Clades of huge phages from across Earth’s ecosystems
Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest ph...
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| Published in | Nature (London) Vol. 578; no. 7795; pp. 425 - 431 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
20.02.2020
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Bacteriophages typically have small genomes
1
and depend on their bacterial hosts for replication
2
. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.
Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes. |
|---|---|
| AbstractList | Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems. Bacteriophages typically have small genomes and depend on their bacterial hosts for replication . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems. Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems. Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems. Bacteriophages typically have small genomes.sup.1 and depend on their bacterial hosts for replication.sup.2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is--to our knowledge--the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems. Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems. Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems. Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes. Bacteriophages typically have small genomes.sup.1 and depend on their bacterial hosts for replication.sup.2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is--to our knowledge--the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems. Genomic analyses of major clades of huge phages sampled from across Earth's ecosystems show that they have diverse genetic inventories, including a variety of CRISPR-Cas systems and translation-relevant genes. |
| Audience | Academic |
| Author | Munk, Patrick Lavy, Adi Lane, Katherine R. Borton, Mikayla A. Keren, Ray Ward, Fred Morowitz, Michael Matheus-Carnevali, Paula Nelson, Tara C. Relman, David A. Brooks, Brandon Li, Wen-Jun Doudna, Jennifer A. Sachdeva, Rohan Méheust, Raphaël Farag, Ibrahim F. Devoto, Audra Al-Shayeb, Basem Olm, Matthew R. Cate, Jamie H. D. Power, Mary E. Zhou, Jinglie Wrighton, Kelly Finstad, Kari Chen, Lin-Xing Warren, Lesley Sharrar, Allison Lehours, Anne-Catherine Santini, Joanne M. Kantor, Rose Probst, Alexander J. Jaffe, Alexander L. Thomas, Alex Tringe, Susannah G. Castelle, Cindy J. Goltsman, Daniela S. A. Lei, Shufei Bouma-Gregson, Keith Amundson, Ronald Anantharaman, Karthik Banfield, Jillian F. He, Christine Sun, Christine Amano, Yuki Harrison, Sue |
| Author_xml | – sequence: 1 givenname: Basem surname: Al-Shayeb fullname: Al-Shayeb, Basem organization: Innovative Genomics Institute, University of California Berkeley – sequence: 2 givenname: Rohan surname: Sachdeva fullname: Sachdeva, Rohan organization: Innovative Genomics Institute, University of California Berkeley – sequence: 3 givenname: Lin-Xing surname: Chen fullname: Chen, Lin-Xing organization: Innovative Genomics Institute, University of California Berkeley – sequence: 4 givenname: Fred surname: Ward fullname: Ward, Fred organization: Innovative Genomics Institute, University of California Berkeley – sequence: 5 givenname: Patrick surname: Munk fullname: Munk, Patrick organization: National Food Institute, Technical University of Denmark – sequence: 6 givenname: Audra surname: Devoto fullname: Devoto, Audra organization: Innovative Genomics Institute, University of California Berkeley – sequence: 7 givenname: Cindy J. surname: Castelle fullname: Castelle, Cindy J. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 8 givenname: Matthew R. surname: Olm fullname: Olm, Matthew R. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 9 givenname: Keith surname: Bouma-Gregson fullname: Bouma-Gregson, Keith organization: Earth and Planetary Science, University of California Berkeley – sequence: 10 givenname: Yuki surname: Amano fullname: Amano, Yuki organization: Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency – sequence: 11 givenname: Christine surname: He fullname: He, Christine organization: Innovative Genomics Institute, University of California Berkeley – sequence: 12 givenname: Raphaël surname: Méheust fullname: Méheust, Raphaël organization: Innovative Genomics Institute, University of California Berkeley – sequence: 13 givenname: Brandon surname: Brooks fullname: Brooks, Brandon organization: Innovative Genomics Institute, University of California Berkeley – sequence: 14 givenname: Alex surname: Thomas fullname: Thomas, Alex organization: Innovative Genomics Institute, University of California Berkeley – sequence: 15 givenname: Adi surname: Lavy fullname: Lavy, Adi organization: Innovative Genomics Institute, University of California Berkeley – sequence: 16 givenname: Paula surname: Matheus-Carnevali fullname: Matheus-Carnevali, Paula organization: Innovative Genomics Institute, University of California Berkeley – sequence: 17 givenname: Christine surname: Sun fullname: Sun, Christine organization: Department of Microbiology & Immunology, Stanford University – sequence: 18 givenname: Daniela S. A. surname: Goltsman fullname: Goltsman, Daniela S. A. organization: Department of Microbiology & Immunology, Stanford University – sequence: 19 givenname: Mikayla A. surname: Borton fullname: Borton, Mikayla A. organization: Department of Soil and Crop Sciences, Colorado State University – sequence: 20 givenname: Allison surname: Sharrar fullname: Sharrar, Allison organization: Earth and Planetary Science, University of California Berkeley – sequence: 21 givenname: Alexander L. surname: Jaffe fullname: Jaffe, Alexander L. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 22 givenname: Tara C. surname: Nelson fullname: Nelson, Tara C. organization: Department of Civil and Mineral Engineering, University of Toronto – sequence: 23 givenname: Rose surname: Kantor fullname: Kantor, Rose organization: Innovative Genomics Institute, University of California Berkeley – sequence: 24 givenname: Ray surname: Keren fullname: Keren, Ray organization: Innovative Genomics Institute, University of California Berkeley – sequence: 25 givenname: Katherine R. surname: Lane fullname: Lane, Katherine R. