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Abstract
Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time, and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and 6 algae, resulting in the annotation of more than 120,000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organized in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/) . This chapter contains a detailed explanation of the content of GreeNC and how to access both programmatically and with a web browser.
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102
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Rahman F, Hassan M, Hanano A, Fitzpatrick DA, McCarthy CGP, Murphy DJ. Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi. BMC Genomics 2018; 19:976. [PMID: 30593269 PMCID: PMC6309107 DOI: 10.1186/s12864-018-5334-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim of this study was to investigate the evolution and functions of the CLO/PXGs in the Fungi and other non-plant clades and to elucidate the overall origin of this gene family. RESULTS CLO/PXG-like genes are distributed across the full range of fungal groups from the basal clades, Cryptomycota and Microsporidia, to the largest and most complex Dikarya species. However, the genes were only present in 243 out of 844 analysed fungal genomes. CLO/PXG-like genes have been retained in many pathogenic or parasitic fungi that have undergone considerable genomic and structural simplification, indicating that they have important functions in these species. Structural and functional analyses demonstrate that CLO/PXGs are multifunctional proteins closely related to similar proteins found in all major taxa of the Chlorophyte Division of the Viridiplantae. Transcriptome and physiological data show that fungal CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression and are upregulated in response to a range of biotic and abiotic stresses as well as participating in key metabolic and developmental processes such as lipid metabolism, signalling, reproduction and pathogenesis. Biochemical data also reveal that the Aspergillus flavus CLO/PXG has specific functions in sporulation and aflatoxin production as well as playing roles in lipid droplet function. CONCLUSIONS In contrast to plants, CLO/PXGs only occur in about 30% of sequenced fungal genomes but are present in all major taxa. Fungal CLO/PXGs have similar but not identical roles to those in plants, including stress-related oxylipin signalling, lipid metabolism, reproduction and pathogenesis. While the presence of CLO/PXG orthologs in all plant genomes sequenced to date would suggest that they have core housekeeping functions in plants, the selective loss of CLO/PXGs in many fungal genomes suggests more restricted functions in fungi as accessory genes useful in particular environments or niches. We suggest an ancient origin of CLO/PXG-like genes in the 'last eukaryotic common ancestor' (LECA) and their subsequent loss in ancestors of the Metazoa, after the latter had diverged from the ancestral fungal lineage.
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Affiliation(s)
- Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
| | - Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | | | | | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
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103
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Broberg M, Dubey M, Sun MH, Ihrmark K, Schroers HJ, Li SD, Jensen DF, Brandström Durling M, Karlsson M. Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping. Front Microbiol 2018; 9:2844. [PMID: 30524411 PMCID: PMC6262169 DOI: 10.3389/fmicb.2018.02844] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/05/2018] [Indexed: 01/16/2023] Open
Abstract
There is an increasing importance for using biocontrol agents in combating plant diseases sustainably and in the long term. As large scale genomic sequencing becomes economically viable, the impact of single nucleotide polymorphisms (SNPs) on biocontrol-associated phenotypes can be easily studied across entire genomes of fungal populations. Here, we improved a previously reported genome assembly of the biocontrol fungus Clonostachys rosea strain IK726 using the PacBio sequencing platform, which resulted in a total genome size of 70.7 Mbp and 21,246 predicted genes. We further performed whole-genome re-sequencing of 52 additional C. rosea strains isolated globally using Illumina sequencing technology, in order to perform genome-wide association studies in conditions relevant for biocontrol activity. One such condition is the ability to grow at lower temperatures commonly encountered in cryic or frigid soils in temperate regions, as these will be prevalent for protecting growing crops in temperate climates. Growth rates at 10°C on potato dextrose agar of the 53 sequenced strains of C. rosea were measured and ranged between 0.066 and 0.413 mm/day. Performing a genome wide association study, a total of 1,478 SNP markers were significantly associated with the trait and located in 227 scaffolds, within or close to (< 1000 bp distance) 265 different genes. The predicted gene products included several chaperone proteins, membrane transporters, lipases, and proteins involved in chitin metabolism with possible roles in cold tolerance. The data reported in this study provides a foundation for future investigations into the genetic basis for cold tolerance in fungi, with important implications for biocontrol.
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Affiliation(s)
- Martin Broberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Man-Hong Sun
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Shi-Dong Li
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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104
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Pardo-De la Hoz CJ, Magain N, Lutzoni F, Goward T, Restrepo S, Miadlikowska J. Contrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera. Front Microbiol 2018; 9:2770. [PMID: 30505297 PMCID: PMC6250826 DOI: 10.3389/fmicb.2018.02770] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.
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Affiliation(s)
- Carlos José Pardo-De la Hoz
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
- Department of Biology, Duke University, Durham, NC, United States
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, NC, United States
| | - François Lutzoni
- Department of Biology, Duke University, Durham, NC, United States
| | - Trevor Goward
- UBC Herbarium, Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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105
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Cao S, Zhang F, Zheng H, Peng F, Liu C, Zhou Q. Coccomyxagreatwallensis sp. nov. (Trebouxiophyceae, Chlorophyta), a lichen epiphytic alga from Fildes Peninsula, Antarctica. PHYTOKEYS 2018; 110:39-50. [PMID: 30473613 PMCID: PMC6236199 DOI: 10.3897/phytokeys.110.26961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/15/2018] [Indexed: 06/09/2023]
Abstract
A single-celled green alga Coccomyxagreatwallensis Shunan Cao & Qiming Zhou, sp. nov., isolated from a specimen of Antarctic lichen Psoromahypnorum (Vahl) Gray, is described and illustrated based on a comprehensive investigation of morphology, ultrastructure, ecology and phylogeny. The cells of C.greatwallensis are ovoid to long ellipsoidal and measured 3-5 µm × 6-12 µm. The new species has distinct ITS rDNA and SSU rDNA sequences and differs from the phylogenetic closely related species C.antarctica, C.arvernensis and C.viridis in cell size, distribution and habitat.
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Affiliation(s)
- Shunan Cao
- Key Laboratory for Polar Science SOA, Polar Research Institute of China, No.451 Jinqiao Road, Pudong Avenue, Shanghai, 200136, ChinaPolar Research Institute of ChinaShanghaiChina
| | - Fang Zhang
- Key Laboratory for Polar Science SOA, Polar Research Institute of China, No.451 Jinqiao Road, Pudong Avenue, Shanghai, 200136, ChinaPolar Research Institute of ChinaShanghaiChina
| | - Hongyuan Zheng
- Key Laboratory for Polar Science SOA, Polar Research Institute of China, No.451 Jinqiao Road, Pudong Avenue, Shanghai, 200136, ChinaPolar Research Institute of ChinaShanghaiChina
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, ChinaTongji UniversityShanghaiChina
| | - Fang Peng
- China Centre for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, No. 299 Bayi Road, Wuchang District, Wuhan 430072, ChinaWuhan UniversityWuhanChina
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Nangang Distinct, Harbin, 150080, ChinaHarbin Institute of TechnologyHarbinChina
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Nangang Distinct, Harbin, 150080, ChinaHarbin Institute of TechnologyHarbinChina
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106
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Schmidt JJ, Gagnon GA, Jamieson RC. Predicting microalgae growth and phosphorus removal in cold region waste stabilization ponds using a stochastic modelling approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:32952-32963. [PMID: 28660515 DOI: 10.1007/s11356-017-9583-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
A stochastic ecological model with an integrated equilibrium temperature model was developed to predict microalgae growth and phosphorus removal in cold region waste stabilization ponds (WSPs). The model utilized a Monte Carlo simulation to account for parameter uncertainty. The equilibrium temperature model was parameterized using field data collected from two WSPs in Nunavut, Canada, from 2012 to 2014. The equilibrium temperature model provided good agreement with field data on a daily time step. The full model was run using historic (1956-2005) temperature and solar radiation data from five communities (Baker Lake, Cambridge Bay, Coral Harbour, Hall Beach, Resolute) in Nunavut, Canada. The communities represented a range of geographical locations and environmental conditions. Logistic regression on pooled model outputs showed that mean July temperature and mean treatment season temperature (June 1-September 15, ice-free period) provided the best predictors for microalgae growth. They had a predictive success rate of 93 and 88%, respectively. The modelled threshold (50% probability from the Monte Carlo simulation) for microalgae growth was 8.7 and 5.6 °C for the July temperature and mean treatment season temperature, respectively. The logistic regression was applied to each community (except Sanikiluaq) in Nunavut using historic climate data and a probability of microalgae growth was calculated. Based on the model results, soluble phosphorus concentrations consistent with secondary treatment could be achieved if WSP depth is less than 2 m. The model demonstrated a robust method to predict whether a microalgae bloom will occur under a range of model parameters.
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Affiliation(s)
- Jordan J Schmidt
- Centre for Water Resources Studies, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada
| | - Graham A Gagnon
- Centre for Water Resources Studies, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada
| | - Rob C Jamieson
- Centre for Water Resources Studies, Dalhousie University, 1360 Barrington Street, Halifax, NS, Canada.
