Mirusviruses link herpesviruses to giant viruses.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
04 2023
04 2023
Historique:
received:
27
10
2022
accepted:
16
03
2023
medline:
28
4
2023
pubmed:
20
4
2023
entrez:
19
04
2023
Statut:
ppublish
Résumé
DNA viruses have a major influence on the ecology and evolution of cellular organisms
Identifiants
pubmed: 37076623
doi: 10.1038/s41586-023-05962-4
pii: 10.1038/s41586-023-05962-4
pmc: PMC10132985
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
783-789Informations de copyright
© 2023. The Author(s).
Références
Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021).
pubmed: 33707211
pmcid: 7980383
doi: 10.1073/pnas.2021586118
Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. https://doi.org/10.1038/nrmicro1750 (2007).
Irwin, N. A. T., Pittis, A. A., Richards, T. A. & Keeling, P. J. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat. Microbiol. 7, 327–336 (2022).
pubmed: 34972821
doi: 10.1038/s41564-021-01026-3
Moniruzzaman, M., Weinheimer, A. R., Martinez-Gutierrez, C. A. & Aylward, F. O. Widespread endogenization of giant viruses shapes genomes of green algae. Nature https://doi.org/10.1038/s41586-020-2924-2 (2020).
Koonin, E. V., Dolja, V. V. & Krupovic, M. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology 479–480, 2–25 (2015).
pubmed: 25771806
doi: 10.1016/j.virol.2015.02.039
Koonin, E. V. et al. Global organization and proposed megataxonomy of the virus world. Microbiol. Mol. Biol. Rev. 84, e00061-19 (2020).
pubmed: 32132243
pmcid: 7062200
doi: 10.1128/MMBR.00061-19
Krupovic, M., Dolja, V. V. & Koonin, E. V. The LUCA and its complex virome. Nat. Rev. Microbiol. 18, 661–670 (2020).
pubmed: 32665595
doi: 10.1038/s41579-020-0408-x
Krupovic, M. & Koonin, E. V. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat. Rev. Microbiol. 13, 105–115 (2015).
pubmed: 25534808
doi: 10.1038/nrmicro3389
Guglielmini, J., Woo, A. C., Krupovic, M., Forterre, P. & Gaia, M. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proc. Natl Acad. Sci. USA 116, 19585–19592 (2019).
pubmed: 31506349
pmcid: 6765235
doi: 10.1073/pnas.1912006116
Woo, A. C., Gaia, M., Guglielmini, J., da Cunha, V. & Forterre, P. Phylogeny of the Varidnaviria morphogenesis module: congruence and incongruence with the tree of life and viral taxonomy. Front. Microbiol. 12, 1708 (2021).
doi: 10.3389/fmicb.2021.704052
Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature https://doi.org/10.1038/s41586-020-1957-x (2020).
Moniruzzaman, M., Martinez-Gutierrez, C. A., Weinheimer, A. R. & Aylward, F. O. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat. Commun. 11, 1710 (2020).
doi: 10.1038/s41467-020-15507-2
Endo, H. et al. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat. Ecol. Evol. 4, 1639–1649 (2020).
pubmed: 32895519
doi: 10.1038/s41559-020-01288-w
Mann, N. H. Phages of the marine cyanobacterial picophytoplankton. FEMS Microbiol. Rev. 27, 17–34 (2003).
pubmed: 12697340
doi: 10.1016/S0168-6445(03)00016-0
Kaneko, H. et al. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience 24, 102002 (2021).
pubmed: 33490910
doi: 10.1016/j.isci.2020.102002
Gregory, A. C. et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177, 1109–1123 (2019).
pubmed: 31031001
pmcid: 6525058
doi: 10.1016/j.cell.2019.03.040
Laber, C. P. et al. Coccolithovirus facilitation of carbon export in the North Atlantic. Nat. Microbiol. 3, 537–547 (2018).
pubmed: 29531367
doi: 10.1038/s41564-018-0128-4
Sunagawa, S. et al. Tara Oceans: towards global ocean ecosystems biology. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-020-0364-5 (2020).
Delmont, T. O. et al. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME J. https://doi.org/10.1038/s41396-021-01135-1 (2021).
Delmont, T. O. et al. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genomics https://doi.org/10.1016/J.XGEN.2022.100123 (2022).
