate-glutathione cycle. The EgLCY cDNA sequence was obtained via homology searching E. gracilis transcriptome data. An enzyme assay using Escherichia coli demonstrated that EgLCY converts lycopene to β-carotene. E. gracilis treated with EgLCY double-stranded RNA (dsRNA) produced colorless cells with hypertrophic appearance, inhibited growth, and marked decrease in carotenoid and chlorophyll content, suggesting that EgLCY is essential for the synthesis of β-carotene and downstream carotenoids, which are abundant and physiologically functional. In EgLCY dsRNA-treated cells, the ascorbate-glutathione cycle, composed of ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDAR), and glutathione reductase (GR), was unusually modulated; APX and GR activities significantly decreased, whereas DHAR and MDAR activities increased. Ascorbate content was significantly increased and glutathione content significantly decreased in EgLCY dsRNA-treated cells and was correlated with their recycling enzyme activities. Fluorescent imaging demonstrated that EgLCY dsRNA-treated cells accumulated higher levels of H2O2 compared to wild-type cells. Taken together, this study revealed that EgLCY-mediated synthesis of β-carotene and downstream carotenoid species upregulates APX activity and increases glutathione pool size for H2O2 scavenging. Our study suggests a possible relationship between carotenoid synthesis and the ascorbate-glutathione cycle for ROS scavenging in E. gracilis.
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Affiliation(s)
- Shun Tamaki
- Department of Biosciences, School of Science and Engineering, Teikyo University, Tochigi, Japan
| | - Ryosuke Sato
- Department of Biosciences, School of Science and Engineering, Teikyo University, Tochigi, Japan
| | - Yuki Koshitsuka
- Department of Biosciences, School of Science and Engineering, Teikyo University, Tochigi, Japan
| | - Masashi Asahina
- Department of Biosciences, School of Science and Engineering, Teikyo University, Tochigi, Japan
- Advanced Instrumental Analysis Center, Teikyo University, Tochigi, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
| | - Tomoko Shinomura
- Department of Biosciences, School of Science and Engineering, Teikyo University, Tochigi, Japan
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Nakazawa M, Takahashi M, Hayashi R, Matsubara Y, Kashiyama Y, Ueda M, Inui H, Sakamoto T. NADPH-to-NADH conversion by mitochondrial transhydrogenase is indispensable for sustaining anaerobic metabolism in Euglena gracilis. FEBS Lett 2021; 595:2922-2930. [PMID: 34738635 DOI: 10.1002/1873-3468.14221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/06/2022]
Abstract
Euglena gracilis produces ATP in the anaerobic mitochondria with concomitant wax ester formation, and NADH is essential for ATP formation and fatty acid synthesis in the mitochondria. This study demonstrated that mitochondrial cofactor conversion by nicotinamide nucleotide transhydrogenase (NNT), converting NADPH/NAD+ to NADP+ /NADH, is indispensable for sustaining anaerobic metabolism. Silencing of NNT genes significantly decreased wax ester production and cellular viability during anaerobiosis but had no such marked effects under aerobic conditions. An analogous phenotype was observed in the silencing of the gene encoding a mitochondrial NADP+ -dependent malic enzyme. These results suggest that the reducing equivalents produced in glycolysis are shuttled to the mitochondria as malate, where cytosolic NAD+ regeneration is coupled with mitochondrial NADPH generation.
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Affiliation(s)
- Masami Nakazawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Mutsuki Takahashi
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Ryuta Hayashi
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Yuki Matsubara
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Mitsuhiro Ueda
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Hiroshi Inui
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan.,Department of Health and Nutrition, Otemae University, Osaka, Japan
| | - Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
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15
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Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Sci Rep 2021; 11:13070. [PMID: 34158556 PMCID: PMC8219788 DOI: 10.1038/s41598-021-92174-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.
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16
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Cordoba J, Perez E, Van Vlierberghe M, Bertrand AR, Lupo V, Cardol P, Baurain D. De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. Genes (Basel) 2021; 12:842. [PMID: 34072576 PMCID: PMC8227486 DOI: 10.3390/genes12060842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.
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Affiliation(s)
- Javier Cordoba
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Emilie Perez
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Mick Van Vlierberghe
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Amandine R. Bertrand
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Valérian Lupo
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Pierre Cardol
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Denis Baurain
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
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17
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Muchut RJ, Calloni RD, Arias DG, Arce AL, Iglesias AA, Guerrero SA. Elucidating carbohydrate metabolism in Euglena gracilis: Reverse genetics-based evaluation of genes coding for enzymes linked to paramylon accumulation. Biochimie 2021; 184:125-131. [PMID: 33675853 DOI: 10.1016/j.biochi.2021.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/24/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Euglena gracilis is a eukaryotic single-celled and photosynthetic organism grouped under the kingdom Protista. This phytoflagellate can accumulate the carbon photoassimilate as a linear β-1,3-glucan chain called paramylon. This storage polysaccharide can undergo degradation to provide glucose units to obtain ATP and reducing power both in aerobic and anaerobic growth conditions. Our group has recently characterized an essential enzyme for accumulating the polysaccharide, the UDP-glucose pyrophosphorylase (Biochimie vol 154, 2018, 176-186), which catalyzes the synthesis of UDP-glucose (the substrate for paramylon synthase). Additionally, the identification of nucleotide sequences coding for putative UDP-sugar pyrophosphorylases suggests the occurrence of an alternative source of UDP-glucose. In this study, we demonstrate the active involvement of both pyrophosphorylases in paramylon accumulation. Using techniques of single and combined knockdown of transcripts coding for these proteins, we evidenced a substantial decrease in the polysaccharide synthesis from 39 ± 7 μg/106 cells determined in the control at day 21st of growth. Thus, the paramylon accumulation in Euglena gracilis cells decreased by 60% and 30% after a single knockdown of the expression of genes coding for UDP-glucose pyrophosphorylase and UDP-sugar pyrophosphorylase, respectively. Besides, the combined knockdown of both genes resulted in a ca. 65% reduction in the level of the storage polysaccharide. Our findings indicate the existence of a physiological dependence between paramylon accumulation and the partitioning of sugar nucleotides into other metabolic routes, including the Leloir pathway's functionality in Euglena gracilis.
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Affiliation(s)
- Robertino J Muchut
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Rodrigo D Calloni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Diego G Arias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL), Argentina, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Argentina.
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18
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Tomečková L, Tomčala A, Oborník M, Hampl V. The Lipid Composition of Euglena gracilis Middle Plastid Membrane Resembles That of Primary Plastid Envelopes. PLANT PHYSIOLOGY 2020; 184:2052-2063. [PMID: 33008834 PMCID: PMC7723114 DOI: 10.1104/pp.20.00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Euglena gracilis is a photosynthetic flagellate possessing chlorophyte-derived secondary plastids that are enclosed by only three enveloping membranes, unlike most secondary plastids, which are surrounded by four membranes. It has generally been assumed that the two innermost E. gracilis plastid envelopes originated from the primary plastid, while the outermost is of eukaryotic origin. It was suggested that nucleus-encoded plastid proteins pass through the middle and innermost plastid envelopes of E. gracilis by machinery homologous to the translocons of outer and inner chloroplast membranes, respectively. Although recent genomic, transcriptomic, and proteomic data proved the presence of a reduced form of the translocon of inner membrane, they failed to identify any outer-membrane translocon homologs, which raised the question of the origin of E. gracilis's middle plastid envelope. Here, we compared the lipid composition of whole cells of the pigmented E. gracilis strain Z and two bleached mutants that lack detectable plastid structures, W10BSmL and WgmZOflL We determined the lipid composition of E. gracilis strain Z mitochondria and plastids, and of plastid subfractions (thylakoids and envelopes), using HPLC high-resolution tandem mass spectrometry, thin-layer chromatography, and gas chromatography-flame ionization detection analytical techniques. Phosphoglycerolipids are the main structural lipids in mitochondria, while glycosyldiacylglycerols are the major structural lipids of plastids and also predominate in extracts of whole mixotrophic cells. Glycosyldiacylglycerols were detected in both bleached mutants, indicating that mutant cells retain some plastid remnants. Additionally, we discuss the origin of the E. gracilis middle plastid envelope based on the lipid composition of envelope fraction.