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107
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Allen JW, Tevatia R, Demirel Y, DiRusso CC, Black PN. Induction of oil accumulation by heat stress is metabolically distinct from N stress in the green microalgae Coccomyxa subellipsoidea C169. PLoS One 2018; 13:e0204505. [PMID: 30261009 PMCID: PMC6160078 DOI: 10.1371/journal.pone.0204505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
Algae are often promoted as feedstock organisms to produce a sustainable petroleum fossil fuel alternative. However, to induce lipid accumulation most often requires a severe stress that is difficult to induce in large batch cultures. The objective of this study is to analyze and mathematically model heat stress on growth, chlorophyll content, triacylglyceride, and starch synthesis in algae. We initially screened 30 algal species for the most pronounced induction of lipid droplets from heat stress using confocal microscopy and mass spectroscopy techniques. One species, Coccomyxa subellipsoidea C169, was selected and subjected to further biochemical analyses using a jacketed bioreactor amended with 1% CO2 at 25°C, 30°C, 32°C, 33°C, 34°C, 35°C, and 36°C. Lipid and starch accumulation was less extreme than N stress. Growth was reduced above 25°C, but heat stress induced lipid droplet synthesis was negatively correlated with growth only past a demonstrated threshold temperature above 32°C. The optimal temperature for lipid accumulation was 35°C, which led to 6% of dry weight triglyceride content and a 72% reduction from optimal growth after 5 days. Fatty acid influx rates into triglycerides and 15N labeling of amino acids and proteins indicate that heat stress is mechanistically distinct from N stress. Thus, this study lends support to a novel hypothesis that lipid droplet triglycerides result from a redistribution of carbon flux as fatty acids to neutral storage lipids over membrane or other lipids.
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Affiliation(s)
- James W. Allen
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Rahul Tevatia
- Department of Chemical and Biomolecular Engineering, Othmer Hall, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Yaşar Demirel
- Department of Chemical and Biomolecular Engineering, Othmer Hall, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Concetta C. DiRusso
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Paul N. Black
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, University of Nebraska-Lincoln, Lincoln, NE, United States of America
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108
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Raven JA. The potential effect of low cell osmolarity on cell function through decreased concentration of enzyme substrates. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4667-4673. [PMID: 29992331 DOI: 10.1093/jxb/ery254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/03/2018] [Indexed: 06/08/2023]
Abstract
Some freshwater algae have lower (<130 osmol m-3) intracellular osmolarities than most others (>180 osmol m-3). Low osmolarities are related to the presence of flagella and the low energy cost of active water efflux following downhill water influx unconstrained by cell walls covering the plasmalemma, and the low resource cost of cell wall synthesis with the same mechanical degree of safety. One consequence of low intracellular osmolarity is limitation on the concentration of metabolites, that is, substrates and products of enzyme activity. Models of the flux through metabolic pathways, and hence the specific growth rate, using steady-state concentrations of enzymes and metabolites have involved organisms with intracellular metabolite osmolarities >280 osmol m-3, where the metabolite concentrations are much greater than the total osmolarity of some freshwater algae. Since the protein concentration (mol m-3) in the cells and the specific growth rates of freshwater cells with low and with higher intracellular osmolarity are highly similar, the models of trade-offs between enzyme and metabolite concentrations for cells with high intracellular osmolarity need modification for cells with low intracellular osmolarity. The soluble free-radical scavenger ascorbate can constitute as little as 0.2% of the low intracellular metabolite concentration (mol m-3) of low-intracellular-osmolarity cells.
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Affiliation(s)
- John A Raven
- Division of Plant Science, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, UK
- School of Biological Sciences, University of Western Australia, Crawley (Perth), WA, Australia
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109
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Uchida H, Sumimoto K, Oki T, Nishii I, Mizohata E, Matsunaga S, Okada S. Isolation and characterization of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase gene from Botryococcus braunii, race B. JOURNAL OF PLANT RESEARCH 2018; 131:839-848. [PMID: 29725892 DOI: 10.1007/s10265-018-1039-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/12/2018] [Indexed: 05/27/2023]
Abstract
The B race of a green microalga Botryococcus braunii Kützing produces triterpene hydrocarbons that is a promising source for biofuel. In this algal race, precursors of triterpene hydrocarbons are provided from the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. The terminal enzyme of this pathway, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) is regarded as one of the key enzymes that affect yields of products in terpene biosynthesis. In order to better understand the MEP pathway of the alga, cDNA and genomic clones of HDR were obtained from B. braunii Showa strain. B. braunii HDR (BbHDR) is encoded on a single copy gene including a 1509-bp open reading frame that was intervened by 6 introns. The exon-intron structure of BbHDR genes did not show clear relation to phylogeny, while its amino acid sequence reflected phyla and classes well. BbHDR sequence was distinctive from that of the HDR protein from Escherichia coli in the residues involved in hydrogen-bond network that surrounds substrate. Introduction of BbHDR cDNA into an E. coli HDR deficient mutant resulted in recovery of its auxotrophy. BbHDR expression level was upregulated from the onset of liquid culture to the 24th day after inoculation with a 2.5-fold increase and retained its level in the subsequent period.
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Affiliation(s)
- Hidenobu Uchida
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo, 102-0076, Japan
| | - Koremitsu Sumimoto
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo, 102-0076, Japan
| | - Tomoka Oki
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo, 102-0076, Japan
| | - Ichiro Nishii
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo, 102-0076, Japan
- Department of Biological Science, Nara Women's University, Kitauoya, Higashimachi, Nara, Nara, 630-8506, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo, 102-0076, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo, 102-0076, Japan.
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110
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Hamada M, Schröder K, Bathia J, Kürn U, Fraune S, Khalturina M, Khalturin K, Shinzato C, Satoh N, Bosch TC. Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. eLife 2018; 7:35122. [PMID: 29848439 PMCID: PMC6019070 DOI: 10.7554/elife.35122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/26/2018] [Indexed: 11/13/2022] Open
Abstract
Many multicellular organisms rely on symbiotic associations for support of metabolic activity, protection, or energy. Understanding the mechanisms involved in controlling such interactions remains a major challenge. In an unbiased approach we identified key players that control the symbiosis between Hydra viridissima and its photosynthetic symbiont Chlorella sp. A99. We discovered significant up-regulation of Hydra genes encoding a phosphate transporter and glutamine synthetase suggesting regulated nutrition supply between host and symbionts. Interestingly, supplementing the medium with glutamine temporarily supports in vitro growth of the otherwise obligate symbiotic Chlorella, indicating loss of autonomy and dependence on the host. Genome sequencing of Chlorella sp. A99 revealed a large number of amino acid transporters and a degenerated nitrate assimilation pathway, presumably as consequence of the adaptation to the host environment. Our observations portray ancient symbiotic interactions as a codependent partnership in which exchange of nutrients appears to be the primary driving force.
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Affiliation(s)
- Mayuko Hamada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Ushimado Marine Institute, Okayama University, Okayama, Japan
| | - Katja Schröder
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Jay Bathia
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Ulrich Kürn
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Sebastian Fraune
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Mariia Khalturina
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Thomas Cg Bosch
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
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111
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Berthelier J, Casse N, Daccord N, Jamilloux V, Saint-Jean B, Carrier G. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics 2018. [PMID: 29783941 DOI: 10.17882/52231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. RESULTS To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795 ), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. CONCLUSION This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.
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Affiliation(s)
- Jérémy Berthelier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
| | - Nathalie Casse
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences, INRA of Angers, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d'Angers, Angers, France
- Université Bretagne Loire, Angers, France
| | | | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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Berthelier J, Casse N, Daccord N, Jamilloux V, Saint-Jean B, Carrier G. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics 2018; 19:378. [PMID: 29783941 PMCID: PMC5963040 DOI: 10.1186/s12864-018-4763-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
Background Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. Results To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: 10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. Conclusion This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4763-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jérémy Berthelier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France. .,Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
| | - Nathalie Casse
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences, INRA of Angers, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d'Angers, Angers, France.,Université Bretagne Loire, Angers, France
| | | | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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Rahman F, Hassan M, Rosli R, Almousally I, Hanano A, Murphy DJ. Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae. PLoS One 2018; 13:e0196669. [PMID: 29771926 PMCID: PMC5957377 DOI: 10.1371/journal.pone.0196669] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 03/06/2018] [Indexed: 12/04/2022] Open
Abstract
Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta). CLO/PXG-like sequences are also present in all of the >300 sequenced Embryophyte genomes, where some species contain as many as 10–12 genes that have arisen via selective gene duplication. Angiosperm genomes harbour at least one copy each of two distinct CLO/PX isoforms, termed H (high) and L (low), where H-forms contain an additional C-terminal motif of about 30–50 residues that is absent from L-forms. In contrast, species in other Viridiplantae taxa, including green algae, non-vascular plants, ferns and gymnosperms, contain only one (or occasionally both) of these isoforms per genome. Transcriptome and biochemical data show that CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression. CLO/PXG proteins can associate with cytosolic lipid droplets and/or bilayer membranes. Many of the analysed isoforms also have peroxygenase activity and are involved in oxylipin metabolism. The distribution of CLO/PXG-like genes is consistent with an origin >1 billion years ago in at least two of the earliest diverging groups of the Viridiplantae, namely the Chlorophyta and the Streptophyta, after the Viridiplantae had already diverged from other Archaeplastidal groups such as the Rhodophyta and Glaucophyta. While algal CLO/PXGs have roles in lipid packaging and stress responses, the Embryophyte proteins have a much wider spectrum of roles and may have been instrumental in the colonisation of terrestrial habitats and the subsequent diversification as the major land flora.
