Author
Ansgar Gruber
Other affiliations: Academy of Sciences of the Czech Republic, Dalhousie University, Alfred Wegener Institute for Polar and Marine Research
Bio: Ansgar Gruber is an academic researcher from University of Konstanz. The author has contributed to research in topics: Phaeodactylum tricornutum & Plastid. The author has an hindex of 22, co-authored 41 publications receiving 3651 citations. Previous affiliations of Ansgar Gruber include Academy of Sciences of the Czech Republic & Dalhousie University.
Topics: Phaeodactylum tricornutum, Plastid, Diatom, Chloroplast, Endosymbiosis
Papers
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École Normale Supérieure1, J. Craig Venter Institute2, Joint Genome Institute3, Alfred Wegener Institute for Polar and Marine Research4, University of Konstanz5, University of Wisconsin–Milwaukee6, University of Melbourne7, University of Washington8, University of Nantes9, University of Wisconsin-Madison10, Ghent University11, University of Rhode Island12, Sewanee: The University of the South13, University of Arizona14, Hebrew University of Jerusalem15, Georgia Institute of Technology16, Leibniz Institute for Neurobiology17, Stazione Zoologica Anton Dohrn18, University of British Columbia19, Stanford University20, Scottish Association for Marine Science21, University of North Carolina at Wilmington22
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
1,500 citations
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TL;DR: A detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum is presented, which provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diats, which is of significance for an improved understanding of global carbon cycles.
Abstract: Background
Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids.
408 citations
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Dalhousie University1, University of British Columbia2, University of Konstanz3, University of Toronto4, Centre national de la recherche scientifique5, United States Department of Energy6, University of Freiburg7, University of Ostrava8, University of Alberta9, Academy of Sciences of the Czech Republic10, Sewanee: The University of the South11, University of New Brunswick12, University of Washington13, University of Exeter14, Aix-Marseille University15, Science for Life Laboratory16, University of Tsukuba17, American Museum of Natural History18, Natural History Museum19, Monterey Bay Aquarium Research Institute20, University of East Anglia21, University of Canterbury22, San Francisco State University23, Reed College24, National Center for Genome Resources25, University of Melbourne26
TL;DR: The nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans are sequenced and extensive genetic and biochemical mosaicism is revealed, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosYmbionT cytOSol of both algae.
Abstract: Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
356 citations
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University of East Anglia1, Joint Genome Institute2, Norwich Research Park3, Stazione Zoologica Anton Dohrn4, J. Craig Venter Institute5, Scripps Institution of Oceanography6, Alfred Wegener Institute for Polar and Marine Research7, Université Paris-Saclay8, École Normale Supérieure9, University of Paris10, Leibniz Association11, University of Cologne12, University of Konstanz13, Medical University of South Carolina14, University of Duisburg-Essen15, Leibniz Institute for Neurobiology16, University of Washington17, University of Nevada, Las Vegas18, Monterey Bay Aquarium Research Institute19, University of British Columbia20, University of California, Berkeley21
TL;DR: In this article, the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms was studied.
Abstract: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
287 citations
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TL;DR: This comprehensive mutational analysis found that only the aromatic amino acids phenylalanine, tryptophan, tyrosine and the bulky amino acid leucine at the +1 position of the predicted signal peptidase cleavage site allow plastid import, as expected from the sequence comparison of native plastids targeting presequences of P. tricornutum and the cryptophyte Guillardia theta.
Abstract: Plastids of diatoms and related algae evolved by secondary endocytobiosis, the uptake of a eukaryotic alga into a eukaryotic host cell and its subsequent reduction into an organelle. As a result diatom plastids are sur- rounded by four membranes. Protein targeting of nucleus encoded plastid proteins across these membranes depends on N-terminal bipartite presequences consisting of a signal and a transit peptide-like domain. Diatoms and crypto- phytes share a conserved amino acid motif of unknown function at the cleavage site of the signal peptides (ASA- FAP), which is particularly important for successful plastid targeting. Screening genomic databases we found that in rare cases the very conserved phenylalanine within the motif may be replaced by tryptophan, tyrosine or leucine. To test such unusual presequences for functionality and to better understand the role of the motif and putative receptor proteins involved in targeting, we constructed prese- quence:GFP fusion proteins with or without modifications of the ''ASAFAP''-motif and expressed them in the diatom Phaeodactylum tricornutum. In this comprehensive muta- tional analysis we found that only the aromatic amino acids phenylalanine, tryptophan, tyrosine and the bulky amino acid leucine at the +1 position of the predicted signal peptidase cleavage site allow plastid import, as expected from the sequence comparison of native plastid targeting presequences of P. tricornutum and the cryptophyte Guil- lardia theta. Deletions within the signal peptide domains also impaired plastid import, showing that the presence of F at the N-terminus of the transit peptide together with a cleavable signal peptide is crucial for plastid import.