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Affiliation(s)
- Lucia Tomečková
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
| | - Aleš Tomčala
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Fisheries and Protection of Water, CENAKVA, Institute of Aquaculture and Protection of Waters, 370 05 České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
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19
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Abstract
Most secondary nonphotosynthetic eukaryotes have retained residual plastids whose physiological role is often still unknown. One such example is Euglena longa, a close nonphotosynthetic relative of Euglena gracilis harboring a plastid organelle of enigmatic function. By mining transcriptome data from E. longa, we finally provide an overview of metabolic processes localized to its elusive plastid. The organelle plays no role in the biosynthesis of isoprenoid precursors and fatty acids and has a very limited repertoire of pathways concerning nitrogen-containing metabolites. In contrast, the synthesis of phospholipids and glycolipids has been preserved, curiously with the last step of sulfoquinovosyldiacylglycerol synthesis being catalyzed by the SqdX form of an enzyme so far known only from bacteria. Notably, we show that the E. longa plastid synthesizes tocopherols and a phylloquinone derivative, the first such report for nonphotosynthetic plastids studied so far. The most striking attribute of the organelle could be the presence of a linearized Calvin-Benson (CB) pathway, including RuBisCO yet lacking the gluconeogenetic part of the standard cycle, together with ferredoxin-NADP+ reductase (FNR) and the ferredoxin/thioredoxin system. We hypothesize that the ferredoxin/thioredoxin system activates the linear CB pathway in response to the redox status of the E. longa cell and speculate on the role of the pathway in keeping the redox balance of the cell. Altogether, the E. longa plastid defines a new class of relic plastids that is drastically different from the best-studied organelle of this category, the apicoplast.IMPORTANCE Colorless plastids incapable of photosynthesis evolved in many plant and algal groups, but what functions they perform is still unknown in many cases. Here, we study the elusive plastid of Euglena longa, a nonphotosynthetic cousin of the familiar green flagellate Euglena gracilis We document an unprecedented combination of metabolic functions that the E. longa plastid exhibits in comparison with previously characterized nonphotosynthetic plastids. For example, and truly surprisingly, it has retained the synthesis of tocopherols (vitamin E) and a phylloquinone (vitamin K) derivative. In addition, we offer a possible solution of the long-standing conundrum of the presence of the CO2-fixing enzyme RuBisCO in E. longa Our work provides a detailed account on a unique variant of relic plastids, the first among nonphotosynthetic plastids that evolved by secondary endosymbiosis from a green algal ancestor, and suggests that it has persisted for reasons not previously considered in relation to nonphotosynthetic plastids.
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20
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Xiong R, Chen Z, Wang W, Jiang L, Xiang Y, Fan J. Combined transcriptome sequencing and prokaryotic expression to investigate the key enzyme in the 2-C-methylerythritol-4-phosphate pathway of Osmanthus fragrans. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:945-958. [PMID: 32527366 DOI: 10.1071/fp19365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Terpenoids are one of the main components of plant aromas. In the present study we investigated these compounds in Osmanthus fragrans Lour., which is a fragrant plant widely used for the production of essential oils. Quantitative real-time PCR (qRT-PCR) results of enzymes associated with the 2-C-methylerythritol-4-phosphate pathway confirmed that the TPS is a key enzyme for terpenoid synthesis in O. fragrans. In a series of experiments, we identified the TPS candidate genes in O. fragrans and revealed the underlying catalytic activity and subcellular localisation of the encoded proteins. Because there is no available O. fragrans reference genome, we sequenced and analysed its transcriptome and identified two putative TPS genes, OfTPS1 and OfTPS2. According to qRT-PCR analysis, both genes were most highly expressed at the full-bloom stage, suggesting that OfTPS1 and OfTPS2 contribute to O. fragrans terpenoid synthesis. To verify this hypothesis, we constructed prokaryotic expression vectors to obtain protein. In order to study the function of OfTPS1 and OfTPS2 in the synthesis of monoterpenes, the obtained proteins were reacted with geranyl pyrophosphate. As a result, two kinds of monoterpenes, (E)-β-ocimene and linalool, were detected from reaction products, respectively. In conclusion, OfTPS1 and OfTPS2 are both monoterpene synthases.
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Affiliation(s)
- Rui Xiong
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Zhu Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Weiyu Wang
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Li Jiang
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China; and Corresponding authors. ; ;
| | - Jun Fan
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China; and Corresponding authors. ; ;
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21
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Hammond MJ, Nenarokova A, Butenko A, Zoltner M, Dobáková EL, Field MC, Lukeš J. A Uniquely Complex Mitochondrial Proteome from Euglena gracilis. Mol Biol Evol 2020; 37:2173-2191. [PMID: 32159766 PMCID: PMC7403612 DOI: 10.1093/molbev/msaa061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Euglena gracilis is a metabolically flexible, photosynthetic, and adaptable free-living protist of considerable environmental importance and biotechnological value. By label-free liquid chromatography tandem mass spectrometry, a total of 1,786 proteins were identified from the E. gracilis purified mitochondria, representing one of the largest mitochondrial proteomes so far described. Despite this apparent complexity, protein machinery responsible for the extensive RNA editing, splicing, and processing in the sister clades diplonemids and kinetoplastids is absent. This strongly suggests that the complex mechanisms of mitochondrial gene expression in diplonemids and kinetoplastids occurred late in euglenozoan evolution, arising independently. By contrast, the alternative oxidase pathway and numerous ribosomal subunits presumed to be specific for parasitic trypanosomes are present in E. gracilis. We investigated the evolution of unexplored protein families, including import complexes, cristae formation proteins, and translation termination factors, as well as canonical and unique metabolic pathways. We additionally compare this mitoproteome with the transcriptome of Eutreptiella gymnastica, illuminating conserved features of Euglenida mitochondria as well as those exclusive to E. gracilis. This is the first mitochondrial proteome of a free-living protist from the Excavata and one of few available for protists as a whole. This study alters our views of the evolution of the mitochondrion and indicates early emergence of complexity within euglenozoan mitochondria, independent of parasitism.