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Affiliation(s)
- Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kuala Lumpur, Malaysia
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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Zhang Z, An M, Miao J, Gu Z, Liu C, Zhong B. The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution. BMC PLANT BIOLOGY 2018; 18:53. [PMID: 29614974 PMCID: PMC5883279 DOI: 10.1186/s12870-018-1273-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/27/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The ice alga Chlamydomonas sp. ICE-L is the main contributor to primary productivity in Antarctic sea ice ecosystems and is well adapted to the extremely harsh environment. However, the adaptive mechanism of Chlamydomonas sp. ICE-L to sea-ice environment remains unclear. To study the adaptive strategies in Chlamydomonas sp. ICE-L, we investigated the molecular evolution of chloroplast photosynthetic genes that are essential for the accumulation of carbohydrate and energy living in Antarctic sea ice. RESULTS The 60 chloroplast protein-coding genes of Chlamydomonas sp. ICE-L were obtained, and the branch-site test detected significant signatures of positive selection on atpB, psaB, and rbcL genes in Chlamydomonas sp. ICE-L associated with the photosynthetic machinery. These positively selected genes were further identified as being under convergent evolution between Chlamydomonas sp. ICE-L and the halotolerant alga Dunaliella salina. CONCLUSIONS Our study provides evidence that the phototrophic component of Chlamydomonas sp. ICE-L exhibits adaptive evolution under extreme environment. The positive Darwinian selection operates on the chloroplast protein-coding genes of Antarctic ice algae adapted to extreme environment following functional-specific and lineages-specific patterns. In addition, three positively selected genes with convergent substitutions in Chlamydomonas sp. ICE-L were identified, and the adaptive modifications in these genes were in functionally important regions of the proteins. Our study provides a foundation for future experiments on the biochemical and physiological impacts of photosynthetic genes in green algae.
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Affiliation(s)
- Zhenhua Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Meiling An
- Medical College, Qingdao University, Qingdao, China
| | - Jinlai Miao
- Medical College, Qingdao University, Qingdao, China
- Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Zhiqiang Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Bojian Zhong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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Firdaus-Raih M, Hashim NHF, Bharudin I, Abu Bakar MF, Huang KK, Alias H, Lee BKB, Mat Isa MN, Mat-Sharani S, Sulaiman S, Tay LJ, Zolkefli R, Muhammad Noor Y, Law DSN, Abdul Rahman SH, Md-Illias R, Abu Bakar FD, Najimudin N, Abdul Murad AM, Mahadi NM. The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PLoS One 2018; 13:e0189947. [PMID: 29385175 PMCID: PMC5791967 DOI: 10.1371/journal.pone.0189947] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/05/2017] [Indexed: 01/01/2023] Open
Abstract
Extremely low temperatures present various challenges to life that include ice formation and effects on metabolic capacity. Psyhcrophilic microorganisms typically have an array of mechanisms to enable survival in cold temperatures. In this study, we sequenced and analysed the genome of a psychrophilic yeast isolated in the Antarctic region, Glaciozyma antarctica. The genome annotation identified 7857 protein coding sequences. From the genome sequence analysis we were able to identify genes that encoded for proteins known to be associated with cold survival, in addition to annotating genes that are unique to G. antarctica. For genes that are known to be involved in cold adaptation such as anti-freeze proteins (AFPs), our gene expression analysis revealed that they were differentially transcribed over time and in response to different temperatures. This indicated the presence of an array of adaptation systems that can respond to a changing but persistent cold environment. We were also able to validate the activity of all the AFPs annotated where the recombinant AFPs demonstrated anti-freeze capacity. This work is an important foundation for further collective exploration into psychrophilic microbiology where among other potential, the genes unique to this species may represent a pool of novel mechanisms for cold survival.
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Affiliation(s)
- Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- * E-mail:
| | - Noor Haza Fazlin Hashim
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Izwan Bharudin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mohd Faizal Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Kie Kyon Huang
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Bernard K. B. Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Shuhaila Mat-Sharani
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
| | - Suhaila Sulaiman
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Lih Jinq Tay
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Radziah Zolkefli
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Yusuf Muhammad Noor
- Malaysia Genome Institute, Jalan Bangi Lama, Kajang, Selangor, Malaysia
- Department of Biosciences Engineering, Faculty of Chemical & Natural Resources Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Douglas Sie Nguong Law
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Siti Hamidah Abdul Rahman
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Rosli Md-Illias
- Department of Biosciences Engineering, Faculty of Chemical & Natural Resources Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Ranjan P, Kateriya S. Localization and dimer stability of a newly identified microbial rhodopsin from a polar, non-motile green algae. BMC Res Notes 2018; 11:65. [PMID: 29361974 PMCID: PMC5781313 DOI: 10.1186/s13104-018-3181-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The eukaryotic plasma membrane localized light-gated proton-pumping rhodopsins possesses great optogenetic applications for repolarization (silencing) of the neuronal activity simply by light illumination. Very few plasma membrane localized proton-pumping rhodopsins of a eukaryotic origin are known that have optogenetic potential. Our objective was to identify and characterize microbial rhodopsin of an eukaryotic origin that expresses on plasma membrane. The plasma membrane localized light-gated proton pump of an eukaryotic origin hold great promise to be used as an optogenetic tools for the neurobiology. RESULTS Here, we had characterized the cellular expression and membrane localization of a new rhodopsin in Antarctican algae Coccomyxa subellipsoidea. It is the first algal ion pumping rhodopsin that localizes to the plasma membrane of the eukaryotic cells. Coccomyxa subellipsoidea rhodopsin exists in the monomeric and dimeric state both the in vivo and in vitro. The dimeric form of the Coccomyxa subellipsoidea rhodopsin is resistant to heat and detergent denaturants.
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Affiliation(s)
- Peeyush Ranjan
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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Satjarak A, Graham LE. Genome-wide analysis of carbohydrate-active enzymes in Pyramimonas parkeae (Prasinophyceae). JOURNAL OF PHYCOLOGY 2017; 53:1072-1086. [PMID: 28708263 DOI: 10.1111/jpy.12566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The wall-less green flagellate Pyramimonas parkeae is classified in clade I of the prasinophytes, a paraphyletic assemblage representing the last common ancestor of Viridiplantae, a monophyletic group composed of the green algae and land plants. Consequently, P. parkeae and other prasinophytes illuminate early-evolved Viridiplantae traits likely fundamental in the systems biology of green algae and land plants. Cellular structure and organellar genomes of P. parkeae are now well understood, and transcriptomic sequence data are also publically available for one strain of this species, but corresponding nuclear genomic sequence data are lacking. For this reason, we obtained shotgun genomic sequence and assembled a draft nuclear genome for P. parkeaeNIES254 to use along with existing transcriptomic sequence to focus on carbohydrate-active enzymes. We found that the P. parkeae nuclear genome encodes carbohydrate-active protein families similar to those previously observed for other prasinophytes, green algae, and early-diverging embryophytes for which full nuclear genomic sequence is publically available. Sequences homologous to genes related to biosynthesis of starch and cell wall carbohydrates were identified in the P. parkeae genome, indicating molecular traits common to Viridiplantae. For example, the P. parkeae genome includes sequences clustering with bacterial genes that encode cellulose synthases (Bcs), including regions coding for domains common to bacterial and plant cellulose synthases; these new sequences were incorporated into phylogenies aimed at illuminating the evolutionary history of cellulose production by Viridiplantae. Genomic sequences related to biosynthesis of xyloglucans, pectin, and starch likewise shed light on the origin of key Viridiplantae traits.
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Affiliation(s)
- Anchittha Satjarak
- Department of Botany, Chulalongkorn University, Bangkok, Thailand
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
| | - Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
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Acidophilic green algal genome provides insights into adaptation to an acidic environment. Proc Natl Acad Sci U S A 2017; 114:E8304-E8313. [PMID: 28893987 DOI: 10.1073/pnas.1707072114] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Some microalgae are adapted to extremely acidic environments in which toxic metals are present at high levels. However, little is known about how acidophilic algae evolved from their respective neutrophilic ancestors by adapting to particular acidic environments. To gain insights into this issue, we determined the draft genome sequence of the acidophilic green alga Chlamydomonas eustigma and performed comparative genome and transcriptome analyses between Ceustigma and its neutrophilic relative Chlamydomonas reinhardtii The results revealed the following features in Ceustigma that probably contributed to the adaptation to an acidic environment. Genes encoding heat-shock proteins and plasma membrane H+-ATPase are highly expressed in Ceustigma This species has also lost fermentation pathways that acidify the cytosol and has acquired an energy shuttle and buffering system and arsenic detoxification genes through horizontal gene transfer. Moreover, the arsenic detoxification genes have been multiplied in the genome. These features have also been found in other acidophilic green and red algae, suggesting the existence of common mechanisms in the adaptation to acidic environments.
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121
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Macrander JC, Dimond JL, Bingham BL, Reitzel AM. Transcriptome sequencing and characterization of Symbiodinium muscatinei and Elliptochloris marina, symbionts found within the aggregating sea anemone Anthopleura elegantissima. Mar Genomics 2017; 37:82-91. [PMID: 28888836 DOI: 10.1016/j.margen.2017.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 08/26/2017] [Accepted: 08/27/2017] [Indexed: 12/20/2022]
Abstract
There is a growing body of literature using transcriptomic data to study how tropical cnidarians and their photosynthetic endosymbionts respond to environmental stressors and participate in metabolic exchange. Despite these efforts, our understanding of how essential genes function to facilitate symbiosis establishment and maintenance remains limited. The inclusion of taxonomically and ecologically diverse endosymbionts will enhance our understanding of these interactions. Here we characterize the transcriptomes of two very different symbionts found within the temperate sea anemone Anthopleura elegantissima: the chlorophyte Elliptochloris marina and the dinoflagellate Symbiodinium muscatinei. We use a multi-level approach to assess the diversity of genes found across S. muscatinei and E. marina transcriptomes, and compare their overall protein domains with other dinoflagellates and chlorophytes. Our analysis identified several genes that are potentially involved in mitigating stress response (e.g., heat shock proteins pathways for mediating reactive oxygen species) and metabolic exchange (e.g., ion transporters). Finally, we show that S. muscatinei and other Symbiodinium strains are equipped with a high salt peridinin-chl-protein (HSPCP) gene previously identified only in free-living dinoflagellates. The addition of these transcriptomes to the cnidarian-symbiont molecular toolkit will aid in understanding how these vitally important symbiotic relationships are established and maintained across a variety of environmental conditions.
