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Sun X, LaVoie M, Lefebvre PA, Gallaher SD, Glaesener AG, Strenkert D, Mehta R, Merchant SS, Silflow CD. Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii. bioRxiv 2024:2024.03.22.586359. [PMID: 38586028 PMCID: PMC10996464 DOI: 10.1101/2024.03.22.586359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation of HYDA1 transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of the HYDA1 promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termed cehc1-1 , leads to constitutive expression of HYDA1 and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway. CRR1 was required for the constitutive expression of the HYDA1 reporter gene in cehc1-1 mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized in cehc1-1 cells, supporting the conclusion that CEHC1 acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in the CRR1 pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
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Davidi L, Gallaher SD, Ben-David E, Purvine SO, Fillmore TL, Nicora CD, Craig RJ, Schmollinger S, Roje S, Blaby-Haas CE, Auber RP, Wisecaver JH, Merchant SS. Pumping iron: A multi-omics analysis of two extremophilic algae reveals iron economy management. Proc Natl Acad Sci U S A 2023; 120:e2305495120. [PMID: 37459532 PMCID: PMC10372677 DOI: 10.1073/pnas.2305495120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Marine algae are responsible for half of the world's primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species of marine algae, Dunaliella tertiolecta, is remarkable for its ability to maintain photosynthesis and thrive in low-iron environments. A related species, Dunaliella salina Bardawil, shares this attribute but is an extremophile found in hypersaline environments. To elucidate how algae manage their iron requirements, we produced high-quality genome assemblies and transcriptomes for both species to serve as a foundation for a comparative multiomics analysis. We identified a host of iron-uptake proteins in both species, including a massive expansion of transferrins and a unique family of siderophore-iron-uptake proteins. Complementing these multiple iron-uptake routes, ferredoxin functions as a large iron reservoir that can be released by induction of flavodoxin. Proteomic analysis revealed reduced investment in the photosynthetic apparatus coupled with remodeling of antenna proteins by dramatic iron-deficiency induction of TIDI1, which is closely related but identifiably distinct from the chlorophyll binding protein, LHCA3. These combinatorial iron scavenging and sparing strategies make Dunaliella unique among photosynthetic organisms.
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Affiliation(s)
- Lital Davidi
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Eyal Ben-David
- Department of Human Genetics, University of California, Los Angeles, CA 90095
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Rory J Craig
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163
| | - Crysten E Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert P Auber
- Department of Biochemistry, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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Craig RJ, Gallaher SD, Shu S, Salomé PA, Jenkins JW, Blaby-Haas CE, Purvine SO, O’Donnell S, Barry K, Grimwood J, Strenkert D, Kropat J, Daum C, Yoshinaga Y, Goodstein DM, Vallon O, Schmutz J, Merchant SS. The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory. Plant Cell 2023; 35:644-672. [PMID: 36562730 PMCID: PMC9940879 DOI: 10.1093/plcell/koac347] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 10/12/2022] [Accepted: 12/16/2022] [Indexed: 05/20/2023]
Abstract
Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.
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Affiliation(s)
- Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean D Gallaher
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| | - Jerry W Jenkins
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Crysten E Blaby-Haas
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O’Donnell
- Laboratory of Computational and Quantitative Biology, UMR 7238, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris 75005, France
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chris Daum
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - David M Goodstein
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris 75005, France
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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4
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Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen JH, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SS, Niyogi KK. Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis. Plant Cell 2019; 31:579-601. [PMID: 30787178 PMCID: PMC6482638 DOI: 10.1105/tpc.18.00742] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/18/2018] [Accepted: 02/15/2019] [Indexed: 05/04/2023]
Abstract
Light and nutrients are critical regulators of photosynthesis and metabolism in plants and algae. Many algae have the metabolic flexibility to grow photoautotrophically, heterotrophically, or mixotrophically. Here, we describe reversible Glc-dependent repression/activation of oxygenic photosynthesis in the unicellular green alga Chromochloris zofingiensis. We observed rapid and reversible changes in photosynthesis, in the photosynthetic apparatus, in thylakoid ultrastructure, and in energy stores including lipids and starch. Following Glc addition in the light, C. zofingiensis shuts off photosynthesis within days and accumulates large amounts of commercially relevant bioproducts, including triacylglycerols and the high-value nutraceutical ketocarotenoid astaxanthin, while increasing culture biomass. RNA sequencing reveals reversible changes in the transcriptome that form the basis of this metabolic regulation. Functional enrichment analyses show that Glc represses photosynthetic pathways while ketocarotenoid biosynthesis and heterotrophic carbon metabolism are upregulated. Because sugars play fundamental regulatory roles in gene expression, physiology, metabolism, and growth in both plants and animals, we have developed a simple algal model system to investigate conserved eukaryotic sugar responses as well as mechanisms of thylakoid breakdown and biogenesis in chloroplasts. Understanding regulation of photosynthesis and metabolism in algae could enable bioengineering to reroute metabolism toward beneficial bioproducts for energy, food, pharmaceuticals, and human health.