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Affiliation(s)
- Michael J Hammond
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
| | - Anna Nenarokova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Anzhelika Butenko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Eva Lacová Dobáková
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
| | - Mark C Field
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, Czech Republic
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Tanno Y, Kato S, Takahashi S, Tamaki S, Takaichi S, Kodama Y, Sonoike K, Shinomura T. Light dependent accumulation of β-carotene enhances photo-acclimation of Euglena gracilis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 209:111950. [PMID: 32682285 DOI: 10.1016/j.jphotobiol.2020.111950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/30/2020] [Accepted: 06/29/2020] [Indexed: 01/04/2023]
Abstract
Carotenoids are essential components of photosynthetic organisms including land plants, algae, cyanobacteria, and photosynthetic bacteria. Although the light-mediated regulation of carotenoid biosynthesis, including the light/dark cycle as well as the dependence of carotenoid biosynthesis-related gene translation on light wavelength, has been investigated in land plants, these aspects have not been studied in microalgae. Here, we investigated carotenoid biosynthesis in Euglena gracilis and found that zeaxanthin accumulates in the dark. The major carotenoid species in E. gracilis, namely β-carotene, neoxanthin, diadinoxanthin and diatoxanthin, accumulated corresponding to the duration of light irradiation under the light/dark cycle, although the translation of carotenoid biosynthesis genes hardly changed. Irradiation with either blue or red-light (3 μmol photons m-2 s-1) caused a 1.3-fold increase in β-carotene content compared with the dark control. Blue-light irradiation (300 μmol photons m-2 s-1) caused an increase in the cellular content of both zeaxanthin and all trans-diatoxanthin, and this increase was proportional to blue-light intensity. In addition, pre-irradiation with blue-light of 3 or 30 μmol photons m-2 s-1 enhanced the photosynthetic activity and tolerance to high-light stress. These findings suggest that the accumulation of β-carotene is regulated by the intensity of light, which may contribute to the acclimation of E. gracilis to the light environment in day night conditions.
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Affiliation(s)
- Yuri Tanno
- Plant Molecular and Cellular Biology Laboratory, Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan
| | - Shota Kato
- Plant Molecular and Cellular Biology Laboratory, Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan; Laboratory of Complex Biology, Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 42988, Republic of Korea; Center for Bioscience Research and Education, Utsunomiya University, 350 mine-machi, Utsunomiya, Tochigi 321-8505, Japan
| | - Senji Takahashi
- Plant Molecular and Cellular Biology Laboratory, Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan; Plant Molecular and Cellular Biology Laboratory, Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan
| | - Shun Tamaki
- Plant Molecular and Cellular Biology Laboratory, Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, 350 mine-machi, Utsunomiya, Tochigi 321-8505, Japan
| | - Kintake Sonoike
- Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Tomoko Shinomura
- Plant Molecular and Cellular Biology Laboratory, Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan; Plant Molecular and Cellular Biology Laboratory, Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan.
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23
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A Global Analysis of Enzyme Compartmentalization to Glycosomes. Pathogens 2020; 9:pathogens9040281. [PMID: 32290588 PMCID: PMC7237986 DOI: 10.3390/pathogens9040281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/28/2022] Open
Abstract
In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. We found that while metabolic pathways were consistently represented across kinetoplastids, individual proteins within those pathways may not universally exhibit evidence of glycosome localization.
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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25
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Sugiyama K, Takahashi K, Nakazawa K, Yamada M, Kato S, Shinomura T, Nagashima Y, Suzuki H, Ara T, Harada J, Takaichi S. Oxygenic Phototrophs Need ζ-Carotene Isomerase (Z-ISO) for Carotene Synthesis: Functional Analysis in Arthrospira and Euglena. PLANT & CELL PHYSIOLOGY 2020; 61:276-282. [PMID: 31593237 DOI: 10.1093/pcp/pcz192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/26/2019] [Indexed: 05/02/2023]
Abstract
For carotenogenesis, two biosynthetic pathways from phytoene to lycopene are known. Most bacteria and fungi require only phytoene desaturase (PDS, CrtI), whereas land plants require four enzymes: PDS (CrtP), ζ-carotene desaturase (ZDS, CrtQ), ζ-carotene isomerase (Z-ISO) and cis-carotene isomerase (CrtISO, CrtH). The gene encoding Z-ISO has been functionally identified in only two species, Arabidopsis thaliana and Zea mays, and has been little studied in other organisms. In this study, we found that the deduced amino acid sequences of Arthrospira Z-ISO and Euglena Z-ISO have 58% and 62% identity, respectively, with functional Z-ISO from Arabidopsis. We studied the function of Z-ISO genes from the cyanobacterium Arthrospira platensis and eukaryotic microalga Euglena gracilis. The Z-ISO genes of Arthrospira and Euglena were transformed into Escherichia coli strains that produced mainly 9,15,9'-tri-cis-ζ-carotene in darkness. In the resulting E. coli transformants cultured under darkness, 9,9'-di-cis-ζ-carotene was accumulated predominantly as Z-ISO in Arabidopsis. This indicates that the Z-ISO genes were involved in the isomerization of 9,15,9'-tri-cis-ζ-carotene to 9,9'-di-cis-ζ-carotene in darkness. This is the first functional analysis of Z-ISO as a ζ-carotene isomerase in cyanobacteria and eukaryotic microalgae. Green sulfur bacteria and Chloracidobacterium also use CrtP, CrtQ and CrtH for lycopene synthesis as cyanobacteria, but their genomes did not comprise Z-ISO genes. Consequently, Z-ISO is needed in oxygenic phototrophs, whereas it is not found in anoxygenic species.
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Affiliation(s)
- Kenjiro Sugiyama
- Department of Applied Chemistry, School of Advanced Engineering, Kogakuin University, Hachioji, Tokyo, 192-0015 Japan
| | - Koh Takahashi
- Department of Applied Chemistry, School of Advanced Engineering, Kogakuin University, Hachioji, Tokyo, 192-0015 Japan
| | - Keisuke Nakazawa
- Department of Applied Chemistry, School of Advanced Engineering, Kogakuin University, Hachioji, Tokyo, 192-0015 Japan
| | - Masaharu Yamada
- Department of Applied Chemistry, School of Advanced Engineering, Kogakuin University, Hachioji, Tokyo, 192-0015 Japan
| | - Shota Kato
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, Utsunomiya, Tochigi, 320-8551 Japan
| | - Tomoko Shinomura
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, Utsunomiya, Tochigi, 320-8551 Japan
| | | | - Hideyuki Suzuki
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0812 Japan
| | - Takeshi Ara
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011 Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Faculty of Life Science, Tokyo University of Agriculture, Setagaya, Tokyo, 156-8502 Japan
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26
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Novák Vanclová AMG, Zoltner M, Kelly S, Soukal P, Záhonová K, Füssy Z, Ebenezer TE, Lacová Dobáková E, Eliáš M, Lukeš J, Field MC, Hampl V. Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid. THE NEW PHYTOLOGIST 2020; 225:1578-1592. [PMID: 31580486 DOI: 10.1111/nph.16237] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 05/20/2023]
Abstract
Euglena spp. are phototrophic flagellates with considerable ecological presence and impact. Euglena gracilis harbours secondary green plastids, but an incompletely characterised proteome precludes accurate understanding of both plastid function and evolutionary history. Using subcellular fractionation, an improved sequence database and MS we determined the composition, evolutionary relationships and hence predicted functions of the E. gracilis plastid proteome. We confidently identified 1345 distinct plastid protein groups and found that at least 100 proteins represent horizontal acquisitions from organisms other than green algae or prokaryotes. Metabolic reconstruction confirmed previously studied/predicted enzymes/pathways and provided evidence for multiple unusual features, including uncoupling of carotenoid and phytol metabolism, a limited role in amino acid metabolism, and dual sets of the SUF pathway for FeS cluster assembly, one of which was acquired by lateral gene transfer from Chlamydiae. Plastid paralogues of trafficking-associated proteins potentially mediating fusion of transport vesicles with the outermost plastid membrane were identified, together with derlin-related proteins, potential translocases across the middle membrane, and an extremely simplified TIC complex. The Euglena plastid, as the product of many genomes, combines novel and conserved features of metabolism and transport.