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Affiliation(s)
- Jason C Macrander
- Department of Biological Sciences, University of North Carolina, Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.
| | - James L Dimond
- Shannon Point Marine Center, Western Washington University, 1900 Shannon Point Road, Anacortes, WA 98221, USA
| | - Brian L Bingham
- Shannon Point Marine Center, Western Washington University, 1900 Shannon Point Road, Anacortes, WA 98221, USA; Department of Environmental Sciences, Western Washington University, 516 High Street, Bellingham, WA 98225, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes. Sci Rep 2017; 7:10101. [PMID: 28855622 PMCID: PMC5577192 DOI: 10.1038/s41598-017-10388-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/08/2017] [Indexed: 11/20/2022] Open
Abstract
Ancient endosymbiotic relationships have led to extreme genomic reduction in many bacterial and eukaryotic algal endosymbionts. Endosymbionts in more recent and/or facultative relationships can also experience genomic reduction to a lesser extent, but little is known about the effects of the endosymbiotic transition on the organellar genomes of eukaryotes. To understand how the endosymbiotic lifestyle has affected the organellar genomes of photosynthetic green algae, we generated the complete plastid genome (plastome) and mitochondrial genome (mitogenome) sequences from three green algal endosymbionts (Chlorella heliozoae, Chlorella variabilis and Micractinium conductrix). The mitogenomes and plastomes of the three newly sequenced endosymbionts have a standard set of genes compared with free-living trebouxiophytes, providing no evidence for functional genomic reduction. Instead, their organellar genomes are generally larger and more intron rich. Intron content is highly variable among the members of Chlorella, suggesting very high rates of gain and/or loss of introns during evolution. Phylogenetic analysis of plastid and mitochondrial genes demonstrated that the three endosymbionts do not form a monophyletic group, indicating that the endosymbiotic lifestyle has evolved multiple times in Chlorellaceae. In addition, M. conductrix is deeply nested within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera.
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123
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Tsou CY, Matsunaga S, Okada S. Molecular cloning and functional characterization of NADPH-dependent cytochrome P450 reductase from the green microalga Botryococcus braunii, B race. J Biosci Bioeng 2017; 125:30-37. [PMID: 28818427 DOI: 10.1016/j.jbiosc.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/08/2017] [Accepted: 07/16/2017] [Indexed: 10/19/2022]
Abstract
The green microalga Botryococcus braunii of the B race accumulates various lipophilic compounds containing a 10,11-oxidosqualene epoxide moiety in addition to large amounts of triterpene hydrocarbons. While 2,3-squalene epoxidases have already been isolated and characterized from the alga, the enzyme that catalyzes the 10,11-epoxidation of squalene has remained elusive. In order to obtain a molecular tool to explore a 10,11-squalene epoxidase, cDNA cloning of an NADPH-dependent cytochrome P450 reductase (CPR) that is required by both squalene epoxidases and cytochrome P450 enzymes was carried out. The isolated cDNA contained an open reading frame (1998 bp) that encoded for a protein with 665 amino acid residues with a predicted molecular weight of 71.46 kDa and a theoretical pI of 5.49. Analysis of the deduced amino acid sequence revealed the presence of conserved motifs, including FMN, FAD, and NADPH binding domains, which are typical of other CPRs and necessary for enzyme activity. By truncation of the N-terminal transmembrane anchor and addition of a 6× His-tag, BbCPR was heterologously produced in Escherichia coli and purified by Ni-NTA affinity chromatography. The purified recombinant enzyme showed optimal reducing activity of cytochrome c at around a neutral pH at a temperature range of 30-37°C. For steady state kinetic parameters, the recombinant enzyme had a km for cytochrome c and NADPH of 11.7±1.6 and 9.4±1.4 μM, and a kcat for cytochrome c and NADPH of 2.78±0.09 and 3.66±0.11 μmol/min/mg protein, respectively. This is the first study to perform the functional characterization of a CPR from eukaryotic microalgae.
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Affiliation(s)
- Chung-Yau Tsou
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural & Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural & Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural & Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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The augmented lipid productivity in an emerging oleaginous model alga Coccomyxa subellipsoidea by nitrogen manipulation strategy. World J Microbiol Biotechnol 2017; 33:160. [DOI: 10.1007/s11274-017-2324-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/21/2017] [Indexed: 01/22/2023]
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125
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Nelson DR, Khraiwesh B, Fu W, Alseekh S, Jaiswal A, Chaiboonchoe A, Hazzouri KM, O'Connor MJ, Butterfoss GL, Drou N, Rowe JD, Harb J, Fernie AR, Gunsalus KC, Salehi-Ashtiani K. The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization. eLife 2017. [PMID: 28623667 PMCID: PMC5509433 DOI: 10.7554/elife.25783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline. DOI:http://dx.doi.org/10.7554/eLife.25783.001 Single-celled green algae, also known as green microalgae, play an important role for the world’s ecosystems, in part, because they can harness energy from sunlight to produce carbon-rich compounds. Microalgae are also important for biotechnology and people have harnessed them to make food, fuel and medicines. Green microalgae live in many types of habitats from streams to oceans, and they can also be found on the land, including in deserts. Like plants that live in the desert, these microalgae have likely evolved specific traits that allow them to live in these hot and dry regions. Yet, fewer scientists have studied microalgae compared to land plants, and until now it was not well understood how microalgae could survive in the desert. Nelson et al. analyzed green microalgae from different locations around the United Arab Emirates and found that one microalga, known as Chloroidium, is one of the most dominant algae in this area. This included samples from beaches, mangroves, desert oases, buildings and public fresh water sources. Chloroidium has a unique set of genes and proteins and grew particularly well in freshwater and saltwater. Rather than just harnessing sunlight, the microalgae were able to consume over 40 different varieties of carbon sources to produce energy. The microalgae also accumulated oily molecules with a similar composition to palm oil, which may help this species to survive in desert regions. A next step will be to develop biotechnological assets based on the information obtained. In the future, microalgae could be used to make an oil that represents an alternative to palm oil; this would reduce the demand for palm tree plantations, which pose a major threat to the natural environment. Moreover, understanding how microalgae can colonize a desert region will help us to understand the effects of climate change in the region. DOI:http://dx.doi.org/10.7554/eLife.25783.002
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Affiliation(s)
- David R Nelson
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Basel Khraiwesh
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Weiqi Fu
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ashish Jaiswal
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Khaled M Hazzouri
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Matthew J O'Connor
- Core Technology Platform, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nizar Drou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Jillian D Rowe
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Jamil Harb
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology and Department of Biology, New York University, New York, United States
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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126
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Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proc Natl Acad Sci U S A 2017; 114:E4296-E4305. [PMID: 28484037 PMCID: PMC5448231 DOI: 10.1073/pnas.1619928114] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microalgae have potential to help meet energy and food demands without exacerbating environmental problems. There is interest in the unicellular green alga Chromochloris zofingiensis, because it produces lipids for biofuels and a highly valuable carotenoid nutraceutical, astaxanthin. To advance understanding of its biology and facilitate commercial development, we present a C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions. The assembly, derived from a combination of short- and long-read sequencing in conjunction with optical mapping, revealed a compact genome of ∼58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. The genome has uniform gene density over chromosomes, low repetitive sequence content (∼6%), and a high fraction of protein-coding sequence (∼39%) with relatively long coding exons and few coding introns. Functional annotation of gene models identified orthologous families for the majority (∼73%) of genes. Synteny analysis uncovered localized but scrambled blocks of genes in putative orthologous relationships with other green algae. Two genes encoding beta-ketolase (BKT), the key enzyme synthesizing astaxanthin, were found in the genome, and both were up-regulated by high light. Isolation and molecular analysis of astaxanthin-deficient mutants showed that BKT1 is required for the production of astaxanthin. Moreover, the transcriptome under high light exposure revealed candidate genes that could be involved in critical yet missing steps of astaxanthin biosynthesis, including ABC transporters, cytochrome P450 enzymes, and an acyltransferase. The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production.
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127
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Ramesh SA, Tyerman SD, Gilliham M, Xu B. γ-Aminobutyric acid (GABA) signalling in plants. Cell Mol Life Sci 2017; 74:1577-1603. [PMID: 27838745 PMCID: PMC11107511 DOI: 10.1007/s00018-016-2415-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 01/11/2023]
Abstract
The role of γ-aminobutyric acid (GABA) as a signal in animals has been documented for over 60 years. In contrast, evidence that GABA is a signal in plants has only emerged in the last 15 years, and it was not until last year that a mechanism by which this could occur was identified-a plant 'GABA receptor' that inhibits anion passage through the aluminium-activated malate transporter family of proteins (ALMTs). ALMTs are multigenic, expressed in different organs and present on different membranes. We propose GABA regulation of ALMT activity could function as a signal that modulates plant growth, development, and stress response. In this review, we compare and contrast the plant 'GABA receptor' with mammalian GABAA receptors in terms of their molecular identity, predicted topology, mode of action, and signalling roles. We also explore the implications of the discovery that GABA modulates anion flux in plants, its role in signal transduction for the regulation of plant physiology, and predict the possibility that there are other GABA interaction sites in the N termini of ALMT proteins through in silico evolutionary coupling analysis; we also explore the potential interactions between GABA and other signalling molecules.