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Affiliation(s)
- Melissa S Roth
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569
| | - Daniel J Westcott
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Masakazu Iwai
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Katherine B Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Maria Mueller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Andreas Walter
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Fatima Foflonker
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Nassim N Ataii
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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5
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Li M, van Zee M, Riche CT, Tofig B, Gallaher SD, Merchant SS, Damoiseaux R, Goda K, Di Carlo D. A Gelatin Microdroplet Platform for High-Throughput Sorting of Hyperproducing Single-Cell-Derived Microalgal Clones. Small 2018; 14:e1803315. [PMID: 30369052 DOI: 10.1002/smll.201803315] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/06/2018] [Indexed: 05/08/2023]
Abstract
Microalgae are an attractive feedstock organism for sustainable production of biofuels, chemicals, and biomaterials, but the ability to rationally engineer microalgae to enhance production has been limited. To enable the evolution-based selection of new hyperproducing variants of microalgae, a method is developed that combines phase-transitioning monodisperse gelatin hydrogel droplets with commercial flow cytometric instruments for high-throughput screening and selection of clonal populations of cells with desirable properties, such as high lipid productivity per time traced over multiple cell cycles. It is found that gelatin microgels enable i) the growth and metabolite (e.g., chlorophyll and lipids) production of single microalgal cells within the compartments, ii) infusion of fluorescent reporter molecules into the hydrogel matrices following a sol-gel transition, iii) selection of high-producing clonal populations of cells using flow cytometry, and iv) cell recovery under mild conditions, enabling regrowth after sorting. This user-friendly method is easily integratable into directed cellular evolution pipelines for strain improvement and can be adopted for other applications that require high-throughput processing, e.g., cellular secretion phenotypes and intercellular interactions.
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Affiliation(s)
- Ming Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- School of Engineering, Macquarie University, Sydney, NSW, 2122, Australia
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Carson T Riche
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Bobby Tofig
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Robert Damoiseaux
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Molecular and Medicinal Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo, 113-8655, Japan
- Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
- Department of Electrical Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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6
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Gallaher SD, Roth MS. RNA Purification from the Unicellular Green Alga, Chromochloris zofingiensis. Bio Protoc 2018; 8:e2792. [PMID: 34286015 DOI: 10.21769/bioprotoc.2793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/22/2018] [Accepted: 03/25/2018] [Indexed: 11/02/2022] Open
Abstract
Chromochloris zofingiensis is a unicellular green alga that is an emerging model species for studies in fields such as biofuel production, ketocarotenoid biosynthesis and metabolism. The recent availability of a high-quality genome assembly facilitates systems-level analysis, such as RNA-Seq. However, cells of this alga have a tough cell wall, which is a challenge for RNA purification. This protocol was designed specifically to breach the cell wall and isolate high-quality RNA suitable for RNA-Seq studies.
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Affiliation(s)
- Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Melissa S Roth
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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7
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Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. Plant J 2018; 93:545-565. [PMID: 29172250 PMCID: PMC5775909 DOI: 10.1111/tpj.13788] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205-kbp circular chloroplast genome and ~15.8-kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. Forty-six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3'-end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.
