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Dorrell RG. Convergence in the RNA processing of fractured algal organelle genomes. JOURNAL OF PHYCOLOGY 2020; 56:1121-1123. [PMID: 33460118 DOI: 10.1111/jpy.13039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
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Klinger CM, Paoli L, Newby RJ, Wang MYW, Carroll HD, Leblond JD, Howe CJ, Dacks JB, Bowler C, Cahoon AB, Dorrell RG, Richardson E. Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage-Specific Application but Conserved Trends. Genome Biol Evol 2018; 10:1019-1038. [PMID: 29617800 PMCID: PMC5888634 DOI: 10.1093/gbe/evy057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2018] [Indexed: 11/24/2022] Open
Abstract
Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage.
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Affiliation(s)
- Christen M Klinger
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Lucas Paoli
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Robert J Newby
- Department of Biology, Middle Tennessee State University
| | - Matthew Yu-Wei Wang
- Center for Computational Science and Department of Computer Science, Columbus State University, Columbus, GA 31907
| | - Hyrum D Carroll
- Center for Computational Science and Department of Computer Science, Columbus State University, Columbus, GA 31907
| | | | | | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Aubery Bruce Cahoon
- Department of Natural Sciences, The University of Virginia's College at Wise
| | - Richard G Dorrell
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
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Cavalier-Smith T. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. PROTOPLASMA 2018; 255:297-357. [PMID: 28875267 PMCID: PMC5756292 DOI: 10.1007/s00709-017-1147-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/18/2017] [Indexed: 05/18/2023]
Abstract
In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated 'endocytosis' from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.
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Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes. Curr Biol 2017; 27:3771-3782.e6. [PMID: 29199074 DOI: 10.1016/j.cub.2017.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/28/2022]
Abstract
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Kenny A Bogaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine, Québec City, QC G1V 0A6, Canada
| | - Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, New Kirk Building, Kelburn Parade, P.O. Box 600, Wellington 6012, New Zealand
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Juan M Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35484-0345, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Professors Walk, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium.
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Dorrell RG, Howe CJ. Integration of plastids with their hosts: Lessons learned from dinoflagellates. Proc Natl Acad Sci U S A 2015; 112:10247-54. [PMID: 25995366 PMCID: PMC4547248 DOI: 10.1073/pnas.1421380112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function.
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Affiliation(s)
- Richard G Dorrell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; School of Biology, École Normale Superieure, Paris 75005, France
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
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Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci U S A 2015; 112:10177-84. [PMID: 25814499 DOI: 10.1073/pnas.1422049112] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial and plastid genomes show a wide array of architectures, varying immensely in size, structure, and content. Some organelle DNAs have even developed elaborate eccentricities, such as scrambled coding regions, nonstandard genetic codes, and convoluted modes of posttranscriptional modification and editing. Here, we compare and contrast the breadth of genomic complexity between mitochondrial and plastid chromosomes. Both organelle genomes have independently evolved many of the same features and taken on similar genomic embellishments, often within the same species or lineage. This trend is most likely because the nuclear-encoded proteins mediating these processes eventually leak from one organelle into the other, leading to a high likelihood of processes appearing in both compartments in parallel. However, the complexity and intensity of genomic embellishments are consistently more pronounced for mitochondria than for plastids, even when they are found in both compartments. We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.
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Richardson E, Dorrell RG, Howe CJ. Genome-wide transcript profiling reveals the coevolution of plastid gene sequences and transcript processing pathways in the fucoxanthin dinoflagellate Karlodinium veneficum. Mol Biol Evol 2014; 31:2376-86. [PMID: 24925926 PMCID: PMC4137713 DOI: 10.1093/molbev/msu189] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Plastids utilize a complex gene expression machinery, which has coevolved with the underlying genome sequence. Relatively, little is known about the genome-wide evolution of transcript processing in algal plastids that have undergone complex endosymbiotic events. We present the first genome-wide study of transcript processing in a plastid acquired through serial endosymbiosis, in the fucoxanthin-containing dinoflagellate Karlodinium veneficum. The fucoxanthin dinoflagellate plastid has an extremely divergent genome and utilizes two unusual transcript processing pathways, 3'-poly(U) tail addition and sequence editing, which were acquired following the serial endosymbiosis event. We demonstrate that poly(U) addition and sequence editing are widespread features across the Karl. veneficum plastid transcriptome, whereas other dinoflagellate plastid lineages that have arisen through independent serial endosymbiosis events do not utilize either RNA processing pathway. These pathways constrain the effects of divergent sequence evolution in fucoxanthin plastids, for example by correcting mutations in the genomic sequence that would otherwise be deleterious, and are specifically associated with transcripts that encode functional plastid proteins over transcripts of recently generated pseudogenes. These pathways may have additionally facilitated divergent evolution within the Karl. veneficum plastid. Transcript editing, for example, has contributed to the evolution of a novel C-terminal sequence extension on the Karl. veneficum AtpA protein. We furthermore provide the first complete sequence of an episomal minicircle in a fucoxanthin dinoflagellate plastid, which contains the dnaK gene, and gives rise to polyuridylylated and edited transcripts. Our results indicate that RNA processing in fucoxanthin dinoflagellate plastids is evolutionarily dynamic, coevolving with the underlying genome sequence.
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Affiliation(s)
| | - Richard G Dorrell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Mackiewicz P, Bodył A, Moszczyński K. The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome. Mob Genet Elements 2013; 3:e25845. [PMID: 24195014 PMCID: PMC3812789 DOI: 10.4161/mge.25845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/14/2013] [Accepted: 07/22/2013] [Indexed: 12/19/2022] Open
Abstract
Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Genomics; Faculty of Biotechnology; University of Wrocław; Wrocław, Poland
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Dorrell RG, Howe CJ. Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors. Proc Natl Acad Sci U S A 2012; 109:18879-84. [PMID: 23112181 PMCID: PMC3503182 DOI: 10.1073/pnas.1212270109] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chloroplasts originate through the endosymbiotic integration of a host and a photosynthetic symbiont, with processes established within the host for the biogenesis and maintenance of the nascent chloroplast. It is thought that several photosynthetic eukaryotes have replaced their original chloroplasts with others derived from different source organisms in a process termed "serial endosymbiosis of chloroplasts." However, it is not known whether replacement chloroplasts are affected by the biogenesis and maintenance pathways established to support their predecessors. Here, we investigate whether pathways established during a previous chloroplast symbiosis function in the replacement chloroplasts of the dinoflagellate alga Karenia mikimotoi. We show that chloroplast transcripts in K. mikimotoi are subject to 3' polyuridylylation and extensive sequence editing. We confirm that these processes do not occur in free-living relatives of the replacement chloroplast lineage, but are otherwise found only in the ancestral, red algal-derived chloroplasts of dinoflagellates and their closest relatives. This indicates that these unusual RNA-processing pathways have been retained from the original symbiont lineage and made use of by the replacement chloroplast. Our results constitute an addition to current theories of chloroplast evolution in which chloroplast biogenesis may be radically remodeled by pathways remaining from previous symbioses.
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Affiliation(s)
- Richard G Dorrell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.
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