Aylward, F. O., Moniruzzaman, M., Ha, A. D. & Koonin, E. V. A phylogenomic framework for charting the diversity and evolution of giant viruses. PLoS Biol. 19, e3001430 (2021).
pubmed: 34705818
pmcid: 8575486
doi: 10.1371/journal.pbio.3001430
de Vargas, C. et al. Eukaryotic plankton diversity in the sunlit ocean. Science 348, 1261605 (2015).
pubmed: 25999516
doi: 10.1126/science.1261605
Carradec, Q. et al. A global ocean atlas of eukaryotic genes. Nat. Commun. 9, 373 (2018).
pubmed: 29371626
pmcid: 5785536
doi: 10.1038/s41467-017-02342-1
Mihara, T. et al. Taxon richness of ‘Megaviridae’ exceeds those of Bacteria and Archaea in the ocean. Microbes Environ. 33, 162–171 (2018).
pubmed: 29806626
pmcid: 6031395
doi: 10.1264/jsme2.ME17203
Okoye, M. E., Sexton, G. L., Huang, E., McCaffery, J. M. & Desai, P. Functional analysis of the triplex proteins (VP19C and VP23) of herpes simplex virus type 1. J. Virol. 80, 929–940 (2006).
pubmed: 16378995
pmcid: 1346874
doi: 10.1128/JVI.80.2.929-940.2006
Zhang, Y. et al. Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes. Nat. Commun. 10, 5346 (2019).
pubmed: 31767868
pmcid: 6877594
doi: 10.1038/s41467-019-13064-x
Duda, R. L. & Teschke, C. M. The amazing HK97 fold: versatile results of modest differences. Curr. Opin. Virol. 36, 9–16 (2019).
pubmed: 30856581
pmcid: 6626583
doi: 10.1016/j.coviro.2019.02.001
Hua, J. et al. Capsids and genomes of jumbo-sized bacteriophages reveal the evolutionary reach of the HK97 fold. mBio 8, e01579-17 (2017).
pubmed: 29042498
pmcid: 5646251
doi: 10.1128/mBio.01579-17
Kazlauskas, D., Krupovic, M., Guglielmini, J., Forterre, P. & Venclovas, C. S. Diversity and evolution of B-family DNA polymerases. Nucleic Acids Res. 48, 10142 (2020).
pubmed: 32976577
pmcid: 7544198
doi: 10.1093/nar/gkaa760
Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature https://doi.org/10.1038/s41586-022-04862-3 (2022).
Legendre, M. et al. Diversity and evolution of the emerging Pandoraviridae family. Nat. Commun. 9, 2285 (2018).
pubmed: 29891839
pmcid: 5995976
doi: 10.1038/s41467-018-04698-4
Talbert, P. B., Armache, K. J. & Henikoff, S. Viral histones: pickpocket’s prize or primordial progenitor? Epigenetics Chromatin 15, 21 (2022).
doi: 10.1186/s13072-022-00454-7
Hososhima, S. et al. Proton-transporting heliorhodopsins from marine giant viruses. Elife 11, e78416 (2022).
pubmed: 36065640
pmcid: 9448325
doi: 10.7554/eLife.78416
Weinheimer, A. R. & Aylward, F. O. Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages. ISME J. https://doi.org/10.1038/s41396-022-01214-x (2022).
Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020).
pubmed: 32051592
pmcid: 7162821
doi: 10.1038/s41586-020-2007-4
Weinheimer, A. R. & Aylward, F. O. A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase. Nat. Commun. 11, 4506 (2020).
pubmed: 32908149
pmcid: 7481178
doi: 10.1038/s41467-020-18281-3
Adler, B., Sattler, C. & Adler, H. Herpesviruses and their host cells: a successful liaison. Trends Microbiol. 25, 229–241 (2017).
pubmed: 27956142
doi: 10.1016/j.tim.2016.11.009
Yutin, N., Shevchenko, S., Kapitonov, V., Krupovic, M. & Koonin, E. V. A novel group of diverse Polinton-like viruses discovered by metagenome analysis. BMC Biol. 13, 95 (2015).
pubmed: 26560305
pmcid: 4642659
doi: 10.1186/s12915-015-0207-4
Boratto, P. V. M. et al. Yaravirus: a novel 80-nm virus infecting Acanthamoeba castellanii. Proc. Natl Acad. Sci. USA 117, 16579–16586 (2020).
pubmed: 32601223
pmcid: 7368276
doi: 10.1073/pnas.2001637117
Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2014).
doi: 10.1093/bioinformatics/btv033
Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).
pubmed: 26500826
pmcid: 4614810
doi: 10.7717/peerj.1319
Eren, A. M. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat. Microbiol. 6, 3–6 (2021).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).