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Affiliation(s)
- Sean D. Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Corresponding author:
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
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Wittkopp TM, Schmollinger S, Saroussi S, Hu W, Zhang W, Fan Q, Gallaher SD, Leonard MT, Soubeyrand E, Basset GJ, Merchant SS, Grossman AR, Duanmu D, Lagarias JC. Bilin-Dependent Photoacclimation in Chlamydomonas reinhardtii. Plant Cell 2017; 29:2711-2726. [PMID: 29084873 PMCID: PMC5728120 DOI: 10.1105/tpc.17.00149] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/26/2017] [Accepted: 10/27/2017] [Indexed: 05/18/2023]
Abstract
In land plants, linear tetrapyrrole (bilin)-based phytochrome photosensors optimize photosynthetic light capture by mediating massive reprogramming of gene expression. But, surprisingly, many green algal genomes lack phytochrome genes. Studies of the heme oxygenase mutant (hmox1) of the green alga Chlamydomonas reinhardtii suggest that bilin biosynthesis in plastids is essential for proper regulation of a nuclear gene network implicated in oxygen detoxification during dark-to-light transitions. hmox1 cannot grow photoautotrophically and photoacclimates poorly to increased illumination. We show that these phenotypes are due to reduced accumulation of photosystem I (PSI) reaction centers, the PSI electron acceptors 5'-monohydroxyphylloquinone and phylloquinone, and the loss of PSI and photosystem II antennae complexes during photoacclimation. The hmox1 mutant resembles chlorophyll biosynthesis mutants phenotypically, but can be rescued by exogenous biliverdin IXα, the bilin produced by HMOX1. This rescue is independent of photosynthesis and is strongly dependent on blue light. RNA-seq comparisons of hmox1, genetically complemented hmox1, and chemically rescued hmox1 reveal that tetrapyrrole biosynthesis and known photoreceptor and photosynthesis-related genes are not impacted in the hmox1 mutant at the transcript level. We propose that a bilin-based, blue-light-sensing system within plastids evolved together with a bilin-based retrograde signaling pathway to ensure that a robust photosynthetic apparatus is sustained in light-grown Chlamydomonas.
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Affiliation(s)
- Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Department of Biology, Stanford University, Stanford, California 94305
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Wei Hu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Weiqing Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuling Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Michael T Leonard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Eric Soubeyrand
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Gilles J Basset
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Deqiang Duanmu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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Chambers M, Turki-Judeh W, Kim MW, Chen K, Gallaher SD, Courey AJ. Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity. BMC Genomics 2017; 18:215. [PMID: 28245789 PMCID: PMC5331681 DOI: 10.1186/s12864-017-3589-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/13/2017] [Indexed: 12/24/2022] Open
Abstract
Background The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting. Results Our chromatin immunoprecipitation sequencing analysis of temporally staged Drosophila embryos shows that Gro binds in a highly dynamic manner primarily to clusters of discrete (<1 kb) segments. Consistent with the idea that Gro may facilitate communication between silencers and promoters, Gro binding is enriched at both cis-regulatory modules, as well as within the promotors of potential target genes. While this Gro-recruitment is required for repression, our data show that it is not sufficient for repression. Integration of Gro binding data with transcriptomic analysis suggests that, contrary to what has been observed for another Gro family member, Drosophila Gro is probably a dedicated repressor. This analysis also allows us to define a set of high confidence Gro repression targets. Using publically available data regarding the physical and genetic interactions between these targets, we are able to place them in the regulatory network controlling development. Through analysis of chromatin associated pre-mRNA levels at these targets, we find that genes regulated by Gro in the embryo are enriched for characteristics of promoter proximal paused RNA polymerase II. Conclusions Our findings are inconsistent with a one-dimensional spreading model for long-range repression and suggest that Gro-mediated repression must be regulated at a post-recruitment step. They also show that Gro is likely a dedicated repressor that sits at a prominent highly interconnected regulatory hub in the developmental network. Furthermore, our findings suggest a role for RNA polymerase II pausing in Gro-mediated repression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3589-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Chambers
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Wiam Turki-Judeh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Min Woo Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Kenny Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Department of Energy, Institute of Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Albert J Courey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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10
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Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels 2016; 9:258. [PMID: 27933100 PMCID: PMC5124317 DOI: 10.1186/s13068-016-0670-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. CONCLUSIONS Functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.
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Affiliation(s)
- Jesse C. Traller
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Shawn J. Cokus
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - David A. Lopez
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Olga Gaidarenko
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Sarah R. Smith
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - John P. McCrow
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sean D. Gallaher
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Michael Thompson
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Orna Cook
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Marco Morselli
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Artur Jaroszewicz
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Eric E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
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11
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Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol 2015; 169:2730-43. [PMID: 26450704 PMCID: PMC4677889 DOI: 10.1104/pp.15.00861] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/07/2015] [Indexed: 05/02/2023]
Abstract
The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.
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Affiliation(s)
- David Lopez
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Takashi Hamaji
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Janette Kropat
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Peter De Hoff
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Marco Morselli
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Liudmilla Rubbi
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sorel Fitz-Gibbon
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sean D Gallaher
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sabeeha S Merchant
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - James Umen
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Matteo Pellegrini
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
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12
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Gallaher SD, Fitz-Gibbon ST, Glaesener AG, Pellegrini M, Merchant SS. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies. Plant Cell 2015; 27:2335-52. [PMID: 26307380 PMCID: PMC4815092 DOI: 10.1105/tpc.15.00508] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/13/2015] [Accepted: 08/07/2015] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas.