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Affiliation(s)
| | - Martin Zoltner
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Petr Soukal
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
| | - Kristína Záhonová
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - ThankGod E Ebenezer
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Eva Lacová Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Marek Eliáš
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czechia
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Vladimír Hampl
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
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27
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Tamaki S, Nishino K, Ogawa T, Maruta T, Sawa Y, Arakawa K, Ishikawa T. Comparative proteomic analysis of mitochondria isolated from Euglena gracilis under aerobic and hypoxic conditions. PLoS One 2019; 14:e0227226. [PMID: 31891638 PMCID: PMC6938325 DOI: 10.1371/journal.pone.0227226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/13/2019] [Indexed: 12/26/2022] Open
Abstract
The unicellular microalga Euglena gracilis produces wax esters for ATP acquisition under low-oxygen conditions. The regulatory mechanism of wax ester production is not yet understood. Indeed, our previous transcriptomic analysis showed that transcript levels of genes involved in the wax ester synthesis hardly changed under hypoxic conditions, suggesting contribution of post-transcriptional regulation. In this study, we conducted a proteome analysis of E. gracilis mitochondria, as this organelle employs the fatty-acid synthesis pathway under hypoxic conditions. Mitochondria were isolated from E. gracilis SM-ZK strain treated with both aerobic and hypoxic conditions and used for shotgun proteomic analysis. Three independent proteomic analyses succeeded in identifying a total of 714 non-redundant proteins. Of these, 229 were detected in common to all experiments, and 116 were significantly recognized as differentially expressed proteins. GO enrichment analysis suggested dynamic changes in mitochondrial metabolic pathways and redox reactions under aerobic and hypoxic conditions. Protein levels of bifunctional enzymes isocitrate lyase and malate synthase in glyoxylate cycle were 1.35-fold higher under hypoxic conditions. Abundances of the propionyl-CoA synthetic enzymes, succinyl-CoA synthetase and propionyl-CoA carboxylase, were also 1.35- and 1.47-fold higher, respectively, under hypoxic conditions. Protein levels of pyruvate:NADP+ oxidoreductase, a key enzyme for anaerobic synthesis of acetyl-CoA, which serves as a C2 donor for fatty acids, showed a 1.68-fold increase under hypoxic conditions, whereas those of pyruvate dehydrogenase subunits showed a 0.77–0.81-fold decrease. Protein levels of the fatty-acid synthesis enzymes, 3-ketoacyl-CoA thiolase isoforms (KAT1 and KAT2), 3-hydroxyacyl-CoA dehydrogenases, and acyl-CoA dehydrogenase were up-regulated by 1.20- to 1.42-fold in response to hypoxic treatment. Overall, our proteomic analysis revealed that wax ester synthesis-related enzymes are up-regulated at the protein level post-transcriptionally to promote wax ester production in E. gracilis under low-oxygen conditions.
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Affiliation(s)
- Shun Tamaki
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Kohei Nishino
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Takahisa Ogawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Takanori Maruta
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Yoshihiro Sawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
- * E-mail:
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28
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Hasan MT, Sun A, Khatiwada B, McQuade L, Mirzaei M, Te'o J, Hobba G, Sunna A, Nevalainen H. Comparative proteomics investigation of central carbon metabolism in Euglena gracilis grown under predominantly phototrophic, mixotrophic and heterotrophic cultivations. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Krüger J, Richter P, Stoltze J, Strauch SM, Krüger M, Daiker V, Prasad B, Sonnewald S, Reid S, Lebert M. Changes of Gene Expression in Euglena gracilis Obtained During the 29 th DLR Parabolic Flight Campaign. Sci Rep 2019; 9:14260. [PMID: 31582787 PMCID: PMC6776534 DOI: 10.1038/s41598-019-50611-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/02/2019] [Indexed: 01/14/2023] Open
Abstract
Parabolic flight maneuvers of Novespace's Airbus A310 ZERO-G produce subsequent phases of hypergravity (about 20 s), microgravity (about 22 s) and another 20 s hypergravity on experiments located in the experiment area of the aircraft. The 29th DLR parabolic flight campaign consisted of four consecutive flight days with thirty-one parabolas each day. Euglena gracilis cells were fixed with TRIzol during different acceleration conditions at the first and the last parabola of each flight. Samples were collected and analyzed with microarrays for one-color gene expression analysis. The data indicate significant changes in gene expression in E. gracilis within short time. Hierarchical clustering shows that changes induced by the different accelerations yield reproducible effects at independent flight days. Transcription differed between the first and last parabolas indicating adaptation effects in the course of the flight. Different gene groups were found to be affected in different phases of the parabolic flight, among others, genes involved in signal transduction, calcium signaling, transport mechanisms, metabolic pathways, and stress-response as well as membrane and cytoskeletal proteins. In addition, transcripts of other areas, e.g., DNA and protein modification, were altered. The study contributes to the understanding of short-term effects of microgravity and different accelerations on cells at a molecular level.
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Affiliation(s)
- Julia Krüger
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Peter Richter
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Julia Stoltze
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Sebastian M Strauch
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
- Postgraduate Program in Health and Environment, University of Joinville Region, Rua Paulo Malschitzki, 10 - Zona Industrial Norte, Joinville, SC, CEP 89219-710, Brazil
| | - Marcus Krüger
- Clinic for Plastic, Aesthetic and Hand Surgery, Otto von Guericke University Magdeburg, Leipziger Straße 44, 39120, Magdeburg, Germany
| | - Viktor Daiker
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Binod Prasad
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Sophia Sonnewald
- Biochemistry Division, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Stephen Reid
- Biochemistry Division, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Michael Lebert
- Cell Biology Division: Gravitational Biology Group, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany.
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30
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Inwongwan S, Kruger NJ, Ratcliffe RG, O'Neill EC. Euglena Central Metabolic Pathways and Their Subcellular Locations. Metabolites 2019; 9:E115. [PMID: 31207935 PMCID: PMC6630311 DOI: 10.3390/metabo9060115] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023] Open
Abstract
Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know where the component enzymes are in the cell, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. We analysed bioinformatic, biochemical, and proteomic information from a variety of sources to assess the subcellular location of the enzymes of the central metabolic pathways, and we use these assignments to propose a model of the metabolic network of Euglena. Other than photosynthesis, all major pathways present in the chloroplast are also present elsewhere in the cell. Our model demonstrates how Euglena can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Nicholas J Kruger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ellis C O'Neill
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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31
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Vesteg M, Hadariová L, Horváth A, Estraño CE, Schwartzbach SD, Krajčovič J. Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa. Biol Rev Camb Philos Soc 2019; 94:1701-1721. [PMID: 31095885 DOI: 10.1111/brv.12523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/23/2023]
Abstract
Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.
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Affiliation(s)
- Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Lucia Hadariová
- Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), 252 50, Vestec, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University in Prague, 128 44, Prague, Czech Republic
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Carlos E Estraño
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Steven D Schwartzbach
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Juraj Krajčovič
- Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia
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Gissibl A, Sun A, Care A, Nevalainen H, Sunna A. Bioproducts From Euglena gracilis: Synthesis and Applications. Front Bioeng Biotechnol 2019; 7:108. [PMID: 31157220 PMCID: PMC6530250 DOI: 10.3389/fbioe.2019.00108] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/29/2019] [Indexed: 11/24/2022] Open
Abstract
In recent years, the versatile phototrophic protist Euglena gracilis has emerged as an interesting candidate for application-driven research and commercialisation, as it is an excellent source of dietary protein, pro(vitamins), lipids, and the β-1,3-glucan paramylon only found in euglenoids. From these, paramylon is already marketed as an immunostimulatory agent in nutraceuticals. Bioproducts from E. gracilis can be produced under various cultivation conditions discussed in this review, and their yields are relatively high when compared with those achieved in microalgal systems. Future challenges include achieving the economy of large-scale cultivation. Recent insights into the complex metabolism of E. gracilis have highlighted unique metabolic pathways, which could provide new leads for product enhancement by genetic modification of the organism. Also, development of molecular tools for strain improvement are emerging rapidly, making E. gracilis a noteworthy challenger for microalgae such as Chlorella spp. and their products currently on the market.