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Affiliation(s)
- Sunita A Ramesh
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Stephen D Tyerman
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Matthew Gilliham
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Bo Xu
- Plant Transport and Signalling Lab, ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia.
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128
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Fang L, Qi S, Xu Z, Wang W, He J, Chen X, Liu J. De novo transcriptomic profiling of Dunaliella salina reveals concordant flows of glycerol metabolic pathways upon reciprocal salinity changes. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.01.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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129
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Wei L, Xin Y, Wang Q, Yang J, Hu H, Xu J. RNAi-based targeted gene knockdown in the model oleaginous microalgae Nannochloropsis oceanica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1236-1250. [PMID: 28188644 DOI: 10.1111/tpj.13411] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/02/2016] [Accepted: 10/24/2016] [Indexed: 05/09/2023]
Abstract
Microalgae are promising feedstock for renewable fuels such as biodiesel, yet development of industrial oleaginous strains has been hindered by the paucity and inefficiency of reverse genetics tools. Here we established an efficient RNAi-based targeted gene-knockdown method for Nannochloropsis spp., which are emerging model organisms for industrial microalgal oil production. The method achieved a 40-80% success rate in Nannochloropsis oceanica strain IMET1. When transcript level of one carbonic anhydrase (CA) was inhibited by 62-83% via RNAi, mutant cells exhibited photosynthetic oxygen evolution (POE) rates that were 68-100% higher than wild-type (WT) at pH 6.0, equivalent to WT at pH 8.2, yet 39-45% lower than WT at pH 9.0. Moreover, the mutant POE rates were negatively correlated with the increase of culture pH, an exact opposite of WT. Thus, a dynamic carbon concentration mechanism (CCM) that is highly sensitive to pH homeostasis was revealed, where the CA inhibition likely partially abrogated the mechanism that normally deactivates CCM under a high level of dissolved CO2 . Extension of the method to another sequenced N. oceanica strain of CCMP 1779 demonstrated comparable performance. Finally, McrBC-PCR followed by bisulfite sequencing revealed that the gene knockdown is mediated by the CG, CHG and CHH types of DNA methylation at the coding region of the targeted gene. The efficiency, robustness and general applicability of this reverse genetics approach suggested the possibility of large-scale RNAi-based gene function screening in industrial microalgae.
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Affiliation(s)
- Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Yang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
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130
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Yao L, Tan KWM, Tan TW, Lee YK. Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing. BMC Bioinformatics 2017; 18:122. [PMID: 28228091 PMCID: PMC5322580 DOI: 10.1186/s12859-017-1551-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/16/2017] [Indexed: 12/31/2022] Open
Abstract
Background RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microalgal strains with potential as biofuel sources. However, insufficient genomic or transcriptomic information of non-model microalgae has limited the understanding of their regulatory mechanisms and hampered genetic manipulation to enhance biofuel production. As such, an optimal microalgal transcriptomic database construction is a subject of urgent investigation. Results Dunaliella tertiolecta, a non-model oleaginous microalgal species, was sequenced via Illumina MISEQ and HISEQ 4000 in RNA-Seq studies. The high quality high-throughout sequencing data were explored using high performance computing (HPC) in a petascale data center and subjected to de novo assembly and parallelized mpiBLASTX search with multiple species. As a result, a transcriptome database of 17,845 was constructed (~95% completeness). This enlarged database constructed fueled the RNA-Seq data analysis, which was validated by a nitrogen deprivation (ND) study that induces triacylglycerol (TAG) production. Conclusions The new paralleled assembly and annotation method under HPC presented here allows the solution of large-scale data processing problems in acceptable computation time. There is significant increase in the number of transcriptomic data achieved and observable heterogeneity in the performance to identify differentially expressed genes in the ND treatment paradigm. The results provide new insights as to how response to ND treatment in microalgae is regulated. ND analyses highlight the advantages of this database generated in this study that could also serve as a useful resource for future gene manipulation and transcriptome-wide analysis. We thus demonstrate the usefulness of exploring the transcriptome as an informative platform for functional studies and genetic manipulations in similar species. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1551-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lina Yao
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Kenneth Wei Min Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.,National Supercomputing Centre (NSCC), Singapore, 138632, Singapore
| | - Yuan Kun Lee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
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Olsson S, Penacho V, Puente-Sánchez F, Díaz S, Gonzalez-Pastor JE, Aguilera A. Horizontal Gene Transfer of Phytochelatin Synthases from Bacteria to Extremophilic Green Algae. MICROBIAL ECOLOGY 2017; 73:50-60. [PMID: 27592346 DOI: 10.1007/s00248-016-0848-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Transcriptomic sequencing together with bioinformatic analyses and an automated annotation process led us to identify novel phytochelatin synthase (PCS) genes from two extremophilic green algae (Chlamydomonas acidophila and Dunaliella acidophila). These genes are of intermediate length compared to known PCS genes from eukaryotes and PCS-like genes from prokaryotes. A detailed phylogenetic analysis gives new insight into the complicated evolutionary history of PCS genes and provides evidence for multiple horizontal gene transfer events from bacteria to eukaryotes within the gene family. A separate subgroup containing PCS-like genes within the PCS gene family is not supported since the PCS genes are monophyletic only when the PCS-like genes are included. The presence and functionality of the novel genes in the organisms were verified by genomic sequencing and qRT-PCR. Furthermore, the novel PCS gene in Chlamydomonas acidophila showed very strong induction by cadmium. Cloning and expression of the gene in Escherichia coli clearly improves its cadmium resistance. The gene in Dunaliella was not induced, most likely due to gene duplication.
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Affiliation(s)
- Sanna Olsson
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland.
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
| | - Vanessa Penacho
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
- Bioarray, S.L., Parque Científico y Empresarial de la UMH. Edificio Quorum III, Avenida de la Universidad s/n, 03202, Elche, Alicante, Spain
| | - Fernando Puente-Sánchez
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Silvia Díaz
- Departamento de Microbiología-III, Facultad de Biología, Universidad Complutense (UCM), Madrid, Spain
| | | | - Angeles Aguilera
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
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132
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Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Microbiol Mol Biol Rev 2016; 81:81/1/e00040-16. [PMID: 28031352 DOI: 10.1128/mmbr.00040-16] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
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133
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Allen JW, DiRusso CC, Black PN. Carbon and Acyl Chain Flux during Stress-induced Triglyceride Accumulation by Stable Isotopic Labeling of the Polar Microalga Coccomyxa subellipsoidea C169. J Biol Chem 2016; 292:361-374. [PMID: 27903654 DOI: 10.1074/jbc.m116.760843] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/29/2016] [Indexed: 01/06/2023] Open
Abstract
Deriving biofuels and other lipoid products from algae is a promising future technology directly addressing global issues of atmospheric CO2 balance. To better understand the metabolism of triglyceride synthesis in algae, we examined their metabolic origins in the model species, Coccomyxa subellipsoidea C169, using stable isotopic labeling. Labeling patterns arising from [U-13C]glucose, 13CO2, or D2O supplementation were analyzed by GC-MS and/or LC-MS over time courses during nitrogen starvation to address the roles of catabolic carbon recycling, acyl chain redistribution, and de novo fatty acid (FA) synthesis during the expansion of the lipid bodies. The metabolic origin of stress-induced triglyceride was found to be a continuous 8:2 ratio between de novo synthesized FA and acyl chain transfer from pre-stressed membrane lipids with little input from lipid remodeling. Membrane lipids were continually synthesized with associated acyl chain editing during nitrogen stress, in contrast to an overall decrease in total membrane lipid. The incorporation rates of de novo synthesized FA into lipid classes were measured over a time course of nitrogen starvation. The synthesis of triglycerides, phospholipids, and galactolipids followed a two-stage pattern where nitrogen starvation resulted in a 2.5-fold increase followed by a gradual decline. Acyl chain flux into membrane lipids was dominant in the first stage followed by triglycerides. These data indicate that the level of metabolic control that determines acyl chain flux between membrane lipids and triglycerides during nitrogen stress relies primarily on the Kennedy pathway and de novo FA synthesis with limited, defined input from acyl editing reactions.
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Affiliation(s)
- James W Allen
- From the Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Concetta C DiRusso
- From the Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Paul N Black
- From the Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664
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134
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Chilling out: the evolution and diversification of psychrophilic algae with a focus on Chlamydomonadales. Polar Biol 2016. [DOI: 10.1007/s00300-016-2045-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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135
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Galindo-Trigo S, Gray JE, Smith LM. Conserved Roles of CrRLK1L Receptor-Like Kinases in Cell Expansion and Reproduction from Algae to Angiosperms. FRONTIERS IN PLANT SCIENCE 2016; 7:1269. [PMID: 27621737 PMCID: PMC5002434 DOI: 10.3389/fpls.2016.01269] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/10/2016] [Indexed: 05/20/2023]
Abstract
Receptor-like kinases (RLKs) are regulators of plant development through allowing cells to sense their extracellular environment. They facilitate detection of local endogenous signals, in addition to external biotic and abiotic stimuli. The Catharanthus roseus RLK1-like (CrRLK1L) protein kinase subfamily, which contains FERONIA, plays a central role in regulating fertilization and in cell expansion mechanisms such as cell elongation and tip growth, as well as having indirect links to plant-pathogen interactions. Several components of CrRLK1L signaling pathways have been identified, including an extracellular ligand, coreceptors, and downstream signaling elements. The presence and abundance of the CrRLK1L proteins in the plant kingdom suggest an origin within the Streptophyta lineage, with a notable increase in prevalence in the seeded land plants. Given the function of the sole CrRLK1L protein in a charophycean alga, the possibility of a conserved role in detection and/or regulation of cell wall integrity throughout the Strephtophytes is discussed. Orthologs of signaling pathway components are also present in extant representatives of non-vascular land plants and early vascular land plants including the liverwort Marchantia polymorpha, the moss Physcomitrella patens and the lycophyte Selaginella moellendorffii. Deciphering the roles in development of the CrRLK1L protein kinases in early diverging land plants will provide insights into their ancestral function, furthering our understanding of this diversified subfamily of receptors in higher plants.