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Affiliation(s)
- Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Sorel T Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Anne G Glaesener
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
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13
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Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nat Chem Biol 2014; 10:1034-42. [PMID: 25344811 PMCID: PMC4232477 DOI: 10.1038/nchembio.1662] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/05/2014] [Indexed: 12/03/2022]
Abstract
We identified a Cu accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulated Cu, dependent on the nutritional Cu sensor CRR1, but was functionally Cu-deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. NanoSIMS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy (XAS) was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu+ became bio-available for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mis-metallation during Zn deficiency and enabling efficient cuproprotein (re)-metallation upon Zn resupply.
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Affiliation(s)
- Anne Hong-Hermesdorf
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Marcus Miethke
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Sheel C Dodani
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Jefferson Chan
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Dulmini Barupala
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Dylan W Domaille
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Dyna I Shirasaki
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California, USA
| | - Joseph A Loo
- 1] Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA. [2] Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California, USA. [3] Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, USA
| | - Peter K Weber
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Jennifer Pett-Ridge
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Christopher J Chang
- 1] Department of Chemistry, University of California-Berkeley, Berkeley, California, USA. [2] Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, California, USA
| | - Sabeeha S Merchant
- 1] Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA. [2] Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, USA
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14
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Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS. Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell 2013; 25:4305-23. [PMID: 24280389 PMCID: PMC3875720 DOI: 10.1105/tpc.113.117580] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 10/08/2013] [Accepted: 10/31/2013] [Indexed: 05/17/2023]
Abstract
To understand the molecular basis underlying increased triacylglycerol (TAG) accumulation in starchless (sta) Chlamydomonas reinhardtii mutants, we undertook comparative time-course transcriptomics of strains CC-4348 (sta6 mutant), CC-4349, a cell wall-deficient (cw) strain purported to represent the parental STA6 strain, and three independent STA6 strains generated by complementation of sta6 (CC-4565/STA6-C2, CC-4566/STA6-C4, and CC-4567/STA6-C6) in the context of N deprivation. Despite N starvation-induced dramatic remodeling of the transcriptome, there were relatively few differences (5 × 10(2)) observed between sta6 and STA6, the most dramatic of which were increased abundance of transcripts encoding key regulated or rate-limiting steps in central carbon metabolism, specifically isocitrate lyase, malate synthase, transaldolase, fructose bisphosphatase and phosphoenolpyruvate carboxykinase (encoded by ICL1, MAS1, TAL1, FBP1, and PCK1 respectively), suggestive of increased carbon movement toward hexose-phosphate in sta6 by upregulation of the glyoxylate pathway and gluconeogenesis. Enzyme assays validated the increase in isocitrate lyase and malate synthase activities. Targeted metabolite analysis indicated increased succinate, malate, and Glc-6-P and decreased Fru-1,6-bisphosphate, illustrating the effect of these changes. Comparisons of independent data sets in multiple strains allowed the delineation of a sequence of events in the global N starvation response in C. reinhardtii, starting within minutes with the upregulation of alternative N assimilation routes and carbohydrate synthesis and subsequently a more gradual upregulation of genes encoding enzymes of TAG synthesis. Finally, genome resequencing analysis indicated that (1) the deletion in sta6 extends into the neighboring gene encoding respiratory burst oxidase, and (2) a commonly used STA6 strain (CC-4349) as well as the sequenced reference (CC-503) are not congenic with respect to sta6 (CC-4348), underscoring the importance of using complemented strains for more rigorous assignment of phenotype to genotype.
