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Cooney EC, Holt CC, Hehenberger E, Adams JA, Leander BS, Keeling PJ. Investigation of heterotrophs reveals new insights in dinoflagellate evolution. Mol Phylogenet Evol 2024; 196:108086. [PMID: 38677354 DOI: 10.1016/j.ympev.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Corey C Holt
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Jayd A Adams
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Brian S Leander
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, 4200 - 6270, University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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3
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024:10.1038/s41564-024-01707-9. [PMID: 38806669 DOI: 10.1038/s41564-024-01707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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4
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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. Genome Biol 2024; 25:115. [PMID: 38711126 PMCID: PMC11071213 DOI: 10.1186/s13059-024-03261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/28/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties are originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. RESULTS In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays. CONCLUSIONS Our results provide the first window into the 5-hmU and chromatin accessibility landscapes in dinoflagellates.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Matthew P Swaffer
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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5
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Holt CC, Hehenberger E, Tikhonenkov DV, Jacko-Reynolds VKL, Okamoto N, Cooney EC, Irwin NAT, Keeling PJ. Multiple parallel origins of parasitic Marine Alveolates. Nat Commun 2023; 14:7049. [PMID: 37923716 PMCID: PMC10624901 DOI: 10.1038/s41467-023-42807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) are consistently both abundant and diverse in global environmental sequencing surveys. MALVs are dinoflagellates that are thought to be parasites of other protists and animals, but the lack of data beyond ribosomal RNA gene sequences from all but a few described species means much of their biology and evolution remain unknown. Using single-cell transcriptomes from several MALVs and their free-living relatives, we show that MALVs evolved independently from two distinct, free-living ancestors and that their parasitism evolved in parallel. Phylogenomics shows one subgroup (MALV-II and -IV, or Syndiniales) is related to a novel lineage of free-living, eukaryovorous predators, the eleftherids, while the other (MALV-I, or Ichthyodinida) is related to the free-living predator Oxyrrhis and retains proteins targeted to a non-photosynthetic plastid. Reconstructing the evolution of photosynthesis, plastids, and parasitism in early-diverging dinoflagellates shows a number of parallels with the evolution of their apicomplexan sisters. In both groups, similar forms of parasitism evolved multiple times and photosynthesis was lost many times. By contrast, complete loss of the plastid organelle is infrequent and, when this does happen, leaves no residual genes.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
- Hakai Institute, Heriot Bay, British Columbia, Canada.
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
- AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russia
| | | | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558303. [PMID: 37781619 PMCID: PMC10541103 DOI: 10.1101/2023.09.18.558303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties were originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | | | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Moniruzzaman M, Erazo Garcia MP, Farzad R, Ha AD, Jivaji A, Karki S, Sheyn U, Stanton J, Minch B, Stephens D, Hancks DC, Rodrigues RAL, Abrahao JS, Vardi A, Aylward FO. Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses. FEMS Microbiol Rev 2023; 47:fuad053. [PMID: 37740576 PMCID: PMC10583209 DOI: 10.1093/femsre/fuad053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.