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Affiliation(s)
- Alexander Gissibl
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
| | - Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
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33
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Sello CT, Liu C, Sun Y, Msuthwana P, Hu J, Sui Y, Chen S, Zhou Y, Lu H, Xu C, Sun Y, Liu J, Li S, Yang W. De Novo Assembly and Comparative Transcriptome Profiling of Anser anser and Anser cygnoides Geese Species' Embryonic Skin Feather Follicles. Genes (Basel) 2019; 10:genes10050351. [PMID: 31072014 PMCID: PMC6562822 DOI: 10.3390/genes10050351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Geese feather production and the quality of downy feathers are additional economically important traits in the geese industry. However, little information is available about the molecular mechanisms fundamental to feather formation and the quality of feathers in geese. This study conducted de novo transcriptome sequencing analysis of two related geese species using the Illumina 4000 platform to determine the genes involved in embryonic skin feather follicle development. A total of 165,564,278 for Anser anser and 144,595,262 for Anser cygnoides clean reads were generated, which were further assembled into 77,134 unigenes with an average length of 906 base pairs in Anser anser and 66,041 unigenes with an average length of 922 base pairs in Anser cygnoides. To recognize the potential regulatory roles of differentially expressed genes (DEGs) during geese embryonic skin feather follicle development, the obtained unigenes were annotated to Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analysis. In both species, GO and KOG had shown similar distribution patterns during functional annotation except for KEGG, which showed significant variation in signaling enrichment. Anser asnser was significantly enriched in the calcium signaling pathway, whereas Anser cygnoides was significantly enriched with glycerolipid metabolism. Further analysis indicated that 14,227 gene families were conserved between the species, among which a total of 20,715 specific gene families were identified. Comparative RNA-Seq data analysis may reveal inclusive knowledge to assist in the identification of genetic regulators at a molecular level to improve feather quality production in geese and other poultry species.
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Affiliation(s)
- Cornelius Tlotliso Sello
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Chang Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
- Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Changchun 130118, China.
| | - Petunia Msuthwana
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Jingtao Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Yujian Sui
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Shaokang Chen
- Beijing General Station of Animal Husbandry, Beijing 100107, China.
| | - Yuxuan Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Hongtao Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Chenguang Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Yue Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Jing Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Shengyi Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Wei Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
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Ebenezer TE, Zoltner M, Burrell A, Nenarokova A, Novák Vanclová AMG, Prasad B, Soukal P, Santana-Molina C, O'Neill E, Nankissoor NN, Vadakedath N, Daiker V, Obado S, Silva-Pereira S, Jackson AP, Devos DP, Lukeš J, Lebert M, Vaughan S, Hampl V, Carrington M, Ginger ML, Dacks JB, Kelly S, Field MC. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol 2019; 17:11. [PMID: 30732613 PMCID: PMC6366073 DOI: 10.1186/s12915-019-0626-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 01/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts. RESULTS We report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500 Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids. CONCLUSIONS Our data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the 'shopping bag' hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.
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Affiliation(s)
- ThankGod E Ebenezer
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Alana Burrell
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Anna Nenarokova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Binod Prasad
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Petr Soukal
- Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Ellis O'Neill
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Nerissa N Nankissoor
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, T6G, Canada
| | - Nithya Vadakedath
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Viktor Daiker
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Samson Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Sara Silva-Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Michael Lebert
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Vladimίr Hampl
- Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Michael L Ginger
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, T6G, Canada. .,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. .,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic.
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Kato S, Tanno Y, Takaichi S, Shinomura T. Low Temperature Stress Alters the Expression of Phytoene Desaturase Genes (crtP1 and crtP2) and the ζ-Carotene Desaturase Gene (crtQ) Together with the Cellular Carotenoid Content of Euglena gracilis. PLANT & CELL PHYSIOLOGY 2019; 60:274-284. [PMID: 30346581 DOI: 10.1093/pcp/pcy208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/15/2018] [Indexed: 05/02/2023]
Abstract
Carotenoids participate in photosynthesis and photoprotection in oxygenic phototrophs. Euglena gracilis, a eukaryotic phytoflagellate, synthesizes several carotenoids: β-carotene, neoxanthin, diadinoxanthin and diatoxanthin. Temperature is one of the most striking external stimuli altering carotenoid production. In the present study, to elucidate the regulation of carotenoid synthesis of E. gracilis in response to environmental stimuli, we functionally identified phytoene desaturase genes (crtP1 and crtP2) and the ζ-carotene desaturase gene (crtQ) of this alga and analyzed expression of those genes and the composition of major carotenoids in cells grown under cold (20�C) and high-intensity light (HL; 240 �mol photon m-2 s-1) conditions. 20�C-HL treatment increased the transcriptional level of the phytoene synthase gene (crtB), and crtP1 and crtP2, whose products catalyze the early steps of carotenoid biosynthesis in this alga. Cultivation at 20�C under illumination at 55 �mol photon m-2 s-1 (low-intensity light; LL) decreased the cell concentration, Chl and total major carotenoid content by 61, 75 and 50%, respectively, relative to control (25�C-LL) cells. When grown at 20�C-HL, the cells showed a greater decrease in cell concentration and photosynthetic pigment contents than those in 20�C-LL. β-Carotene, neoxanthin and diadinoxanthin contents were decreased by more than half in 20�C-LL and 20�C-HL treatments. On the other hand, when subjected to 20�C-LL and 20�C-HL, the cells retained a diatoxanthin content comparable with control cells. Our findings suggested that diatoxanthin plays crucial roles in the acclimation to cold and intense light condition. To the best of our knowledge, this is the first report on a photosynthetic organism possessing dual crtP genes.
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Affiliation(s)
- Shota Kato
- Plant Molecular and Cellular Biology Laboratory, Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, Japan
| | - Yuri Tanno
- Plant Molecular and Cellular Biology Laboratory, Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya, Tokyo, Japan
| | - Tomoko Shinomura
- Plant Molecular and Cellular Biology Laboratory, Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, Japan
- Plant Molecular and Cellular Biology Laboratory, Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1-1 Toyosatodai, Utsunomiya, Tochigi, Japan
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36
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Yamada K, Nitta T, Atsuji K, Shiroyama M, Inoue K, Higuchi C, Nitta N, Oshiro S, Mochida K, Iwata O, Ohtsu I, Suzuki K. Characterization of sulfur-compound metabolism underlying wax-ester fermentation in Euglena gracilis. Sci Rep 2019; 9:853. [PMID: 30696857 PMCID: PMC6351624 DOI: 10.1038/s41598-018-36600-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/22/2018] [Indexed: 12/03/2022] Open
Abstract
Euglena gracilis is a microalga, which has been used as a model organism for decades. Recent technological advances have enabled mass cultivation of this species for industrial applications such as feedstock in nutritional foods and cosmetics. E. gracilis degrades its storage polysaccharide (paramylon) under hypoxic conditions for energy acquisition by an oxygen-independent process and accumulates high amount of wax-ester as a by-product. Using this sequence of reactions referred to as wax-ester fermentation, E. gracilis is studied for its application in biofuel production. Although the wax-ester production pathway is well characterized, little is known regarding the biochemical reactions underlying the main metabolic route, especially, the existence of an unknown sulfur-compound metabolism implied by the nasty odor generation accompanying the wax-ester fermentation. In this study, we show sulfur-metabolomics of E. gracilis in aerobic and hypoxic conditions, to reveal the biochemical reactions that occur during wax-ester synthesis. Our results helped us in identifying hydrogen sulfide (H2S) as the nasty odor-producing component in wax-ester fermentation. In addition, the results indicate that glutathione and protein degrades during hypoxia, whereas cysteine, methionine, and their metabolites increase in the cells. This indicates that this shift of abundance in sulfur compounds is the cause of H2S synthesis.