doi: 10.1186/1471-2105-11-119
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 2705234
doi: 10.1093/bioinformatics/btp324
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
doi: 10.1093/bioinformatics/btp352
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).
pubmed: 25218180
doi: 10.1038/nmeth.3103
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
pubmed: 22039361
pmcid: 3197634
doi: 10.1371/journal.pcbi.1002195
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
pubmed: 16731699
doi: 10.1093/bioinformatics/btl158
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
pubmed: 23329690
pmcid: 3603318
doi: 10.1093/molbev/mst010
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
pubmed: 28481363
pmcid: 5453245
doi: 10.1038/nmeth.4285
Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
pubmed: 25371430
doi: 10.1093/molbev/msu300
Delmont, T. O. & Eren, A. M. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies. PeerJ 4, e1839 (2016).
pubmed: 27069789
pmcid: 4824900
doi: 10.7717/peerj.1839
Needham, D. M. et al. Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. Philos. Trans. R. Soc. B 374, 20190086 (2019).
doi: 10.1098/rstb.2019.0086
Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478–2483 (2002).
pubmed: 12034836
pmcid: 117189
doi: 10.1093/nar/30.11.2478
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
pubmed: 2231712
doi: 10.1016/S0022-2836(05)80360-2
Yoshikawa, G. et al. Medusavirus, a novel large DNA virus discovered from hot spring water. J. Virol. 93, e02130-18 (2019).
pubmed: 30728258
pmcid: 6450098
doi: 10.1128/JVI.02130-18
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
pubmed: 20525638
doi: 10.1093/sysbio/syq010
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
pubmed: 29077904
doi: 10.1093/molbev/msx281
Menardo, F. et al. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinform. 19, 164 (2018).
doi: 10.1186/s12859-018-2164-8
Wang, H. C., Minh, B. Q., Susko, E. & Roger, A. J. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. 67, 216–235 (2018).
pubmed: 28950365
doi: 10.1093/sysbio/syx068
Delmont, T. O. et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat. Microbiol. 3, 804–813 (2018).
pubmed: 29891866
pmcid: 6792437
doi: 10.1038/s41564-018-0176-9
Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).
pubmed: 26243257
pmcid: 4531804
doi: 10.1186/s13059-015-0721-2
Vanni, C. et al. Unifying the known and unknown microbial coding sequence space. Elife 11, e67667 (2022).
pubmed: 35356891
pmcid: 9132574
doi: 10.7554/eLife.67667
Gabler, F. et al. Protein sequence analysis using the MPI Bioinformatics Toolkit. Curr. Protoc. Bioinform. 72, e108 (2020).
Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinform. 20, 473 (2019).
doi: 10.1186/s12859-019-3019-7
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
pubmed: 35637307
pmcid: 9184281
doi: 10.1038/s41592-022-01488-1
Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).
pubmed: 34282049
pmcid: 7612213
doi: 10.1126/science.abj8754
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
pubmed: 32881101
doi: 10.1002/pro.3943
Mihara, T. et al. Linking virus genomes with host taxonomy. Viruses 8, 66 (2016).
pubmed: 26938550
pmcid: 4810256
doi: 10.3390/v8030066
Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61–D65 (2007).
pubmed: 17130148
doi: 10.1093/nar/gkl842
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B. & Wu, C. H. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932 (2015).
pubmed: 25398609
doi: 10.1093/bioinformatics/btu739
Yutin, N., Wolf, Y. I., Raoult, D. & Koonin, E. V. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol. J. 6, 223 (2009).
pubmed: 20017929
pmcid: 2806869
doi: 10.1186/1743-422X-6-223
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
pubmed: 25402007
doi: 10.1038/nmeth.3176
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
pubmed: 30418610
doi: 10.1093/nar/gky1085
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).
pubmed: 9023104
pmcid: 146525
doi: 10.1093/nar/25.5.955
Holm, L. & Rosenström, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545 (2010).
pubmed: 20457744
pmcid: 2896194
doi: 10.1093/nar/gkq366
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Preprint at bioRxiv https://doi.org/10.1101/2022.02.07.479398 (2022).
Hauser, M., Steinegger, M. & Söding, J. MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics 32, 1323–1330 (2016).
pubmed: 26743509
doi: 10.1093/bioinformatics/btw006
Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–W37 (2011).
pubmed: 21593126
pmcid: 3125773
doi: 10.1093/nar/gkr367