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Affiliation(s)
- Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Maria Paula Erazo Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Roxanna Farzad
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Abdeali Jivaji
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Sangita Karki
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Uri Sheyn
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Joshua Stanton
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Benjamin Minch
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Danae Stephens
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, United States
| | - Rodrigo A L Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Jonatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA 24061, United States
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Kalvelage J, Wöhlbrand L, Schoon RA, Zink FM, Correll C, Senkler J, Eubel H, Hoppenrath M, Rhiel E, Braun HP, Winklhofer M, Klingl A, Rabus R. The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum. mSphere 2023; 8:e0003823. [PMID: 37358287 PMCID: PMC10449503 DOI: 10.1128/msphere.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 06/27/2023] Open
Abstract
The marine, bloom-forming dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) has a genome atypical of eukaryotes, with a large size of ~4.15 Gbp, organized in plentiful, highly condensed chromosomes and packed in a dinoflagellate-specific nucleus (dinokaryon). Here, we apply microscopic and proteogenomic approaches to obtain new insights into this enigmatic nucleus of axenic P. cordatum. High-resolution focused ion beam/scanning electron microscopy analysis of the flattened nucleus revealed highest density of nuclear pores in the vicinity of the nucleolus, a total of 62 tightly packed chromosomes (~0.4-6.7 µm3), and interaction of several chromosomes with the nucleolus and other nuclear structures. A specific procedure for enriching intact nuclei was developed to enable proteomic analyses of soluble and membrane protein-enriched fractions. These were analyzed with geLC and shotgun approaches employing ion-trap and timsTOF (trapped-ion-mobility-spectrometry time-of-flight) mass spectrometers, respectively. This allowed identification of 4,052 proteins (39% of unknown function), out of which 418 were predicted to serve specific nuclear functions; additional 531 proteins of unknown function could be allocated to the nucleus. Compaction of DNA despite very low histone abundance could be accomplished by highly abundant major basic nuclear proteins (HCc2-like). Several nuclear processes including DNA replication/repair and RNA processing/splicing can be fairly well explained on the proteogenomic level. By contrast, transcription and composition of the nuclear pore complex remain largely elusive. One may speculate that the large group of potential nuclear proteins with currently unknown functions may serve yet to be explored functions in nuclear processes differing from those of typical eukaryotic cells. IMPORTANCE Dinoflagellates form a highly diverse group of unicellular microalgae. They provide keystone species for the marine ecosystem and stand out among others by their very large, unusually organized genomes embedded in the nuclei markedly different from other eukaryotic cells. Functional insights into nuclear and other cell biological structures and processes of dinoflagellates have long been hampered by the paucity of available genomic sequences. The here studied cosmopolitan P. cordatum belongs to the harmful algal bloom-forming, marine dinoflagellates and has a recently de novo assembled genome. We present a detailed 3D reconstruction of the P. cordatum nucleus together with comprehensive proteogenomic insights into the protein equipment mastering the broad spectrum of nuclear processes. This study significantly advances our understanding of mechanisms and evolution of the conspicuous dinoflagellate cell biology.
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Affiliation(s)
- Jana Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Robin-Alexander Schoon
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Fiona-Marine Zink
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Correll
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Jennifer Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Holger Eubel
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Mona Hoppenrath
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Erhard Rhiel
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Michael Winklhofer
- Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Andreas Klingl
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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10
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Cooney EC, Leander BS, Keeling PJ. Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral. PNAS NEXUS 2022; 1:pgac202. [PMID: 36714854 PMCID: PMC9802342 DOI: 10.1093/pnasnexus/pgac202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/19/2022] [Indexed: 02/01/2023]
Abstract
Dinoflagellates are a diverse protist group possessing many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, Noctiluca scintillans, and because its phylogenetic position is unresolved it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse Noctilucales genera: Spatulodinium, Kofoidinium, and a new lineage, Fabadinium gen. nov. We also provide transcriptomes for undescribed species in Amphidinium and Abediniales, critical taxa for clarifying the phylogenetic position of Noctilucales. Phylogenomic analyses suggests that the Noctilucales are sister to Amphidinium rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and Amphidinium and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that Spatulodinium plastids are photosynthetic and of ancestral origin, and show that all non-photosynthetic Noctilucales retain plastid genes indicating a cryptic organelle.
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Affiliation(s)
| | - Brian S Leander
- Department of Botany, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada,Department of Zoology, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada
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11
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Orchestrated translation specializes dinoflagellate metabolism three times per day. Proc Natl Acad Sci U S A 2022; 119:e2122335119. [PMID: 35858433 PMCID: PMC9335273 DOI: 10.1073/pnas.2122335119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many cells specialize for different metabolic tasks at different times over their normal ZT cycle by changes in gene expression. However, in most cases, circadian gene expression has been assessed at the mRNA accumulation level, which may not faithfully reflect protein synthesis rates. Here, we use ribosome profiling in the dinoflagellate Lingulodinium polyedra to identify thousands of transcripts showing coordinated translation. All of the components in carbon fixation are concurrently regulated at ZT0, predicting the known rhythm of carbon fixation, and many enzymes involved in DNA replication are concurrently regulated at ZT12, also predicting the known rhythm in this process. Most of the enzymes in glycolysis and the TCA cycle are also regulated together, suggesting rhythms in these processes as well. Surprisingly, a third cluster of transcripts show peak translation at approximately ZT16, and these transcripts encode enzymes involved in transcription, translation, and amino acid biosynthesis. The latter has physiological consequences, as measured free amino acid levels increase at night and thus represent a previously undocumented rhythm in this model. Our results suggest that ribosome profiling may be a more accurate predictor of changed metabolic state than transcriptomics.