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Affiliation(s)
| | - Julie E. Gray
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Lisa M. Smith
- Department of Animal and Plant Sciences, University of SheffieldSheffield, UK
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136
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The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau. Sci Rep 2016; 6:29404. [PMID: 27381465 PMCID: PMC4933973 DOI: 10.1038/srep29404] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/20/2016] [Indexed: 11/09/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP.
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137
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Carniel FC, Gerdol M, Montagner A, Banchi E, De Moro G, Manfrin C, Muggia L, Pallavicini A, Tretiach M. New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach. PLANT MOLECULAR BIOLOGY 2016; 91:319-339. [PMID: 26992400 DOI: 10.1007/s11103-016-0468-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
Trebouxia is the most common lichen-forming genus of aero-terrestrial green algae and all its species are desiccation tolerant (DT). The molecular bases of this remarkable adaptation are, however, still largely unknown. We applied a transcriptomic approach to a common member of the genus, T. gelatinosa, to investigate the alteration of gene expression occurring after dehydration and subsequent rehydration in comparison to cells kept constantly hydrated. We sequenced, de novo assembled and annotated the transcriptome of axenically cultured T. gelatinosa by using Illumina sequencing technology. We tracked the expression profiles of over 13,000 protein-coding transcripts. During the dehydration/rehydration cycle c. 92 % of the total protein-coding transcripts displayed a stable expression, suggesting that the desiccation tolerance of T. gelatinosa mostly relies on constitutive mechanisms. Dehydration and rehydration affected mainly the gene expression for components of the photosynthetic apparatus, the ROS-scavenging system, Heat Shock Proteins, aquaporins, expansins, and desiccation related proteins (DRPs), which are highly diversified in T. gelatinosa, whereas Late Embryogenesis Abundant Proteins were not affected. Only some of these phenomena were previously observed in other DT green algae, bryophytes and resurrection plants, other traits being distinctive of T. gelatinosa, and perhaps related to its symbiotic lifestyle. Finally, the phylogenetic inference extended to DRPs of other chlorophytes, embryophytes and bacteria clearly pointed out that DRPs of chlorophytes are not orthologous to those of embryophytes: some of them were likely acquired through horizontal gene transfer from extremophile bacteria which live in symbiosis within the lichen thallus.
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Affiliation(s)
- Fabio Candotto Carniel
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
- Institute of Botany, University of Innsbruck, Sternwartestraße, 15, 6020, Innsbruck, Austria
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy.
| | - Alice Montagner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Elisa Banchi
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Gianluca De Moro
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Chiara Manfrin
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Lucia Muggia
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Mauro Tretiach
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
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138
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Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG. Comparative genomics explains the evolutionary success of reef-forming corals. eLife 2016; 5. [PMID: 27218454 PMCID: PMC4878875 DOI: 10.7554/elife.13288] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/20/2016] [Indexed: 12/30/2022] Open
Abstract
Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years. DOI:http://dx.doi.org/10.7554/eLife.13288.001 For millions of years, reef-building stony corals have created extensive habitats for numerous marine plants and animals in shallow tropical seas. Stony corals consist of many small, tentacled animals called polyps. These polyps secrete a mineral called aragonite to create the reef – an external ‘skeleton’ that supports and protects the corals. Photosynthesizing algae live inside the cells of stony corals, and each species depends on the other to survive. The algae produce the coral’s main source of food, although they also produce some waste products that can harm the coral if they build up inside cells. If the oceans become warmer and more acidic, the coral are more likely to become stressed and expel the algae from their cells in a process known as coral bleaching. This makes the coral more likely to die or become diseased. Corals have survived previous periods of ocean warming, although it is not known how they evolved to do so. The evolutionary history of an organism can be traced by studying its genome – its complete set of DNA – and the RNA molecules encoded by these genes. Bhattacharya et al. performed this analysis for twenty stony coral species, and compared the resulting genome and RNA sequences with the genomes of other related marine organisms, such as sea anemones and sponges. In particular, Bhattacharya et al. examined “ortholog” groups of genes, which are present in different species and evolved from a common ancestral gene. This analysis identified the genes in the corals that encode the proteins responsible for constructing the aragonite skeleton. The coral genome also encodes a network of environmental sensors that coordinate how the polyps respond to temperature, light and acidity. Bhattacharya et al. also uncovered a variety of stress-related pathways, including those that detoxify the polyps of the damaging molecules generated by algae, and the pathways that enable the polyps to adapt to environmental stress. Many of these genes were recruited from other species in a process known as horizontal gene transfer. The oceans are expected to become warmer and more acidic in the coming centuries. Provided that humans do not physically destroy the corals’ habitats, the evidence found by Bhattacharya et al. suggests that the genome of the corals contains the diversity that will allow them to adapt to these new conditions. DOI:http://dx.doi.org/10.7554/eLife.13288.002
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Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States.,Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States
| | - Shobhit Agrawal
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Baumgarten
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mahdi Belcaid
- Hawaii Institute of Marine Biology, Kaneohe, United States
| | - Jeana L Drake
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States
| | - Douglas Erwin
- Smithsonian Institution, National Museum of Natural History, Washington, United States
| | - Sylvian Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia.,Research School of Biology, Australian National University, Canberra, Australia
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, United States
| | - David F Gruber
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, United States.,Department of Natural Sciences, City University of New York, Baruch College and The Graduate Center, New York, United States
| | - Bishoy Kamel
- Department of Biology, Mueller Lab, Penn State University, University Park, United States
| | - Michael P Lesser
- School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, United States
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gam, Israel
| | - Yi Jin Liew
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthew MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Tali Mass
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States.,Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Israel
| | - Monica Medina
- Department of Biology, Mueller Lab, Penn State University, University Park, United States
| | - Shaadi Mehr
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, United States.,Biological Science Department, State University of New York, College at Old Westbury, New York, United States
| | - Eli Meyer
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Dana C Price
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, United States
| | | | - Huan Qiu
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexander J Stokes
- Laboratory of Experimental Medicine and Department of Cell and Molecular Biology, John A. Burns School of Medicine, Honolulu, United States.,Chaminade University, Honolulu, United States
| | | | - Dan Tchernov
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Israel
| | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nicole Wagner
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | - Charles W Walker
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Andreas Pm Weber
- Institute of Plant Biochemistry, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Virginia Weis
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, United States
| | | | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, United States.,Department of Earth and Planetary Sciences, Rutgers University, New Jersey, United States
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139
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The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nat Commun 2016; 7:11370. [PMID: 27102219 PMCID: PMC4844696 DOI: 10.1038/ncomms11370] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/18/2016] [Indexed: 12/30/2022] Open
Abstract
The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.
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140
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Shemi A, Ben-Dor S, Vardi A. Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes. Autophagy 2016; 11:701-15. [PMID: 25915714 DOI: 10.1080/15548627.2015.1034407] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Aquatic photosynthetic eukaryotes represent highly diverse groups (green, red, and chromalveolate algae) derived from multiple endosymbiosis events, covering a wide spectrum of the tree of life. They are responsible for about 50% of the global photosynthesis and serve as the foundation for oceanic and fresh water food webs. Although the ecophysiology and molecular ecology of some algal species are extensively studied, some basic aspects of algal cell biology are still underexplored. The recent wealth of genomic resources from algae has opened new frontiers to decipher the role of cell signaling pathways and their function in an ecological and biotechnological context. Here, we took a bioinformatic approach to explore the distribution and conservation of TOR and autophagy-related (ATG) proteins (Atg in yeast) in diverse algal groups. Our genomic analysis demonstrates conservation of TOR and ATG proteins in green algae. In contrast, in all 5 available red algal genomes, we could not detect the sequences that encode for any of the 17 core ATG proteins examined, albeit TOR and its interacting proteins are conserved. This intriguing data suggests that the autophagy pathway is not conserved in red algae as it is in the entire eukaryote domain. In contrast, chromalveolates, despite being derived from the red-plastid lineage, retain and express ATG genes, which raises a fundamental question regarding the acquisition of ATG genes during algal evolution. Among chromalveolates, Emiliania huxleyi (Haptophyta), a bloom-forming coccolithophore, possesses the most complete set of ATG genes, and may serve as a model organism to study autophagy in marine protists with great ecological significance.