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 26 givenname: Ibrahim F. surname: Farag fullname: Farag, Ibrahim F. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 27 givenname: Shufei surname: Lei fullname: Lei, Shufei organization: Earth and Planetary Science, University of California Berkeley – sequence: 28 givenname: Kari surname: Finstad fullname: Finstad, Kari organization: Environmental Science, Policy and Management, University of California Berkeley – sequence: 29 givenname: Ronald surname: Amundson fullname: Amundson, Ronald organization: Environmental Science, Policy and Management, University of California Berkeley – sequence: 30 givenname: Karthik surname: Anantharaman fullname: Anantharaman, Karthik organization: Earth and Planetary Science, University of California Berkeley – sequence: 31 givenname: Jinglie surname: Zhou fullname: Zhou, Jinglie organization: DOE Joint Genome Institute – sequence: 32 givenname: Alexander J. surname: Probst fullname: Probst, Alexander J. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 33 givenname: Mary E. surname: Power fullname: Power, Mary E. organization: Integrative Biology, University of California Berkeley – sequence: 34 givenname: Susannah G. surname: Tringe fullname: Tringe, Susannah G. organization: DOE Joint Genome Institute – sequence: 35 givenname: Wen-Jun surname: Li fullname: Li, Wen-Jun organization: School of Life Sciences, Sun Yat-Sen University – sequence: 36 givenname: Kelly surname: Wrighton fullname: Wrighton, Kelly organization: Department of Soil and Crop Sciences, Colorado State University – sequence: 37 givenname: Sue surname: Harrison fullname: Harrison, Sue organization: Centre for Bioprocess Engineering Research, University of Cape Town – sequence: 38 givenname: Michael surname: Morowitz fullname: Morowitz, Michael organization: Department of Surgery, University of Pittsburgh School of Medicine – sequence: 39 givenname: David A. surname: Relman fullname: Relman, David A. organization: Department of Microbiology & Immunology, Stanford University – sequence: 40 givenname: Jennifer A. surname: Doudna fullname: Doudna, Jennifer A. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 41 givenname: Anne-Catherine surname: Lehours fullname: Lehours, Anne-Catherine organization: Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS – sequence: 42 givenname: Lesley surname: Warren fullname: Warren, Lesley organization: Department of Civil and Mineral Engineering, University of Toronto – sequence: 43 givenname: Jamie H. D. surname: Cate fullname: Cate, Jamie H. D. organization: Innovative Genomics Institute, University of California Berkeley – sequence: 44 givenname: Joanne M. surname: Santini fullname: Santini, Joanne M. organization: Institute of Structural and Molecular Biology, University College London – sequence: 45 givenname: Jillian F. surname: Banfield fullname: Banfield, Jillian F. email: jbanfield@berkeley.edu organization: Innovative Genomics Institute, University of California Berkeley, Earth and Planetary Science, University of California Berkeley, Environmental Science, Policy and Management, University of California Berkeley, School of Earth Sciences, University of Melbourne |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32051592$$D View this record in MEDLINE/PubMed https://www.osti.gov/servlets/purl/1609112$$D View this record in Osti.gov |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Novo Nordisk Foundation USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division Paul Allen Foundation Frontiers Group AC02-05CH11231; APSF-2012-10-05; 1349278; GRT00048468; 1342701; CHE-1740549 National Institutes of Health (NIH) National Research Foundation of South Africa National Science Foundation (NSF) Alfred P. Sloan Foundation German Science Foundation Innovative Genomics Institute |
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| Snippet | Bacteriophages typically have small genomes
1
and depend on their bacterial hosts for replication
2
. Here we sequenced DNA from diverse ecosystems and found... Bacteriophages typically have small genomes and depend on their bacterial hosts for replication . Here we sequenced DNA from diverse ecosystems and found... Bacteriophages typically have small genomes.sup.1 and depend on their bacterial hosts for replication.sup.2. Here we sequenced DNA from diverse ecosystems and... Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found... Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. Here we sequenced DNA from diverse ecosystems and found... |
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| SubjectTerms | 45 45/23 631/326/1321 631/326/171 631/326/2565/2142 Amino Acyl-tRNA Synthetases - genetics Analysis Animals Bacteria Bacteria - genetics Bacteria - virology Bacteriophages Bacteriophages - classification Bacteriophages - genetics Bacteriophages - isolation & purification Bacteriophages - metabolism BASIC BIOLOGICAL SCIENCES Biodiversity Biosynthesis Built environment CRISPR CRISPR-Cas Systems - genetics Deoxyribonucleic acid DNA Earth, Planet Ecosystem Ecosystems Elongation Evolution, Molecular Gene Expression Regulation, Bacterial Gene Expression Regulation, Viral Genes Genetic aspects Genetic diversity Genome, Viral - genetics Genomes Host range Host Specificity Humanities and Social Sciences Humans Lake sediments Lakes Lakes - virology Microbiomes Molecular Sequence Annotation multidisciplinary Natural history Nucleotide sequence Oceans Oceans and Seas Phages Phylogeny Plasmids Prophages - genetics Protein Biosynthesis Proteins Ribosomal proteins Ribosomal Proteins - genetics RNA, Transfer - genetics Science Science (multidisciplinary) Seawater - virology Sediments Soil Microbiology Taxonomy Transcription factors Transcription, Genetic Translation Translation elongation Translation initiation tRNA tRNA Ala Urban environments |
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| Title | Clades of huge phages from across Earth’s ecosystems |
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