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12
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Zaheri B, Morse D. An overview of transcription in dinoflagellates. Gene 2022; 829:146505. [PMID: 35447242 DOI: 10.1016/j.gene.2022.146505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 02/18/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Dinoflagellates are a vital diverse family of unicellular algae widespread in various aquatic environments. Typically large genomes and permanently condensed chromosomes without histones make these organisms unique among eukaryotes in terms of chromatin structure and gene expression. Genomic and transcriptomic sequencing projects have provided new insight into the genetic foundation of dinoflagellate behaviors. Genes in tandem arrays, trans-splicing of mRNAs and lower levels of transcriptional regulation compared to other eukaryotes all contribute to the differences seen. Here we present a general overview of transcription in dinoflagellates based on previously described work.
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Affiliation(s)
- Bahareh Zaheri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada.
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13
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Irwin NAT, Pittis AA, Richards TA, Keeling PJ. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol 2021; 7:327-336. [PMID: 34972821 DOI: 10.1038/s41564-021-01026-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/12/2021] [Indexed: 01/19/2023]
Abstract
Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. Here we systematically characterized viral-eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK. .,Department of Zoology, University of Oxford, Oxford, UK. .,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Alexandros A Pittis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Lynch KL, Dillon MR, Bat-Erdene M, Lewis HC, Kaai RJ, Arnold EA, Avgousti DC. A viral histone-like protein exploits antagonism between linker histones and HMGB proteins to obstruct the cell cycle. Curr Biol 2021; 31:5227-5237.e7. [PMID: 34666003 DOI: 10.1016/j.cub.2021.09.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/30/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022]
Abstract
Virus infection necessarily requires redirecting cellular resources toward viral progeny production. Adenovirus encodes the histone-like protein VII, which causes catastrophic global reorganization of host chromatin to promote virus infection. Protein VII recruits the family of high mobility group box (HMGB) proteins to chromatin along with the histone chaperone SET. As a consequence of this recruitment, we find that protein VII causes chromatin depletion of several linker histone H1 isoforms. The relationship between linker histone H1 and the functionally opposite HMGB proteins is critical for higher-order chromatin structure. However, the physiological consequences of perturbing this relationship are largely unknown. Here, we employ complementary systems in Saccharomyces cerevisiae and human cells to demonstrate that adenovirus protein VII disrupts the H1-HMGB balance to obstruct the cell cycle. We find that protein VII causes an accumulation of G2/M cells both in yeast and human systems, underscoring the high conservation of this chromatin vulnerability. In contrast, adenovirus E1A and E1B proteins are well established to override cell cycle regulation and promote transformation of human cells. Strikingly, we find that protein VII obstructs the cell cycle, even in the presence of E1A and E1B. We further show that, in a protein-VII-deleted infection, several cell cycle markers are regulated differently compared to wild-type infection, supporting our model that protein VII plays an integral role in hijacking cell cycle regulation during infection. Together, our results demonstrate that protein VII targets H1-HMGB1 antagonism to obstruct cell cycle progression, revealing an unexpected chromatin vulnerability exploited for viral benefit.
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Affiliation(s)
- Kelsey L Lynch
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Melanie R Dillon
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Mongoljin Bat-Erdene
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Hannah C Lewis
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Molecular & Cellular Biology in Seattle, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Robin J Kaai
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Molecular & Cellular Biology in Seattle, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Edward A Arnold
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Microbiology Graduate Program, University of Washington, 1705 NE Pacific Street, Box 357735, Seattle, WA 98195, USA
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Molecular & Cellular Biology in Seattle, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA; Microbiology Graduate Program, University of Washington, 1705 NE Pacific Street, Box 357735, Seattle, WA 98195, USA.