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Key Words
- ATG, autophagy related
- ATG8
- ATG9
- DUF, domain of unknown function
- EST, expressed sequence tag
- EhV, Emiliania huxleyi virus
- GABARAP, GABA(A) receptor-associated protein
- PtdIns3K, phosphatidylinositol 3-kinase
- RPTOR, regulatory associated protein of MTOR, complex 1
- TOR, target of rapamycin
- TORC, target of rapamycin complex
- Ubl, ubiquitin-like
- Vps, vacuolar protein sorting
- algae
- autophagy
- blooms
- chromalveolata
- phylogenetics
- phytoplankton
- rhodophyta
- stress
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Affiliation(s)
- Adva Shemi
- a Department of Plant Sciences ; Weizmann Institute of Science ; Rehovot , Israel
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141
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Sun P, Leeson C, Zhi X, Leng F, Pierce RH, Henry MS, Rein KS. Characterization of an epoxide hydrolase from the Florida red tide dinoflagellate, Karenia brevis. PHYTOCHEMISTRY 2016; 122:11-21. [PMID: 26626160 PMCID: PMC4724521 DOI: 10.1016/j.phytochem.2015.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/19/2015] [Accepted: 11/05/2015] [Indexed: 05/11/2023]
Abstract
Epoxide hydrolases (EH, EC 3.3.2.3) have been proposed to be key enzymes in the biosynthesis of polyether (PE) ladder compounds such as the brevetoxins which are produced by the dinoflagellate Karenia brevis. These enzymes have the potential to catalyze kinetically disfavored endo-tet cyclization reactions. Data mining of K. brevis transcriptome libraries revealed two classes of epoxide hydrolases: microsomal and leukotriene A4 (LTA4) hydrolases. A microsomal EH was cloned and expressed for characterization. The enzyme is a monomeric protein with molecular weight 44kDa. Kinetic parameters were evaluated using a variety of epoxide substrates to assess substrate selectivity and enantioselectivity, as well as its potential to catalyze the critical endo-tet cyclization of epoxy alcohols. Monitoring of EH activity in high and low toxin producing cultures of K. brevis over a three week period showed consistently higher activity in the high toxin producing culture implicating the involvement of one or more EH in brevetoxin biosynthesis.
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Affiliation(s)
- Pengfei Sun
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Cristian Leeson
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Xiaoduo Zhi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Richard H Pierce
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA.
| | - Michael S Henry
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA.
| | - Kathleen S Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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142
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Abstract
Microalgae present a huge and still insufficiently tapped resource of very long-chain omega-3 and omega-6 polyunsaturated fatty acids (VLC-PUFA) for human nutrition and medicinal applications. This chapter describes the diversity of unicellular eukaryotic microalgae in respect to VLC-PUFA biosynthesis. Then, we outline the major biosynthetic pathways mediating the formation of VLC-PUFA by sequential desaturation and elongation of C18-PUFA acyl groups. We address the aspects of spatial localization of those pathways and elaborate on the role for VLC-PUFA in microalgal cells. Recent progress in microalgal genetic transformation and molecular engineering has opened the way to increased production efficiencies for VLC-PUFA. The perspectives of photobiotechnology and metabolic engineering of microalgae for altered or enhanced VLC-PUFA production are also discussed.
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Affiliation(s)
- Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel.
| | - Stefan Leu
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
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143
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Peng H, Wei D, Chen G, Chen F. Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:151. [PMID: 27453726 PMCID: PMC4957332 DOI: 10.1186/s13068-016-0571-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/12/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Microalgae are emerging as suitable feedstock for renewable biofuel production and providing a promising way to alleviate green house gas CO2. Characterizing the metabolic pathways involved in the biosynthesis of energy-rich compounds and their global regulation upon elevated CO2 is necessary to explore the mechanism underlying rapid growth and lipid accumulation, so as to realize the full potential of these organisms as energy resources. RESULTS In the present study, 2 and 5 % CO2 increased growth rate and lipid accumulation in autotrophically cultured green alga Coccomyxa subellipsoidea C-169. Overall biomass productivity as 222 mg L(-1) day(-1) and fatty acid content as 48.5 % dry cell weight were attained in 2 % CO2, suggesting C-169 as a great candidate for lipid production via CO2 supplementation. Transcriptomic analysis of 2 % against 0.04 % CO2-cultured C-169 unveiled the global regulation of important metabolic processes. Other than enhancing gene expression in the Calvin cycle, C-169 upregulated the expression of phosphoenolpyruvate carboxylase, pyruvate carboxylase and carbamoyl-phosphate synthetase II to enhance the anaplerotic carbon assimilation reactions upon elevated CO2. Upregulation of ferredoxin and ferredoxin-NADP(+) reductase implied that plentiful energy captured through photosynthesis was transferred through ferredoxin to sustain rapid growth and lipid accumulation. Genes involved in the glycolysis, TCA cycle and oxidative phosphorylation were predominantly upregulated presumably to provide abundant intermediates and metabolic energy for anabolism. Coordinated upregulation of nitrogen acquisition and assimilation genes, together with activation of specific carbamoyl-phosphate synthetase and ornithine pathway genes, might help C-169 to maintain carbon/nitrogen balance upon elevated CO2. Significant downregulation of fatty acid degradation genes, as well as the upregulation of fatty acid synthesis genes at the later stage might contribute to the tremendous lipid accumulation. CONCLUSION Global and collaborative regulation was employed by C-169 to assimilate more carbon and maintain carbon/nitrogen balance upon elevated CO2, which provide abundant carbon skeleton and affluent metabolic energy to sustain rapid growth and lipid accumulation. Data here for the first time bring significant insights into the regulatory profile of metabolism and acclimation to elevated CO2 in C-169, which provide important information for future metabolic engineering in the development of sustainable microalgae-based biofuels.
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Affiliation(s)
- Huifeng Peng
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
| | - Dong Wei
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
| | - Gu Chen
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
| | - Feng Chen
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
- />Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 People’s Republic of China
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Liu M, Lu S. Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering. FRONTIERS IN PLANT SCIENCE 2016; 7:1898. [PMID: 28018418 PMCID: PMC5159609 DOI: 10.3389/fpls.2016.01898] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/30/2016] [Indexed: 05/04/2023]
Abstract
Plastoquinone (PQ) and ubiquinone (UQ) are two important prenylquinones, functioning as electron transporters in the electron transport chain of oxygenic photosynthesis and the aerobic respiratory chain, respectively, and play indispensable roles in plant growth and development through participating in the biosynthesis and metabolism of important chemical compounds, acting as antioxidants, being involved in plant response to stress, and regulating gene expression and cell signal transduction. UQ, particularly UQ10, has also been widely used in people's life. It is effective in treating cardiovascular diseases, chronic gingivitis and periodontitis, and shows favorable impact on cancer treatment and human reproductive health. PQ and UQ are made up of an active benzoquinone ring attached to a polyisoprenoid side chain. Biosynthesis of PQ and UQ is very complicated with more than thirty five enzymes involved. Their synthetic pathways can be generally divided into two stages. The first stage leads to the biosynthesis of precursors of benzene quinone ring and prenyl side chain. The benzene quinone ring for UQ is synthesized from tyrosine or phenylalanine, whereas the ring for PQ is derived from tyrosine. The prenyl side chains of PQ and UQ are derived from glyceraldehyde 3-phosphate and pyruvate through the 2-C-methyl-D-erythritol 4-phosphate pathway and/or acetyl-CoA and acetoacetyl-CoA through the mevalonate pathway. The second stage includes the condensation of ring and side chain and subsequent modification. Homogentisate solanesyltransferase, 4-hydroxybenzoate polyprenyl diphosphate transferase and a series of benzene quinone ring modification enzymes are involved in this stage. PQ exists in plants, while UQ widely presents in plants, animals and microbes. Many enzymes and their encoding genes involved in PQ and UQ biosynthesis have been intensively studied recently. Metabolic engineering of UQ10 in plants, such as rice and tobacco, has also been tested. In this review, we summarize and discuss recent research progresses in the biosynthetic pathways of PQ and UQ and enzymes and their encoding genes involved in side chain elongation and in the second stage of PQ and UQ biosynthesis. Physiological functions of PQ and UQ played in plants as well as the practical application and metabolic engineering of PQ and UQ are also included.
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145
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Zhang L, Wang X, Yu M, Qiao Y, Zhang XH. Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle. BMC Genomics 2015; 16:1092. [PMID: 26690083 PMCID: PMC4687298 DOI: 10.1186/s12864-015-2326-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/15/2015] [Indexed: 01/22/2023] Open
Abstract
Background Luteimonas abyssi XH031T, which was previously isolated from subseafloor environment of the South Pacific Gyre (SPG), was an aerobic, gram-negative bacterium, and was identified to be a novel species of the genus Luteimonas in the family of Xanthomonadaceae. The nutrients utilization and metabolic mechanisms of XH031T indicate its plasticity. In view of the above characteristics, its genome was sequenced, and an in-depth analysis of the XH031T genome was performed to elucidate its adaption to extreme ecological environment. Results Various macromolecules including polysaccharide, protein, lipid and DNA could be degraded at low temperature by XH031T under laboratory conditions, and its degradation abilities to starch, gelatin and casein were considerably strong. Genome sequence analysis indicated that XH031T possesses extensive enzyme-encoding genes compared with four other Luteimonas strains. In addition, intricate systems (such as two-component regulatory systems, secretion systems, etc.), which are often used by bacteria to modulate the interactions of bacteria with their environments, were predicted in the genome of XH031T. Genes encoding a choline-glycine betaine transporter and 99 extracellular peptidases featured with halophilicity were predicted in the genome, which might help the bacterium to adapt to the salty marine environment. Moreover, there were many gene clusters in the genome encoding ATP-binding cassette superfamily transporters, major facilitator superfamily transporters and cytochrome P450s that might function in the process of various substrate transportation and metabolisms. Furthermore, drug resistance genes harbored in the genome might signify that XH031T has evolved hereditary adaptation to toxic environment. Finally, the annotation of metabolic pathways of the elements (such as carbon, nitrogen, sulfur, phosphor and iron) in the genome elucidated the degradation of organic matter in the deep sediment of the SPG. Conclusions The genome analysis showed that XH031T had genetic advantages to adapt to subseafloor environment. The material metabolism manifests that the strain may play an important ecological role in the biogeochemical cycle of the SPG, and various cold-adapted extracelluar enzymes produced by the strain may have significant value in application. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2326-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China. .,College of Life Science, Qingdao Agriculture University, Qingdao, 266109, China.
| | - Xiaolei Wang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
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146
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Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME JOURNAL 2015; 10:1134-46. [PMID: 26613339 PMCID: PMC5029228 DOI: 10.1038/ismej.2015.192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/27/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022]
Abstract
Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often
as a component of retrotransposons, as well as in retroviruses and in
prokaryotic retroelements. We investigated the abundance, classification and
transcriptional status of RTs based on Tara Oceans marine metagenomes
and metatranscriptomes encompassing a wide organism size range. Our analyses
revealed that RTs predominate large-size fraction metagenomes
(>5 μm), where they reached a maximum of 13.5% of the total
gene abundance. Metagenomic RTs were widely distributed across the phylogeny of
known RTs, but many belonged to previously uncharacterized clades.
