51
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Hurwitz BL, U’Ren JM. Viral metabolic reprogramming in marine ecosystems. Curr Opin Microbiol 2016; 31:161-168. [DOI: 10.1016/j.mib.2016.04.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022]
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52
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Ledermann B, Béjà O, Frankenberg-Dinkel N. New biosynthetic pathway for pink pigments from uncultured oceanic viruses. Environ Microbiol 2016; 18:4337-4347. [PMID: 26950653 DOI: 10.1111/1462-2920.13290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/04/2016] [Indexed: 12/18/2022]
Abstract
The pink open-chain tetrapyrrole pigment phycoerythrobilin (PEB) is employed by marine cyanobacteria, red algae and cryptophytes as a light-harvesting chromophore in phycobiliproteins. Genes encoding biosynthesis proteins for PEB have also been discovered in cyanophages, viruses that infect cyanobacteria, and mimic host pigment biosynthesis with the exception of PebS which combines the enzymatic activities of two host enzymes. In this study, we have identified novel members of the PEB biosynthetic enzyme families, heme oxygenases and ferredoxin-dependent bilin reductases. Encoding genes were found in metagenomic datasets and could be traced back to bacteriophage but not cyanophage origin. While the heme oxygenase exhibited standard activity, a new bilin reductase with highest homology to the teal pigment producing enzyme PcyA revealed PEB biosynthetic activity. Although PcyX possesses PebS-like activity both enzymes share only 9% sequence identity and likely catalyze the reaction via two independent mechanisms. Our data point towards the presence of phycobilin biosynthetic genes in phages that probably infect alphaproteobacteria and, therefore, further support a role of phycobilins outside oxygenic phototrophs.
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Affiliation(s)
- Benjamin Ledermann
- Department of Biology, Microbiology, Technical University Kaiserslautern, Kaiserslautern, Germany
| | - Oded Béjà
- Technion-Israel Institute of Technology, Haifa, Israel
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53
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Malitsky S, Ziv C, Rosenwasser S, Zheng S, Schatz D, Porat Z, Ben-Dor S, Aharoni A, Vardi A. Viral infection of the marine alga Emiliania huxleyi triggers lipidome remodeling and induces the production of highly saturated triacylglycerol. THE NEW PHYTOLOGIST 2016; 210:88-96. [PMID: 26856244 DOI: 10.1111/nph.13852] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/15/2015] [Indexed: 05/04/2023]
Abstract
Viruses that infect marine photosynthetic microorganisms are major ecological and evolutionary drivers of microbial food webs, estimated to turn over more than a quarter of the total photosynthetically fixed carbon. Viral infection of the bloom-forming microalga Emiliania huxleyi induces the rapid remodeling of host primary metabolism, targeted towards fatty acid metabolism. We applied a liquid chromatography-mass spectrometry (LC-MS)-based lipidomics approach combined with imaging flow cytometry and gene expression profiling to explore the impact of viral-induced metabolic reprogramming on lipid composition. Lytic viral infection led to remodeling of the cellular lipidome, by predominantly inducing the biosynthesis of highly saturated triacylglycerols (TAGs), coupled with a significant accumulation of neutral lipids within lipid droplets. Furthermore, TAGs were found to be a major component (77%) of the lipidome of isolated virions. Interestingly, viral-induced TAGs were significantly more saturated than TAGs produced under nitrogen starvation. This study highlights TAGs as major products of the viral-induced metabolic reprogramming during the host-virus interaction and indicates a selective mode of membrane recruitment during viral assembly, possibly by budding of the virus from specialized subcellular compartments. These findings provide novel insights into the role of viruses infecting microalgae in regulating metabolism and energy transfer in the marine environment and suggest their possible biotechnological application in biofuel production.