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15
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Kgatle MM, Lawal IO, Mashabela G, Boshomane TMG, Koatale PC, Mahasha PW, Ndlovu H, Vorster M, Rodrigues HG, Zeevaart JR, Gordon S, Moura-Alves P, Sathekge MM. COVID-19 Is a Multi-Organ Aggressor: Epigenetic and Clinical Marks. Front Immunol 2021; 12:752380. [PMID: 34691068 PMCID: PMC8531724 DOI: 10.3389/fimmu.2021.752380] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
The progression of coronavirus disease 2019 (COVID-19), resulting from a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, may be influenced by both genetic and environmental factors. Several viruses hijack the host genome machinery for their own advantage and survival, and similar phenomena might occur upon SARS-CoV-2 infection. Severe cases of COVID-19 may be driven by metabolic and epigenetic driven mechanisms, including DNA methylation and histone/chromatin alterations. These epigenetic phenomena may respond to enhanced viral replication and mediate persistent long-term infection and clinical phenotypes associated with severe COVID-19 cases and fatalities. Understanding the epigenetic events involved, and their clinical significance, may provide novel insights valuable for the therapeutic control and management of the COVID-19 pandemic. This review highlights different epigenetic marks potentially associated with COVID-19 development, clinical manifestation, and progression.
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Affiliation(s)
- Mankgopo Magdeline Kgatle
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Ismaheel Opeyemi Lawal
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, Steve Biko Academic Hospital, Pretoria, South Africa
| | - Gabriel Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tebatso Moshoeu Gillian Boshomane
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, Steve Biko Academic Hospital, Pretoria, South Africa
- Nuclear and Oncology Division, AXIM Medical (Pty), Midrand
| | - Palesa Caroline Koatale
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Phetole Walter Mahasha
- Precision Medicine and SAMRC Genomic Centre, Grants, Innovation, and Product Development (GIPD) Unit, South African Medical Research Council, Pretoria, South Africa
| | - Honest Ndlovu
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Mariza Vorster
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Hosana Gomes Rodrigues
- Laboratory of Nutrients and Tissue Repair, School of Applied Sciences, University of Campinas, Campinas, Brazil
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- South African Nuclear Energy Corporation, Radiochemistry and NuMeRI PreClinical Imaging Facility, Mahikeng, South Africa
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Siamon Gordon
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mike Machaba Sathekge
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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16
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Barreat JGN, Katzourakis A. Paleovirology of the DNA viruses of eukaryotes. Trends Microbiol 2021; 30:281-292. [PMID: 34483047 DOI: 10.1016/j.tim.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
Paleovirology is the study of ancient viruses and how they have coevolved with their hosts. An increasingly detailed understanding of the diversity, origins, and evolution of the DNA viruses of eukaryotes has been obtained through the lens of paleovirology in recent years. Members of multiple viral families have been found integrated in the genomes of eukaryotes, providing a rich fossil record to study. These elements have extended our knowledge of exogenous viral diversity, host ranges, and the timing of viral evolution, and are revealing the existence of entire new families of eukaryotic integrating dsDNA viruses and transposons. Future work in paleovirology will continue to provide insights into antiviral immunity, viral diversity, and potential applications, and reveal other secrets of the viral world.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK.
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17
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Monson EA, Trenerry AM, Laws JL, Mackenzie JM, Helbig KJ. Lipid droplets and lipid mediators in viral infection and immunity. FEMS Microbiol Rev 2021; 45:fuaa066. [PMID: 33512504 PMCID: PMC8371277 DOI: 10.1093/femsre/fuaa066] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Lipid droplets (LDs) contribute to key pathways important for the physiology and pathophysiology of cells. In a homeostatic view, LDs regulate the storage of neutral lipids, protein sequestration, removal of toxic lipids and cellular communication; however, recent advancements in the field show these organelles as essential for various cellular stress response mechanisms, including inflammation and immunity, with LDs acting as hubs that integrate metabolic and inflammatory processes. The accumulation of LDs has become a hallmark of infection, and is often thought to be virally driven; however, recent evidence is pointing to a role for the upregulation of LDs in the production of a successful immune response to viral infection. The fatty acids housed in LDs are also gaining interest due to the role that these lipid species play during viral infection, and their link to the synthesis of bioactive lipid mediators that have been found to have a very complex role in viral infection. This review explores the role of LDs and their subsequent lipid mediators during viral infections and poses a paradigm shift in thinking in the field, whereby LDs may play pivotal roles in protecting the host against viral infection.