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Affiliation(s)
- Koji Yamada
- euglena Co., Ltd., Tokyo, 108-0014, Japan
- Microalgae Production Control Technology Laboratory, RIKEN, Kanagawa, 230-0045, Japan
| | | | - Kohei Atsuji
- euglena Co., Ltd., Tokyo, 108-0014, Japan
- Microalgae Production Control Technology Laboratory, RIKEN, Kanagawa, 230-0045, Japan
| | - Maeka Shiroyama
- Innovation Medical Research Institute, University of Tsukuba, Ibaraki, 305-8577, Japan
| | - Komaki Inoue
- Center for Sustainable Resource Science, RIKEN, Kanagawa, 230-0045, Japan
| | | | | | - Satoshi Oshiro
- Innovation Medical Research Institute, University of Tsukuba, Ibaraki, 305-8577, Japan
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Okinawa, 905-2192, Japan
| | - Keiichi Mochida
- Microalgae Production Control Technology Laboratory, RIKEN, Kanagawa, 230-0045, Japan
- Center for Sustainable Resource Science, RIKEN, Kanagawa, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, 244-0813, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, 710-0046, Japan
| | - Osamu Iwata
- euglena Co., Ltd., Tokyo, 108-0014, Japan
- Microalgae Production Control Technology Laboratory, RIKEN, Kanagawa, 230-0045, Japan
| | - Iwao Ohtsu
- euglena Co., Ltd., Tokyo, 108-0014, Japan
- Innovation Medical Research Institute, University of Tsukuba, Ibaraki, 305-8577, Japan
| | - Kengo Suzuki
- euglena Co., Ltd., Tokyo, 108-0014, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN, Kanagawa, 230-0045, Japan.
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37
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Tomiyama T, Goto K, Tanaka Y, Maruta T, Ogawa T, Sawa Y, Ito T, Ishikawa T. A major isoform of mitochondrial trans-2-enoyl-CoA reductase is dispensable for wax ester production in Euglena gracilis under anaerobic conditions. PLoS One 2019; 14:e0210755. [PMID: 30650145 PMCID: PMC6334954 DOI: 10.1371/journal.pone.0210755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/30/2018] [Indexed: 11/18/2022] Open
Abstract
Under anaerobic conditions, Euglena gracilis produces a large amount of wax ester through mitochondrial fatty acid synthesis from storage polysaccharides termed paramylon, to generate ATP. Trans-2-enoyl-CoA reductases (TERs) in mitochondria have been considered to play a key role in this process, because the enzymes catalyze the reduction of short chain length CoA-substrates (such as crotonyl-CoA). A TER enzyme (EgTER1) has been previously identified and enzymologically characterized; however, its physiological significance remained to be evaluated by genetic analysis. We herein generated EgTER1-knockdown Euglena cells, in which total crotonyl-CoA reductase activity was decreased to 10% of control value. Notably, the knockdown cells showed a severe bleaching phenotype with deficiencies in chlorophylls and glycolipids, but grew normally under heterotrophic conditions (with glucose supplementation). Moreover, the knockdown cells accumulated much greater quantities of wax ester than control cells before and after transfer to anaerobic conditions, which was accompanied by a large metabolomic change. Furthermore, we failed to find any contribution of other potential TER genes in wax ester production. Our findings propose a novel role of EgTER1 in the greening process and demonstrate that this enzyme is dispensable for wax ester production under anaerobic conditions.
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Affiliation(s)
- Takuya Tomiyama
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
| | - Kyo Goto
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
| | - Yuji Tanaka
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Takanori Maruta
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Takahisa Ogawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Yoshihiro Sawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
| | - Takuro Ito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Takahiro Ishikawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
- * E-mail:
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38
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Tomita Y, Takeya M, Suzuki K, Nitta N, Higuchi C, Marukawa-Hashimoto Y, Osanai T. Amino acid excretion from Euglena gracilis cells in dark and anaerobic conditions. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tamaki S, Kato S, Shinomura T, Ishikawa T, Imaishi H. Physiological role of β-carotene monohydroxylase (CYP97H1) in carotenoid biosynthesis in Euglena gracilis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:80-87. [PMID: 30471732 DOI: 10.1016/j.plantsci.2018.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/30/2018] [Accepted: 10/18/2018] [Indexed: 05/02/2023]
Abstract
Some carotenoids are found in the Euglena gracilis, including β-carotene, diadinoxanthin, diatoxanthins, and neoxanthin as the major species; however, the molecular mechanism underlying carotenoid biosynthesis in E. gracilis is not well understood. To clarify the pathway and regulation of carotenoid biosynthesis in this alga, we functionally characterized the cytochrome P450 (CYP)-type carotene hydroxylase gene EgCYP97H1. Heterologous in vivo enzyme assay in E. coli indicated that EgCYP97H1 hydroxylated β-carotene to β-cryptoxanthin. E. gracilis cells suppressing EgCYP97H1 resulted in marked growth inhibition and reductions in total carotenoid and chlorophyll contents. Analysis of carotenoid composition revealed that suppression of EgCYP97H1 resulted in higher level of β-carotene, suggesting that EgCYP97H1 is physiologically essential for carotenoid biosynthesis and thus normal cell growth. To our knowledge, this is the first time EgCYP97H1 has been suggested to be β-carotene monohydroxylase, but not β-carotene dihydroxylase. Moreover, during light adaptation of dark-grown E. gracilis, transcript levels of the carotenoid biosynthetic genes (EgCYP97H1, geranylgeranyl pyrophosphate synthase EgcrtE, and phytoene synthase EgcrtB) remained virtually unchanged. In contrast, carotenoid accumulation in E. gracilis grown under the same conditions was inhibited by treatment with a translational inhibitor but not a transcriptional inhibitor, indicating that photo-responsive carotenoid biosynthesis is regulated post-transcriptionally in this alga.
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Affiliation(s)
- Shun Tamaki
- Division of Signal Responses, Biosignal Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Shota Kato
- Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan
| | - Tomoko Shinomura
- Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi, 320-8551, Japan
| | - Takahiro Ishikawa
- Faculty of Life and Environmental Science, Department of Life Science and Biotechnology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan
| | - Hiromasa Imaishi
- Division of Signal Responses, Biosignal Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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Khatiwada B, Kautto L, Sunna A, Sun A, Nevalainen H. Nuclear transformation of the versatile microalga Euglena gracilis. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Nakazawa M, Ando H, Nishimoto A, Ohta T, Sakamoto K, Ishikawa T, Ueda M, Sakamoto T, Nakano Y, Miyatake K, Inui H. Anaerobic respiration coupled with mitochondrial fatty acid synthesis in wax ester fermentation by Euglena gracilis. FEBS Lett 2018; 592:4020-4027. [PMID: 30328102 PMCID: PMC6587861 DOI: 10.1002/1873-3468.13276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 11/08/2022]
Abstract
In Euglena gracilis, wax ester fermentation produces ATP during anaerobiosis. Here, we report that anaerobic wax ester production is suppressed when the mitochondrial electron transport chain complex I is inhibited by rotenone, whereas it is increased by the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP). The ADP/ATP ratio in anaerobic cells is elevated by treatment with either rotenone or CCCP. Gene silencing experiments indicate that acyl-CoA dehydrogenase, electron transfer flavoprotein (ETF), and rhodoquinone (RQ) participate in wax ester production. These results suggest that fatty acids are synthesized in mitochondria by the reversal of β-oxidation, where trans-2-enoyl-CoA is reduced mainly by acyl-CoA dehydrogenase using the electrons provided by NADH via the electron transport chain complex I, RQ, and ETF, and that ATP production is highly supported by anaerobic respiration utilizing trans-2-enoyl-CoA as a terminal electron acceptor.