193 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
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TL;DR: Although microalgae are not yet produced at large scale for bulk applications, recent advances—particularly in the methods of systems biology, genetic engineering, and biorefining—present opportunities to develop this process in a sustainable and economical way within the next 10 to 15 years.
Abstract: Microalgae are considered one of the most promising feedstocks for biofuels. The productivity of these photosynthetic microorganisms in converting carbon dioxide into carbon-rich lipids, only a step or two away from biodiesel, greatly exceeds that of agricultural oleaginous crops, without competing for arable land. Worldwide, research and demonstration programs are being carried out to develop the technology needed to expand algal lipid production from a craft to a major industrial process. Although microalgae are not yet produced at large scale for bulk applications, recent advances—particularly in the methods of systems biology, genetic engineering, and biorefining—present opportunities to develop this process in a sustainable and economical way within the next 10 to 15 years.
1,712 citations
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École Normale Supérieure1, J. Craig Venter Institute2, Joint Genome Institute3, Alfred Wegener Institute for Polar and Marine Research4, University of Konstanz5, University of Wisconsin–Milwaukee6, University of Melbourne7, University of Washington8, University of Nantes9, University of Wisconsin-Madison10, Ghent University11, University of Rhode Island12, Sewanee: The University of the South13, University of Arizona14, Hebrew University of Jerusalem15, Georgia Institute of Technology16, Leibniz Institute for Neurobiology17, Stazione Zoologica Anton Dohrn18, University of British Columbia19, Stanford University20, Scottish Association for Marine Science21, University of North Carolina at Wilmington22
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
1,500 citations
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TL;DR: Potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes are focused on.
Abstract: There are currently intensive global research efforts aimed at increasing and modifying the accumulation of lipids, alcohols, hydrocarbons, polysaccharides, and other energy storage compounds in photosynthetic organisms, yeast, and bacteria through genetic engineering. Many improvements have been realized, including increased lipid and carbohydrate production, improved H2 yields, and the diversion of central metabolic intermediates into fungible biofuels. Photosynthetic microorganisms are attracting considerable interest within these efforts due to their relatively high photosynthetic conversion efficiencies, diverse metabolic capabilities, superior growth rates, and ability to store or secrete energy-rich hydrocarbons. Relative to cyanobacteria, eukaryotic microalgae possess several unique metabolic attributes of relevance to biofuel production, including the accumulation of significant quantities of triacylglycerol; the synthesis of storage starch (amylopectin and amylose), which is similar to that found in higher plants; and the ability to efficiently couple photosynthetic electron transport to H2 production. Although the application of genetic engineering to improve energy production phenotypes in eukaryotic microalgae is in its infancy, significant advances in the development of genetic manipulation tools have recently been achieved with microalgal model systems and are being used to manipulate central carbon metabolism in these organisms. It is likely that many of these advances can be extended to industrially relevant organisms. This review is focused on potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes.
1,079 citations
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University of British Columbia1, Canadian Institute for Advanced Research2, Monterey Bay Aquarium Research Institute3, Stony Brook University4, University of California, San Diego5, Marine Biological Laboratory6, Brown University7, University of Washington8, Dalhousie University9, National Center for Genome Resources10, Alfred Wegener Institute for Polar and Marine Research11, Rutgers University12, Texas A&M University13, University of Southern California14, University of Delaware15, Victoria University of Wellington16, University of Paris-Sud17, Columbia University18, University of Oslo19, University of Hawaii at Manoa20, University of Prince Edward Island21, University of Rhode Island22, Woods Hole Oceanographic Institution23, Max Planck Society24, Jacobs University Bremen25, Smith College26, University of South Alabama27, University of Geneva28, Saint Petersburg State University29, University of Connecticut30, Laval University31, University of Guelph32, University of North Carolina at Chapel Hill33, University of New Brunswick34, University of Camerino35, University of East Anglia36, Stazione Zoologica Anton Dohrn37, University of Georgia38, University of Technology, Sydney39, University of Puerto Rico40, University of Pisa41, Centre national de la recherche scientifique42, Colorado School of Mines43, Lund University44, University of Western Ontario45, California State University46, University of Texas at Austin47, Los Alamos National Laboratory48, Pierre-and-Marie-Curie University49, University of Oklahoma50, Plymouth Marine Laboratory51, Bigelow Laboratory For Ocean Sciences52, Princeton University53
TL;DR: In this paper, the authors describe a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans and their biology, evolution, and ecology.
Abstract: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
852 citations