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Affiliation(s)
- Ebony A Monson
- School of Life Sciences, La Trobe University, Melbourne, Australia, 3083
| | - Alice M Trenerry
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia, 3000
| | - Jay L Laws
- School of Life Sciences, La Trobe University, Melbourne, Australia, 3083
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia, 3000
| | - Karla J Helbig
- School of Life Sciences, La Trobe University, Melbourne, Australia, 3083
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18
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Soo VWC, Warnecke T. Slaying the last unicorn: discovery of histones in the microalga Nanochlorum eucaryotum. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202023. [PMID: 33972876 PMCID: PMC8074811 DOI: 10.1098/rsos.202023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Histones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3 and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga Nanochlorum eucaryotum. If true, derived histone loss in this lineage would constitute an exceptional case that might help us further understand the principles governing eukaryotic gene regulation. To substantiate these earlier reports of histone loss in N. eucaryotum, we sequenced, assembled and quantified its transcriptome. Following a systematic search for histone-fold domains in the assembled transcriptome, we detect orthologues to all four core histones. We also find histone mRNAs to be highly expressed, comparable to the situation in other eukaryotes. Finally, we obtain characteristic protection patterns when N. eucaryotum chromatin is subjected to micrococcal nuclease digestion, indicating widespread formation of nucleosomal complexes in vivo. We conclude that previous reports of missing histones in N. eucaryotum were mistaken. By all indications, Nanochlorum eucaryotum has histone-based chromatin characteristic of most eukaryotes.
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Affiliation(s)
- Valerie W. C. Soo
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tobias Warnecke
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
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19
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Nand A, Zhan Y, Salazar OR, Aranda M, Voolstra CR, Dekker J. Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nat Genet 2021; 53:618-629. [PMID: 33927399 PMCID: PMC8110479 DOI: 10.1038/s41588-021-00841-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/09/2021] [Indexed: 02/02/2023]
Abstract
Dinoflagellates are main primary producers in the oceans, the cause of algal blooms and endosymbionts of marine invertebrates. Much remains to be understood about their biology, including their peculiar crystalline chromosomes. We assembled 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum and analyzed their organization. Genes are enriched towards the ends of chromosomes and are arranged in alternating unidirectional blocks. Some chromosomes are enriched for genes involved in specific biological processes. The chromosomes fold as linear rods and each is composed of a series of structural domains separated by boundaries. Domain boundaries are positioned at sites where transcription of two gene blocks converges and disappear when cells are treated with chemicals that block transcription, indicating correlations between gene orientation, transcription and chromosome folding. The description of the genetic and spatial organization of the S. microadriaticum genome provides a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.
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Affiliation(s)
- Ankita Nand
- grid.168645.80000 0001 0742 0364Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA USA
| | - Ye Zhan
- grid.168645.80000 0001 0742 0364Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA USA
| | - Octavio R. Salazar
- grid.45672.320000 0001 1926 5090Biological and Environmental Sciences & Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- grid.45672.320000 0001 1926 5090Biological and Environmental Sciences & Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R. Voolstra
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Job Dekker
- grid.168645.80000 0001 0742 0364Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Chevy Chase, MD USA
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20
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Oborník M. Photoparasitism as an Intermediate State in the Evolution of Apicomplexan Parasites. Trends Parasitol 2020; 36:727-734. [PMID: 32680786 DOI: 10.1016/j.pt.2020.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 01/23/2023]
Abstract
Despite the benefits of phototrophy, many algae have lost photosynthesis and have converted back to heterotrophy. Parasitism is a heterotrophic strategy, with apicomplexans being among the most devastating parasites for humans. The presence of a nonphotosynthetic plastid in apicomplexan parasites suggests their phototrophic ancestry. The discovery of related phototrophic chromerids has unlocked the possibility to study the transition between phototrophy and parasitism in the Apicomplexa. The chromerid Chromera velia can live as an intracellular parasite in coral larvae as well as a free-living phototroph, combining phototrophy and parasitism in what I call photoparasitism. Since early-branching apicomplexans live extracellularly, their evolution from an intracellular symbiont is unlikely. In this opinion article I discuss possible evolutionary trajectories from an extracellular photoparasite to an obligatory apicomplexan parasite.
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Affiliation(s)
- Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.