Metatranscriptomic RTs showed distinct abundance patterns across samples
compared with metagenomic RTs. The relative abundances of viral and bacterial
RTs among identified RT sequences were higher in metatranscriptomes than in
metagenomes and these sequences were detected in all metatranscriptome size
fractions. Overall, these observations suggest an active proliferation of
various RT-assisted elements, which could be involved in genome evolution or
adaptive processes of plankton assemblage.
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147
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Kobayashi Y, Takusagawa M, Harada N, Fukao Y, Yamaoka S, Kohchi T, Hori K, Ohta H, Shikanai T, Nishimura Y. Eukaryotic Components Remodeled Chloroplast Nucleoid Organization during the Green Plant Evolution. Genome Biol Evol 2015; 8:1-16. [PMID: 26608058 PMCID: PMC4758235 DOI: 10.1093/gbe/evv233] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chloroplast (cp) DNA is thought to originate from the ancestral endosymbiont genome and is compacted to form nucleoprotein complexes, cp nucleoids. The structure of cp nucleoids is ubiquitously observed in diverse plants from unicellular algae to flowering plants and is believed to be a multifunctional platform for various processes, including cpDNA replication, repair/recombination, transcription, and inheritance. Despite its fundamental functions, the protein composition for cp nucleoids in flowering plants was suggested to be divergent from those of bacteria and algae, but the evolutionary process remains elusive. In this research, we aimed to reveal the evolutionary history of cp nucleoid organization by analyzing the key organisms representing the three evolutionary stages of eukaryotic phototrophs: the chlorophyte alga Chlamydomonas reinhardtii, the charophyte alga Klebsormidium flaccidum, and the most basal land plant Marchantia polymorpha. To clarify the core cp nucleoid proteins in C. reinhardtii, we performed an LC-MS/MS analysis using highly purified cp nucleoid fractions and identified a novel SAP domain-containing protein with a eukaryotic origin as a constitutive core component. Then, homologous genes for cp nucleoid proteins were searched for in C. reinhardtii, K. flaccidum, and M. polymorpha using the genome databases, and their intracellular localizations and DNA binding activities were investigated by cell biological/biochemical analyses. Based on these results, we propose a model that recurrent modification of cp nucleoid organization by eukaryotic factors originally related to chromatin organization might have been the driving force for the diversification of cp nucleoids since the early stage of green plant evolution.
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Affiliation(s)
- Yusuke Kobayashi
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
| | - Mari Takusagawa
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Naomi Harada
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
| | - Yoichiro Fukao
- Plant Global Educational Project, and Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan Department of Bioinformatics, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Koichi Hori
- Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama City, Kanagawa, Japan
| | - Hiroyuki Ohta
- Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama City, Kanagawa, Japan Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-Ku, Tokyo, Japan
| | - Toshiharu Shikanai
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
| | - Yoshiki Nishimura
- Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan
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Yao L, Tan TW, Ng YK, Ban KHK, Shen H, Lin H, Lee YK. RNA-Seq transcriptomic analysis with Bag2D software identifies key pathways enhancing lipid yield in a high lipid-producing mutant of the non-model green alga Dunaliella tertiolecta. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:191. [PMID: 26613001 PMCID: PMC4660794 DOI: 10.1186/s13068-015-0382-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 11/13/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND For many years, increasing demands for fossil fuels have met with limited supply. As a potential substitute and renewable source of biofuel feedstock, microalgae have received significant attention. However, few of the current algal species produce high lipid yields to be commercially viable. To discover more high yielding strains, next-generation sequencing technology is used to elucidate lipid synthetic pathways and energy metabolism involved in lipid yield. When subjected to manipulation by genetic and metabolic engineering, enhancement of such pathways may further enhance lipid yield. RESULTS In this study, transcriptome profiling of a random insertional mutant with enhanced lipid production generated from a non-model marine microalga Dunaliella tertiolecta is presented. D9 mutant has a lipid yield that is 2- to 4-fold higher than that of wild type. Using novel Bag2D-workflow scripts developed and reported here, the non-redundant transcripts from de novo assembly were annotated based on the best hits in five model microalgae, namely Chlamydomonas reinhardtii, Coccomyxa subellipsoidea C-169, Ostreococcus lucimarinus, Volvox carteri, Chlorella variabilis NC64A and a high plant species Arabidopsis thaliana. The assembled contigs (~181 Mb) includes 481,381 contigs, covering 10,185 genes. Pathway analysis showed that a pathway from inositol phosphate metabolism to fatty acid biosynthesis is the most significantly correlated with higher lipid yield in this mutant. CONCLUSIONS Herein, we described a pipeline to analyze RNA-Seq data without pre-existing transcriptomic information. The draft transcriptome of D. tertiolecta was constructed and annotated, which offered useful information for characterizing high lipid-producing mutants. D. tertiolecta mutant was generated with an enhanced photosynthetic efficiency and lipid production. RNA-Seq data of the mutant and wild type were compared, providing biological insights into the expression patterns of contigs associated with energy metabolism and carbon flow pathways. Comparison of D. tertiolecta genes with homologs of five other green algae and a model high plant species can facilitate the annotation of D. tertiolecta and lead to a more complete annotation of its sequence database, thus laying the groundwork for optimization of lipid production pathways based on genetic manipulation.
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Affiliation(s)
- Lina Yao
- />Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tin Wee Tan
- />Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yi-Kai Ng
- />Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kenneth Hon Kim Ban
- />Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- />Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Hui Shen
- />Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Huixin Lin
- />Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yuan Kun Lee
- />Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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149
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Conversion of a light-driven proton pump into a light-gated ion channel. Sci Rep 2015; 5:16450. [PMID: 26597707 PMCID: PMC4657025 DOI: 10.1038/srep16450] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022] Open
Abstract
Interest in microbial rhodopsins with ion pumping activity has been revitalized in the context of optogenetics, where light-driven ion pumps are used for cell hyperpolarization and voltage sensing. We identified an opsin-encoding gene (CsR) in the genome of the arctic alga Coccomyxa subellipsoidea C-169 that can produce large photocurrents in Xenopus oocytes. We used this property to analyze the function of individual residues in proton pumping. Modification of the highly conserved proton shuttling residue R83 or its interaction partner Y57 strongly reduced pumping power. Moreover, this mutation converted CsR at moderate electrochemical load into an operational proton channel with inward or outward rectification depending on the amino acid substitution. Together with molecular dynamics simulations, these data demonstrate that CsR-R83 and its interacting partner Y57 in conjunction with water molecules forms a proton shuttle that blocks passive proton flux during the dark-state but promotes proton movement uphill upon illumination.
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150
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Fulnečková J, Ševčíková T, Lukešová A, Sýkorová E. Transitions between the Arabidopsis-type and the human-type telomere sequence in green algae (clade Caudivolvoxa, Chlamydomonadales). Chromosoma 2015; 125:437-51. [PMID: 26596989 DOI: 10.1007/s00412-015-0557-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022]
Abstract
Telomeres are nucleoprotein structures that distinguish native chromosomal ends from double-stranded breaks. They are maintained by telomerase that adds short G-rich telomeric repeats at chromosomal ends in most eukaryotes and determines the TnAmGo sequence of canonical telomeres. We employed an experimental approach that was based on detection of repeats added by telomerase to identify the telomere sequence type forming the very ends of chromosomes. Our previous studies that focused on the algal order Chlamydomonadales revealed several changes in telomere motifs that were consistent with the phylogeny and supported the concept of the Arabidopsis-type sequence being the ancestral telomeric motif for green algae. In addition to previously described independent transitions to the Chlamydomonas-type sequence, we report that the ancestral telomeric motif was replaced by the human-type sequence in the majority of algal species grouped within a higher order clade, Caudivolvoxa. The Arabidopsis-type sequence was apparently retained in the Polytominia clade. Regarding the telomere sequence, the Chlorogonia clade within Caudivolvoxa bifurcates into two groups, one with the human-type sequence and the other group with the Arabidopsis-type sequence that is solely formed by the Chlorogonium species. This suggests that reversion to the Arabidopsis-type telomeric motif occurred in the common ancestral Chlorogonium species. The human-type sequence is also synthesized by telomerases of algal strains from Arenicolinia, Dunaliellinia and Stephanosphaerinia, except a distinct subclade within Stephanosphaerinia, where telomerase activity was not detected and a change to an unidentified telomeric motif might arise. We discuss plausible reasons why changes in telomeric motifs were tolerated during evolution of green algae.
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Affiliation(s)
- Jana Fulnečková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic.,Faculty of Science, and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Life Science Research Centre & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, CZ-71000, Ostrava, Czech Republic
| | - Alena Lukešová
- Institute of Soil Biology, Biology Centre Academy of Sciences of the Czech Republic, v.vi., Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic. .,Faculty of Science, and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
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