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Affiliation(s)
- Masami Nakazawa
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
- Core Research for Evolutional Science and Technology (CREST)Japan Science and Technology Agency (JST)KawaguchiJapan
| | - Hiroko Ando
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
| | - Ayusa Nishimoto
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
| | - Tsuyoshi Ohta
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
| | - Kimitoshi Sakamoto
- Department of Biochemistry and Molecular BiologyFaculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
| | - Takahiro Ishikawa
- Core Research for Evolutional Science and Technology (CREST)Japan Science and Technology Agency (JST)KawaguchiJapan
- Department of Life Science and BiotechnologyFaculty of Life and Environmental ScienceShimane UniversityMatsueJapan
| | - Mitsuhiro Ueda
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
| | - Tatsuji Sakamoto
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
| | - Yoshihisa Nakano
- Division of Applied Life SciencesGraduate School of Life and Environmental SciencesOsaka Prefecture UniversitySakaiJapan
| | - Kazutaka Miyatake
- Department of Nutrition and Food SciencesFaculty of Human and Cultural StudiesTezukayama Gakuin UniversitySakaiJapan
| | - Hiroshi Inui
- Core Research for Evolutional Science and Technology (CREST)Japan Science and Technology Agency (JST)KawaguchiJapan
- Department of NutritionCollege of Health and Human SciencesOsaka Prefecture UniversityHabikinoJapan
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Pollier J, Vancaester E, Kuzhiumparambil U, Vickers CE, Vandepoele K, Goossens A, Fabris M. A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis. Nat Microbiol 2018; 4:226-233. [DOI: 10.1038/s41564-018-0305-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/24/2018] [Indexed: 11/09/2022]
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43
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Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses. Sci Rep 2018; 8:17012. [PMID: 30451959 PMCID: PMC6242988 DOI: 10.1038/s41598-018-35389-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022] Open
Abstract
Euglenophytes are a familiar algal group with green alga-derived secondary plastids, but the knowledge of euglenophyte plastid function and evolution is still highly incomplete. With this in mind we sequenced and analysed the transcriptome of the non-photosynthetic species Euglena longa. The transcriptomic data confirmed the absence of genes for the photosynthetic machinery, but provided candidate plastid-localised proteins bearing N-terminal bipartite topogenic signals (BTSs) of the characteristic euglenophyte type. Further comparative analyses including transcriptome assemblies available for photosynthetic euglenophytes enabled us to unveil salient aspects of the basic euglenophyte plastid infrastructure, such as plastidial targeting of several proteins as C-terminal translational fusions with other BTS-bearing proteins or replacement of the conventional eubacteria-derived plastidial ribosomal protein L24 by homologs of archaeo-eukaryotic origin. Strikingly, no homologs of any key component of the TOC/TIC system and the plastid division apparatus are discernible in euglenophytes, and the machinery for intraplastidial protein targeting has been simplified by the loss of the cpSRP/cpFtsY system and the SEC2 translocon. Lastly, euglenophytes proved to encode a plastid-targeted homolog of the termination factor Rho horizontally acquired from a Lambdaproteobacteria-related donor. Our study thus further documents a substantial remodelling of the euglenophyte plastid compared to its green algal progenitor.
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Muchut RJ, Calloni RD, Herrera FE, Garay SA, Arias DG, Iglesias AA, Guerrero SA. Elucidating paramylon and other carbohydrate metabolism in Euglena gracilis: Kinetic characterization, structure and cellular localization of UDP-glucose pyrophosphorylase. Biochimie 2018; 154:176-186. [DOI: 10.1016/j.biochi.2018.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022]
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Moore AN, McWatters DC, Hudson AJ, Russell AG. RNA-Seq employing a novel rRNA depletion strategy reveals a rich repertoire of snoRNAs in Euglena gracilis including box C/D and Ψ-guide RNAs targeting the modification of rRNA extremities. RNA Biol 2018; 15:1309-1318. [PMID: 30252600 PMCID: PMC6284569 DOI: 10.1080/15476286.2018.1526561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/21/2018] [Accepted: 09/16/2018] [Indexed: 01/06/2023] Open
Abstract
Previous mRNA transcriptome studies of Euglena gracilis have shown that this organism possesses a large and diverse complement of protein coding genes; however, the study of non-coding RNA classes has been limited. The natural extensive fragmentation of the E. gracilis large subunit ribosomal RNA presents additional barriers to the identification of non-coding RNAs as size-selected small RNA libraries will be dominated by rRNA sequences. In this study we have developed a strategy to significantly reduce rRNA amplification prior to RNA-Seq analysis thereby producing a ncRNA library allowing for the identification of many new E. gracilis small RNAs. Library analysis reveals 113 unique new small nucleolar (sno) RNAs and a large collection of snoRNA isoforms, as well as the first significant collection of nuclear tRNAs in this organism. A 3' end AGAUGN consensus motif and conserved structural features can now be defined for E. gracilis pseudouridine guide RNAs. snoRNAs of both classes were identified that target modification of the 3' extremities of rRNAs utilizing predicted base-pairing interactions with internally transcribed spacers (ITS), providing insight into the timing of steps in rRNA maturation. Cumulatively, this represents the most comprehensive analysis of small ncRNAs in Euglena gracilis to date.
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Affiliation(s)
- Ashley N. Moore
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - David C. McWatters
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Andrew J. Hudson
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Anthony G. Russell
- Department of Biological Sciences, and Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
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Liang J, Cui Y, Meng Y, Li X, Wang X, Liu W, Huang L, Du H. Integrated analysis of transcription factors and targets co-expression profiles reveals reduced correlation between transcription factors and target genes in cancer. Funct Integr Genomics 2018; 19:191-204. [PMID: 30251028 DOI: 10.1007/s10142-018-0636-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022]
Abstract
Transcription factors are recognized as the key regulators of gene expression. However, the changes in the correlation of transcription factors and their target genes between normal and tumor tissues are usually ignored. In this research, we used mRNA expression profile data from The Cancer Genome Atlas which included 5726 samples across 11 major human cancers to perform co-expression analysis by the Pearson correlation coefficients. Then, integrating 81,357 pairs of transcription factors and target genes from transcription factors databases to find out the changes in the co-expression correlation of these gene pairs from normal to tumor tissues. Based on the changes in the number of co-expressed TF-TG pairs and changes in the level of co-expression, we found the generally reduced correlation between transcription factors and their target genes in cancer. Additionally, we screened out universal and specific transcription factors-target genes pairs which may significant influence particular cancer. Then, we obtained 423 cancer cell line expression profiles from Broad Institute Cancer Cell Line Encyclopedia to verify our results. Some of these pairs like XRCC5-XRCC6 have been reported to involve in multiple cancers, while pairs like IRF1-PSMB9 without any previous articles related to tumor but involve in the biological processes of cancer, which are of great potential to be therapeutic targets. Our research may provide insights to better understand the tumor development mechanisms and find potential therapeutic targets.