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21
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Sprecher BN, Zhang H, Lin S. Nuclear Gene Transformation in the Dinoflagellate Oxyrrhis marina. Microorganisms 2020; 8:E126. [PMID: 31963386 PMCID: PMC7022241 DOI: 10.3390/microorganisms8010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
The lack of a robust gene transformation tool that allows proper expression of foreign genes and functional testing for the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of the fundamental biology in this ecologically important and evolutionarily unique lineage of microeukaryotes. Here, we report the development of a dinoflagellate expression vector containing various DNA elements from phylogenetically separate dinoflagellate lineages, an electroporation protocol, and successful expression of introduced genes in an early branching dinoflagellate, Oxyrrhis marina. This protocol, involving the use of Lonza's Nucleofector and a codon-optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments for O. marina. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.
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Affiliation(s)
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
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22
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Pfeifer E, Hünnefeld M, Popa O, Frunzke J. Impact of Xenogeneic Silencing on Phage-Host Interactions. J Mol Biol 2019; 431:4670-4683. [PMID: 30796986 PMCID: PMC6925973 DOI: 10.1016/j.jmb.2019.02.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage-host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage-host interactions.
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Affiliation(s)
- Eugen Pfeifer
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Ovidiu Popa
- Heinrich Heine Universität Düsseldorf, Institute for Quantitative and Theoretical Biology, 40223 Düsseldorf, Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
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23
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Wideman JG, Novick A, Muñoz-Gómez SA, Doolittle WF. Neutral evolution of cellular phenotypes. Curr Opin Genet Dev 2019; 58-59:87-94. [PMID: 31574422 DOI: 10.1016/j.gde.2019.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022]
Abstract
Eukaryotes exhibit a great diversity of cellular and subcellular morphologies, but their basic underlying architecture is fairly constant. All have a nucleus, Golgi, cytoskeleton, plasma membrane, vesicles, ribosomes, and all known lineages but one have mitochondrion-related organelles. Moreover, most eukaryotes undergo processes such as mitosis, meiosis, DNA recombination, and often perform feats such as phagocytosis, and amoeboid and flagellar movement. With all of these commonalities, it is obvious that eukaryotes evolved from a common ancestor, but it is not obvious how eukaryotes came to have their diverse structural phenotypes. Are these phenotypes adaptations to particular niches, their evolution dominated by positive natural selection? Or is eukaryotic cellular diversity substantially the product of neutral evolutionary processes, with adaptation either illusory or a secondary consequence? In this paper, we outline how a hierarchical view of phenotype can be used to articulate a neutral theory of phenotypic evolution, involving processes such as gene loss, gene replacement by homologues or analogues, gene duplication followed by subfunctionalization, and constructive neutral evolution. We suggest that neutral iterations of these processes followed by entrenchment of their products can explain much of the diversity of cellular, developmental, and biochemical phenotypes of unicellular eukaryotes and should be explored in addition to adaptive explanations.
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Affiliation(s)
- Jeremy G Wideman
- Centre for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Aaron Novick
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Purdue University, West Lafayette, IN, 47907, USA
| | - Sergio A Muñoz-Gómez
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - W Ford Doolittle
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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Gornik SG, Hu I, Lassadi I, Waller RF. The Biochemistry and Evolution of the Dinoflagellate Nucleus. Microorganisms 2019; 7:microorganisms7080245. [PMID: 31398798 PMCID: PMC6723414 DOI: 10.3390/microorganisms7080245] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
Dinoflagellates are known to possess a highly aberrant nucleus-the so-called dinokaryon-that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones-the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany.
| | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Verma A, Barua A, Ruvindy R, Savela H, Ajani PA, Murray SA. The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms 2019; 7:E222. [PMID: 31362398 PMCID: PMC6722697 DOI: 10.3390/microorganisms7080222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023] Open
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia.