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Affiliation(s)
- Ian K. Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Anne G. Glaesener
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Tabea Mettler
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany 14476
| | - Sorel T. Fitz-Gibbon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Sean D. Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Bensheng Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Nanette R. Boyle
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany 14476
| | - Shannon Johnson
- Genome Science, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - David Casero
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
- Address correspondence to
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15
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Urzica EI, Vieler A, Hong-Hermesdorf A, Page MD, Casero D, Gallaher SD, Kropat J, Pellegrini M, Benning C, Merchant SS. Remodeling of membrane lipids in iron-starved Chlamydomonas. J Biol Chem 2013; 288:30246-30258. [PMID: 23983122 DOI: 10.1074/jbc.m113.490425] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chlamydomonas reinhardtii cells exposed to abiotic stresses (e.g. nitrogen, zinc, or phosphorus deficiency) accumulate triacylglycerols (TAG), which are stored in lipid droplets. Here, we report that iron starvation leads to formation of lipid droplets and accumulation of TAGs. This occurs between 12 and 24 h after the switch to iron-starvation medium. C. reinhardtii cells deprived of iron have more saturated fatty acid (FA), possibly due to the loss of function of FA desaturases, which are iron-requiring enzymes with diiron centers. The abundance of a plastid acyl-ACP desaturase (FAB2) is decreased to the same degree as ferredoxin. Ferredoxin is a substrate of the desaturases and has been previously shown to be a major target of the iron deficiency response. The increase in saturated FA (C16:0 and C18:0) is concomitant with the decrease in unsaturated FA (C16:4, C18:3, or C18:4). This change was gradual for diacylglyceryl-N,N,N-trimethylhomoserine (DGTS) and digalactosyldiacylglycerol (DGDG), whereas the monogalactosyldiacylglycerol (MGDG) FA profile remained stable during the first 12 h, whereas MGDG levels were decreasing over the same period of time. These changes were detectable after only 2 h of iron starvation. On the other hand, DGTS and DGDG contents gradually decreased until a minimum was reached after 24-48 h. RNA-Seq analysis of iron-starved C. reinhardtii cells revealed notable changes in many transcripts coding for enzymes involved in FA metabolism. The mRNA abundances of genes coding for components involved in TAG accumulation (diacylglycerol acyltransferases or major lipid droplet protein) were increased. A more dramatic increase at the transcript level has been observed for many lipases, suggesting that major remodeling of lipid membranes occurs during iron starvation in C. reinhardtii.
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Affiliation(s)
| | - Astrid Vieler
- the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | | | | | - David Casero
- the Institute of Genomics and Proteomics, and; the Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095 and
| | | | | | - Matteo Pellegrini
- the Institute of Genomics and Proteomics, and; the Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095 and
| | - Christoph Benning
- the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sabeeha S Merchant
- From the Department of Chemistry and Biochemistry,; the Institute of Genomics and Proteomics, and; the Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095 and.
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16
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Gallaher SD, Berk AJ. A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results. J Virol Methods 2013; 192:28-38. [PMID: 23624118 DOI: 10.1016/j.jviromet.2013.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 02/19/2013] [Accepted: 04/15/2013] [Indexed: 12/22/2022]
Abstract
Adenoviruses are employed in the study of cellular processes and as expression vectors used in gene therapy. The success and reproducibility of these studies is dependent in part on having accurate and meaningful titers of replication competent and helper-dependent adenovirus stocks, which is problematic due to the use of varied and divergent titration protocols. Physical titration methods, which quantify the total number of viral particles, are used by many, but are poor at estimating activity. Biological titration methods, such as plaque assays, are more biologically relevant, but are time consuming and not applicable to helper-dependent gene therapy vectors. To address this, a protocol was developed called "infectious genome titration" in which viral DNA is isolated from the nuclei of cells ~3 h post-infection, and then quantified by Q-PCR. This approach ensures that only biologically active virions are counted as part of the titer determination. This approach is rapid, robust, sensitive, reproducible, and applicable to all forms of adenovirus. Unlike other Q-PCR-based methods, titers determined by this protocol are well correlated with biological activity.
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Affiliation(s)
- Sean D Gallaher
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, 611 Young Drive, Box 157005, Los Angeles, CA 90095-1570, USA.
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Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS. Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem 2012; 287:15811-25. [PMID: 22403401 DOI: 10.1074/jbc.m111.334052] [Citation(s) in RCA: 282] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Algae have recently gained attention as a potential source for biodiesel; however, much is still unknown about the biological triggers that cause the production of triacylglycerols. We used RNA-Seq as a tool for discovering genes responsible for triacylglycerol (TAG) production in Chlamydomonas and for the regulatory components that activate the pathway. Three genes encoding acyltransferases, DGAT1, DGTT1, and PDAT1, are induced by nitrogen starvation and are likely to have a role in TAG accumulation based on their patterns of expression. DGAT1 and DGTT1 also show increased mRNA abundance in other TAG-accumulating conditions (minus sulfur, minus phosphorus, minus zinc, and minus iron). Insertional mutants, pdat1-1 and pdat1-2, accumulate 25% less TAG compared with the parent strain, CC-4425, which demonstrates the relevance of the trans-acylation pathway in Chlamydomonas. The biochemical functions of DGTT1 and PDAT1 were validated by rescue of oleic acid sensitivity and restoration of TAG accumulation in a yeast strain lacking all acyltransferase activity. Time course analyses suggest than a SQUAMOSA promoter-binding protein domain transcription factor, whose mRNA increases precede that of lipid biosynthesis genes like DGAT1, is a candidate regulator of the nitrogen deficiency responses. An insertional mutant, nrr1-1, accumulates only 50% of the TAG compared with the parental strain in nitrogen-starvation conditions and is unaffected by other nutrient stresses, suggesting the specificity of this regulator for nitrogen-deprivation conditions.
