1
|
Colson P, Aherfi S, La Scola B. Evidence of giant viruses of amoebae in the human gut. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
2
|
Erives AJ. Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance. Epigenetics Chromatin 2017; 10:55. [PMID: 29179736 PMCID: PMC5704553 DOI: 10.1186/s13072-017-0162-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022] Open
Abstract
Background While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like “doublets” in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. Results Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. Conclusions The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of the four core histone clades. We thus suggest MV histone doublet genes and their DNA topo II gene possibly were acquired from an organism with a chromatinized replisome that diverged prior to the origin of eukaryotic core histone variants for H2/H2A.Z and H3/cenH3. These results also imply that core histones were utilized ancestrally in viral DNA compaction and/or protection from host endonucleases. Electronic supplementary material The online version of this article (10.1186/s13072-017-0162-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Albert J Erives
- Department of Biology, University of Iowa, Iowa City, IA, 52242-1324, USA.
| |
Collapse
|
3
|
Abrahão JS, Araújo R, Colson P, La Scola B. The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses. PLoS Genet 2017; 13:e1006532. [PMID: 28207761 PMCID: PMC5313130 DOI: 10.1371/journal.pgen.1006532] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The giant mimiviruses challenged the well-established concept of viruses, blurring the roots of the tree of life, mainly due to their genetic content. Along with other nucleo-cytoplasmic large DNA viruses, they compose a new proposed order-named Megavirales-whose origin and evolution generate heated debate in the scientific community. The presence of an arsenal of genes not widespread in the virosphere related to important steps of the translational process, including transfer RNAs, aminoacyl-tRNA synthetases, and translation factors for peptide synthesis, constitutes an important element of this debate. In this review, we highlight the main findings to date about the translational machinery of the mimiviruses and compare their distribution along the distinct members of the family Mimiviridae. Furthermore, we discuss how the presence and/or absence of the translation-related genes among mimiviruses raises important insights to boost the debate on their origin and evolutionary history.
Collapse
Affiliation(s)
- Jônatas Santos Abrahão
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France.,Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Araújo
- Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France
| |
Collapse
|
4
|
Zhang W, Zhou J, Liu T, Yu Y, Pan Y, Yan S, Wang Y. Four novel algal virus genomes discovered from Yellowstone Lake metagenomes. Sci Rep 2015; 5:15131. [PMID: 26459929 PMCID: PMC4602308 DOI: 10.1038/srep15131] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022] Open
Abstract
Phycodnaviruses are algae-infecting large dsDNA viruses that are widely distributed in aquatic environments. Here, partial genomic sequences of four novel algal viruses were assembled from a Yellowstone Lake metagenomic data set. Genomic analyses revealed that three Yellowstone Lake phycodnaviruses (YSLPVs) had genome lengths of 178,262 bp, 171,045 bp, and 171,454 bp, respectively, and were phylogenetically closely related to prasinoviruses (Phycodnaviridae). The fourth (YSLGV), with a genome length of 73,689 bp, was related to group III in the extended family Mimiviridae comprising Organic Lake phycodnaviruses and Phaeocystis globosa virus 16 T (OLPG). A pair of inverted terminal repeats was detected in YSLPV1, suggesting that its genome is nearly complete. Interestingly, these four putative YSL giant viruses also bear some genetic similarities to Yellowstone Lake virophages (YSLVs). For example, they share nine non-redundant homologous genes, including ribonucleotide reductase small subunit (a gene conserved in nucleo-cytoplasmic large DNA viruses) and Organic Lake virophage OLV2 (conserved in the majority of YSLVs). Additionally, putative multidrug resistance genes (emrE) were found in YSLPV1 and YSLPV2 but not in other viruses. Phylogenetic trees of emrE grouped YSLPVs with algae, suggesting that horizontal gene transfer occurred between giant viruses and their potential algal hosts.
Collapse
Affiliation(s)
- Weijia Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jinglie Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Taigang Liu
- College of Information Technology, Shanghai Ocean University, Shanghai, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
| | - Shuling Yan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Institute of Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
| |
Collapse
|
5
|
Virophages go nuclear in the marine alga Bigelowiella natans. Proc Natl Acad Sci U S A 2015; 112:11750-1. [PMID: 26330604 DOI: 10.1073/pnas.1515142112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
6
|
Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
Collapse
Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| |
Collapse
|
7
|
Molecular Biosafety. APPLIED BIOSAFETY 2014. [DOI: 10.1177/153567601401900406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
8
|
Affiliation(s)
- Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward M. Rubin
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
9
|
Wilson WH, Gilg IC, Duarte A, Ogata H. Development of DNA mismatch repair gene, MutS, as a diagnostic marker for detection and phylogenetic analysis of algal Megaviruses. Virology 2014; 466-467:123-8. [PMID: 25063474 DOI: 10.1016/j.virol.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/10/2014] [Accepted: 07/01/2014] [Indexed: 12/22/2022]
Abstract
Megaviruses are generically defined as giant viruses with genomes up to 1.26Mb that infect eukaryotic unicellular protists; they are clearly delineated in DNA polymerase B phylogenetic trees; in addition, common features often include an associated virophage observed during infection; the presence of an amino acyl tRNA synthetase gene; and a nucleic acid mismatch repair protein, MutS gene. The archetypal representative of this evolving putative family is Mimivirus, an opportunistic pathogen of Acanthamoeba spp. originally thought to be a bacterium until its genome sequence was published in 2004. Subsequent analysis of marine metagenomic data revealed Megaviruses are likely ubiquitous on the surface ocean. Analysis of genome sequences of giant viruses isolated from naturally occurring marine protists such as microalgae and a microflagellate grazer, started the expansion of the Megaviridae. Here, we explored the possibility of developing Megavirus specific markers for mutS that could be used in virus molecular ecology studies. MutS is split into 15 different clades representing a wide range of cellular life, and two that contain Megaviruses, clade MutS7 and clade MutS8. We developed specific PCR primers that recognized Megavirus clade MutS8, a clade that we propose discriminates most of the algal Megaviruses. Analysis of seawater off the coast of Maine, US, revealed novel groups of algal Megaviruses that were present in all samples tested. The Megavirus clade MutS8 marker should be considered as a tool to reveal new diversity and distribution of this enigmatic group of viruses.
Collapse
Affiliation(s)
- William H Wilson
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME 04544, USA; Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK.
| | - Ilana C Gilg
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME 04544, USA
| | - Amy Duarte
- Humboldt State University, Arcata, CA, USA
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| |
Collapse
|
10
|
Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries. Virol J 2014; 11:120. [PMID: 24976356 PMCID: PMC4083134 DOI: 10.1186/1743-422x-11-120] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/16/2014] [Indexed: 12/30/2022] Open
Abstract
In 2003, Acanthamoeba polyphaga mimivirus (APMV) was first described and began to impact researchers around the world, due to its structural and genetic complexity. This virus founded the family Mimiviridae. In recent years, several new giant viruses have been isolated from different environments and specimens. Giant virus research is in its initial phase and information that may arise in the coming years may change current conceptions of life, diversity and evolution. Thus, this review aims to condense the studies conducted so far about the features and peculiarities of APMV, from its discovery to its clinical relevance.
Collapse
|