| | - Abanti Barua
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
- Department of Microbiology, Noakhali Science and Technology University, Chittagong 3814, Bangladesh
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, 00790 Helsinki, Finland
| | - Penelope A Ajani
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
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Gillespie ZE, Barkhshi T, Sosa Ponce ML, Georgel PT, Ausió J. 40th International Asilomar Chromatin, Chromosomes, and Epigenetics Conference. Biochem Cell Biol 2019; 97:777-782. [PMID: 30974061 DOI: 10.1139/bcb-2019-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The 40th International Asilomar Chromatin, Chromosomes, and Epigenetics Conference was held in the Asilomar Conference Grounds, Pacific Grove, California, USA, on 6-9 December 2018. The organizing committee consisted of established scientists in the fields of chromatin and epigenetics: Sally Pasion and Michael Goldman from the Biology Department, San Francisco State University, California, USA; Philippe Georgel from the Department of Biological Sciences, Marshal University, West Virginia, USA; Juan Ausió from the Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada; and Christopher Eskiw from the Department of Biochemistry, University of Saskatchewan, Saskatchewan, Canada. The meeting had two keynote speakers: Jessica Tyler and Jennifer Mitchell, and it covered topics on transcription, replication and repair, epigenetics, cell differentiation and disease, telomeres, and centromeres and it had two sessions devoted to nuclear and genomic organization. It encompassed the enthusiastic presentations of excellent trainees within the breathtaking natural setting of Pacific Grove.
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Affiliation(s)
- Zoe E Gillespie
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tanner Barkhshi
- Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
| | - Maria Laura Sosa Ponce
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Philippe T Georgel
- Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
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Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water. J Virol 2019; 93:JVI.02130-18. [PMID: 30728258 PMCID: PMC6450098 DOI: 10.1128/jvi.02130-18] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae IMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.
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Dinoflagellate nucleus contains an extensive endomembrane network, the nuclear net. Sci Rep 2019; 9:839. [PMID: 30696854 PMCID: PMC6351617 DOI: 10.1038/s41598-018-37065-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates are some of the most common eukaryotic cells in the ocean, but have very unusual nuclei. Many exhibit a form of closed mitosis (dinomitosis) wherein the nuclear envelope (NE) invaginates to form one or more trans-nuclear tunnels. Rather than contact spindles directly, the chromatids then bind to membrane-based kinetochores on the NE. To better understand these unique mitotic features, we reconstructed the nuclear architecture of Polykrikos kofoidii in 3D using focused ion beam scanning electron microscopy (FIB-SEM) in conjunction with high-pressure freezing, freeze-substitution, TEM, and confocal microscopy. We found that P. kofoidii possessed six nuclear tunnels, which were continuous with a reticulating network of membranes that has thus far gone unnoticed. These membranous extensions interconnect the six tunnels while ramifying throughout the nucleus to form a “nuclear net.” To our knowledge, the nuclear net is the most elaborate endomembrane structure described within a nucleus. Our findings demonstrate the utility of tomographic approaches for detecting 3D membrane networks and show that nuclear complexity has been underestimated in Polykrikos kofoidii and, potentially, in other dinoflagellates.
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Riaz S, Sui Z, Niaz Z, Khan S, Liu Y, Liu H. Distinctive Nuclear Features of Dinoflagellates with A Particular Focus on Histone and Histone-Replacement Proteins. Microorganisms 2018; 6:E128. [PMID: 30558155 PMCID: PMC6313786 DOI: 10.3390/microorganisms6040128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 11/30/2022] Open
Abstract
Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates "dinokaryon" have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed nucleosome-less chromatin, immense genome, low protein to DNA ratio, guanine-cytosine rich methylated DNA, and unique mitosis process. Furthermore, dinoflagellates are the only known group of eukaryotes that apparently lack histone proteins. Over the course of evolution, dinoflagellates have recruited other proteins, e.g., histone-like proteins (HLPs), from bacteria and dinoflagellates/viral nucleoproteins (DVNPs) from viruses as histone substitutes. Expression diversity of these nucleoproteins has greatly influenced the chromatin structure and gene expression regulation in dinoflagellates. Histone replacement proteins (HLPs and DVNPs) are hypothesized to perform a few similar roles as histone proteins do in other eukaryotes, i.e., gene expression regulation and repairing DNA. However, their role in bulk packaging of DNA is not significant as low amounts of proteins are associated with the gigantic genome. This review intends to summarize the discoveries encompassing unique nuclear features of dinoflagellates, particularly focusing on histone and histone replacement proteins. In addition, a comprehensive view of the evolution of dinoflagellate nuclei is presented.
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Affiliation(s)
- Sadaf Riaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Department of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan.
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Zeeshan Niaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Department of Microbiology, Hazara University, Mansehra 21120, Pakistan.
| | - Sohrab Khan
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Department of Microbiology, Hazara University, Mansehra 21120, Pakistan.
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Haoxin Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
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