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Affiliation(s)
- Nanette R Boyle
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
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Gil JS, Gallaher SD, Berk AJ. Delivery of an EBV episome by a self-circularizing helper-dependent adenovirus: long-term transgene expression in immunocompetent mice. Gene Ther 2010; 17:1288-93. [PMID: 20463755 DOI: 10.1038/gt.2010.75] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Epstein-Barr virus (EBV) evolved an episomal system for maintaining life-long, latent infection of human B lymphocytes. Circular episomes engineered from EBV components required for this latent form of infection have the capacity to persist in most types of replicating mammalian cells without DNA integration and the pitfalls of insertional mutagenesis. EBV episomes are typically transduced using low-efficiency methods. Here we present a method for efficient delivery of EBV episomes to nuclei of hepatocytes in living mice using a helper-dependent adenoviral vector and Cre-mediated recombination in vivo to generate circular EBV episomes following infection. Cre is transiently expressed from a hepatocyte-specific promoter so that vector generation and transgene expression are tissue specific. We show long-term persistence of the circularized vector DNA and expression of a reporter gene in hepatocytes of immunocompetent mice.
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Affiliation(s)
- J S Gil
- Molecular Biology Institute, Department of Microbiology, Immunology and Molecular Genetics, University of California-Los Angeles, 611 Young Drive E, Los Angeles, CA 90095-1570, USA
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Gallaher SD, Gil JS, Berk AJ. 14. High Efficiency and Long-Term Persistence In Vivo from a Helper Dependent Adenovirus/Epstein-Barr Virus Hybrid Vector. Mol Ther 2006. [DOI: 10.1016/j.ymthe.2006.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Gil JS, Gallaher SD, Berk AJ. 848. Helper Dependent Adenovirus-Epstein- Barr Virus Hybrid Vector for Long Term Persistance in Hepatocytes. Mol Ther 2006. [DOI: 10.1016/j.ymthe.2006.08.934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Dorigo O, Gil JS, Gallaher SD, Tan BT, Castro MG, Lowenstein PR, Calos MP, Berk AJ. Development of a novel helper-dependent adenovirus-Epstein-Barr virus hybrid system for the stable transformation of mammalian cells. J Virol 2004; 78:6556-66. [PMID: 15163748 PMCID: PMC416543 DOI: 10.1128/jvi.78.12.6556-6566.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) episomes are stably maintained in permissive proliferating cell lines due to EBV nuclear antigen 1 (EBNA-1) protein-mediated replication and segregation. Previous studies showed the ability of EBV episomes to confer long-term transgene expression and correct genetic defects in deficient cells. To achieve quantitative delivery of EBV episomes in vitro and in vivo, we developed a binary helper-dependent adenovirus (HDA)-EBV hybrid system that consists of one HDA vector for the expression of Cre recombinase and a second HDA vector that contains all of the sequences for the EBV episome flanked by loxP sites. Upon coinfection of cells, Cre expressed from the first vector recombined loxP sites on the second vector. The resulting circular EBV episomes expressed a transgene and contained the EBV-derived family of repeats, an EBNA-1 expression cassette, and 19 kb of human DNA that functions as a replication origin in mammalian cells. This HDA-EBV hybrid system transformed 40% of cultured cells. Transgene expression in proliferating cells was observed for over 20 weeks under conditions that selected for the expression of the transgene. In the absence of selection, EBV episomes were lost at a rate of 8 to 10% per cell division. Successful delivery of EBV episomes in vivo was demonstrated in the liver of transgenic mice expressing Cre from the albumin promoter. This novel gene transfer system has the potential to confer long-term episomal transgene expression and therefore to correct genetic defects with reduced vector-related toxicity and without insertional mutagenesis.
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Affiliation(s)
- Oliver Dorigo
- Molecular Biology Institute, University of California at Los Angeles, 611 Charles E. Young Dr. East, Los Angeles, CA 90095-1570, USA
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