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Affiliation(s)
- Jinsheng Liang
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Ying Cui
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Yuhuan Meng
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Xingsong Li
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanli Liu
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, Guangdong, China.
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Sun A, Hasan MT, Hobba G, Nevalainen H, Te'o J. Comparative assessment of the Euglena gracilis var. saccharophila variant strain as a producer of the β-1,3-glucan paramylon under varying light conditions. JOURNAL OF PHYCOLOGY 2018; 54:529-538. [PMID: 29889303 DOI: 10.1111/jpy.12758] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/08/2018] [Indexed: 05/16/2023]
Abstract
Euglena gracilis Z and a "sugar loving" variant strain E. gracilis var. saccharophila were investigated as producers of paramylon, a β-1,3-glucan polysaccharide with potential medicinal and industrial applications. The strains were grown under diurnal or dark growth conditions on a glucose-yeast extract medium supporting high-level paramylon production. Both strains produced the highest paramylon yields (7.4-8 g · L-1 , respectively) while grown in the dark, but the maximum yield was achieved faster by E. gracilis var. saccharophila (48 h vs. 72 h). The glucose-to-paramylon yield coefficient Ypar/glu = 0.46 ± 0.03 in the E. gracilis var. saccharophila cultivation, obtained in this study, is the highest reported to date. Proteomic analysis of the metabolic pathways provided molecular clues for the strain behavior observed during cultivation. For example, overexpression of enzymes in the gluconeogenesis/glycolysis pathways including fructokinase-1 and chloroplastic fructose-1,6-bisphosphatase (FBP) may have contributed to the faster rate of paramylon accumulation in E. gracilis var. saccharophila. Differentially expressed proteins in the early steps of chloroplastogenesis pathway including plastid uroporphyrinogen decarboxylases, photoreceptors, and a highly abundant (68-fold increase) plastid transketolase may have provided the E. gracilis var. saccharophila strain an advantage in paramylon production during diurnal cultivations. In conclusion, the variant strain E. gracilis var. saccharophila seems to be well suited for producing large amounts of paramylon. This work has also resulted in the identification of molecular targets for future improvement of paramylon production in E. gracilis, including the FBP and phosophofructokinase 1, the latter being a key regulator of glycolysis.
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Affiliation(s)
- Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Mafruha Tasnin Hasan
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Graham Hobba
- Agritechnology Pty Ltd, Borenore, New South Wales, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Junior Te'o
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, New South Wales, Australia
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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Shibata S, Arimura SI, Ishikawa T, Awai K. Alterations of Membrane Lipid Content Correlated With Chloroplast and Mitochondria Development in Euglena gracilis. FRONTIERS IN PLANT SCIENCE 2018; 9:370. [PMID: 29636759 PMCID: PMC5881160 DOI: 10.3389/fpls.2018.00370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/06/2018] [Indexed: 05/13/2023]
Abstract
Euglenoids are unique protists that can grow photoautotrophically, photomixotrophically, and heterotrophically. Here we grew Euglena gracilis under these different growth conditions and determined cellular contents of seven membrane lipids and one storage lipid (triacylglycerol), which account for more than 94 mol% of total membrane lipids. We also describe the relationship among chloroplast and mitochondria developments with lipid contents, protein contents, and oxygen evolution/consumption rates. In photoautotrophic growth conditions, E. gracilis cells accumulated chlorophyll, photosynthetic proteins, and glycolipids typical to thylakoid membranes. The same occurred for the cells grown under photomixotrophic conditions with higher respiration rates. In heterotrophic conditions, E. gracilis cells had higher respiration rates compared to cells grown in other conditions with the accumulation of pyruvate: NADP+ oxidoreductase, a mitochondrial protein and phospholipid common in mitochondria. Cells were also observed using a confocal laser scanning microscope and found to show more chlorophyll autofluorescence when grown photoautotrophically and photomixotrophycally, and fluorescence of MitoTracker when grown photomixotrophically and heterotrophically. These results suggest that under illumination, E. gracilis develops functional thylakoid membranes with membrane lipids and proteins for photosynthesis. In the medium with glucose, the cells develop mitochondria with phospholipids and proteins for respiration. Possible application based on lipid analysis for the enhancement of wax ester or alkene synthesis is discussed.
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Affiliation(s)
- Shiori Shibata
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Takahiro Ishikawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Koichiro Awai
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
- Research Institute of Electronics, Shizuoka University, Hamamatsu, Japan
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Kuhaudomlarp S, Patron NJ, Henrissat B, Rejzek M, Saalbach G, Field RA. Identification of Euglena gracilis β-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149. J Biol Chem 2018; 293:2865-2876. [PMID: 29317507 PMCID: PMC5827456 DOI: 10.1074/jbc.ra117.000936] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/22/2017] [Indexed: 12/11/2022] Open
Abstract
Glycoside phosphorylases (EC 2.4.x.x) carry out the reversible phosphorolysis of glucan polymers, producing the corresponding sugar 1-phosphate and a shortened glycan chain. β-1,3-Glucan phosphorylase activities have been reported in the photosynthetic euglenozoan Euglena gracilis, but the cognate protein sequences have not been identified to date. Continuing our efforts to understand the glycobiology of E. gracilis, we identified a candidate phosphorylase sequence, designated EgP1, by proteomic analysis of an enriched cellular protein lysate. We expressed recombinant EgP1 in Escherichia coli and characterized it in vitro as a β-1,3-glucan phosphorylase. BLASTP identified several hundred EgP1 orthologs, most of which were from Gram-negative bacteria and had 37-91% sequence identity to EgP1. We heterologously expressed a bacterial metagenomic sequence, Pro_7066 in E. coli and confirmed it as a β-1,3-glucan phosphorylase, albeit with kinetics parameters distinct from those of EgP1. EgP1, Pro_7066, and their orthologs are classified as a new glycoside hydrolase (GH) family, designated GH149. Comparisons between GH94, EgP1, and Pro_7066 sequences revealed conservation of key amino acids required for the phosphorylase activity, suggesting a phosphorylase mechanism that is conserved between GH94 and GH149. We found bacterial GH149 genes in gene clusters containing sugar transporter and several other GH family genes, suggesting that bacterial GH149 proteins have roles in the degradation of complex carbohydrates. The Bacteroidetes GH149 genes located to previously identified polysaccharide utilization loci, implicated in the degradation of complex carbohydrates. In summary, we have identified a eukaryotic and a bacterial β-1,3-glucan phosphorylase and uncovered a new family of phosphorylases that we name GH149.
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Affiliation(s)
- Sakonwan Kuhaudomlarp
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Nicola J Patron
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah 23218, Saudi Arabia
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Gerhard Saalbach
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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Zimorski V, Rauch C, van Hellemond JJ, Tielens AGM, Martin WF. The Mitochondrion of Euglena gracilis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:19-37. [PMID: 28429315 DOI: 10.1007/978-3-319-54910-1_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the presence of oxygen, Euglena gracilis mitochondria function much like mammalian mitochondria. Under anaerobiosis, E. gracilis mitochondria perform a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. Some components (enzymes and cofactors) of Euglena's anaerobic energy metabolism are found among the anaerobic mitochondria of invertebrates, others are found among hydrogenosomes, the H2-producing anaerobic mitochondria of protists.
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Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Cessa Rauch
- Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jaap J van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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