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Affiliation(s)
- Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Carmit Ziv
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shilo Rosenwasser
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shuning Zheng
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ziv Porat
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shifra Ben-Dor
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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54
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Ziv C, Malitsky S, Othman A, Ben-Dor S, Wei Y, Zheng S, Aharoni A, Hornemann T, Vardi A. Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga. Proc Natl Acad Sci U S A 2016; 113:E1907-16. [PMID: 26984500 PMCID: PMC4822627 DOI: 10.1073/pnas.1523168113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine viruses are the most abundant biological entities in the oceans shaping community structure and nutrient cycling. The interaction between the bloom-forming alga Emiliania huxleyi and its specific large dsDNA virus (EhV) is a major factor determining the fate of carbon in the ocean, thus serving as a key host-pathogen model system. The EhV genome encodes for a set of genes involved in the de novo sphingolipid biosynthesis, not reported in any viral genome to date. We combined detailed lipidomic and biochemical analyses to characterize the functional role of this virus-encoded pathway during lytic viral infection. We identified a major metabolic shift, mediated by differential substrate specificity of virus-encoded serine palmitoyltransferase, a key enzyme of sphingolipid biosynthesis. Consequently, unique viral glycosphingolipids, composed of unusual hydroxylated C17 sphingoid bases (t17:0) were highly enriched in the infected cells, and their synthesis was found to be essential for viral assembly. These findings uncover the biochemical bases of the virus-induced metabolic rewiring of the host sphingolipid biosynthesis during the chemical "arms race" in the ocean.
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Affiliation(s)
- Carmit Ziv
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alaa Othman
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland; Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, 23562 Lübeck, Germany
| | - Shifra Ben-Dor
- Biological Services Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yu Wei
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Shuning Zheng
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
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55
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Lin X, Ding H, Zeng Q. Transcriptomic response during phage infection of a marine cyanobacterium under phosphorus-limited conditions. Environ Microbiol 2015; 18:450-60. [DOI: 10.1111/1462-2920.13104] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Xingqin Lin
- Division of Life Science; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Huiming Ding
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Qinglu Zeng
- Division of Life Science; The Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
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56
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57
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Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza JC, Sullivan MB, Cornejo-Castillo FM, Sánchez P, Acinas SG, Dupont CL, Béjà O. Closing the gaps on the viral photosystem-I psaDCAB gene organization. Environ Microbiol 2015; 17:5100-8. [PMID: 26310718 PMCID: PMC5019241 DOI: 10.1111/1462-2920.13036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/20/2015] [Indexed: 11/30/2022]
Abstract
Marine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD→C→A→B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30°N and 30°S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD→C→A→B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF→C→A→B→K→E→D gene organization and most Prochlorococcus strains. This may indicate a co-evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30°N and 30°S equatorial strip.
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Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Pablo Sánchez
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Silvia G Acinas
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J Craig Venter Institute, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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58
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Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:71-97. [PMID: 25381655 DOI: 10.1007/s11120-014-0057-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Viruses infecting the environmentally important marine cyanobacteria Prochlorococcus and Synechococcus encode 'auxiliary metabolic genes' (AMGs) involved in the light and dark reactions of photosynthesis. Here, we discuss progress on the inventory of such AMGs in the ever-increasing number of viral genome sequences as well as in metagenomic datasets. We contextualise these gene acquisitions with reference to a hypothesised fitness gain to the phage. We also report new evidence with regard to the sequence and predicted structural properties of viral petE genes encoding the soluble electron carrier plastocyanin. Viral copies of PetE exhibit extensive modifications to the N-terminal signal peptide and possess several novel residues in a region responsible for interaction with redox partners. We also highlight potential knowledge gaps in this field and discuss future opportunities to discover novel phage-host interactions involved in the photosynthetic process.
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Affiliation(s)
- Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Andrew D Millard
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Evans
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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59
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Davison M, Hall E, Zare R, Bhaya D. Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. PHOTOSYNTHESIS RESEARCH 2015; 126:135-146. [PMID: 25515769 DOI: 10.1007/s11120-014-0066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Cyanobacteria have played a crucial role in the history of early earth and continue to be instrumental in shaping our planet, yet applications of cutting edge technology have not yet been widely used to explore cyanobacterial diversity. To provide adequate background, we briefly review current sequencing technologies and their innovative uses in genomics and metagenomics. Next, we focus on current cell capture technologies and the challenges of using them with cyanobacteria. We illustrate the utility in coupling breakthroughs in DNA amplification with cell capture platforms, with an example of microfluidic isolation and subsequent targeted amplicon sequencing from individual terrestrial thermophilic cyanobacteria. Single cells of thermophilic, unicellular Synechococcus sp. JA-2-3-B'a(2-13) (Syn OS-B') were sorted in a microfluidic device, lysed, and subjected to whole genome amplification by multiple displacement amplification. We amplified regions from specific CRISPR spacer arrays, which are known to be highly diverse, contain semi-palindromic repeats which form secondary structure, and can be difficult to amplify. Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations.
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Affiliation(s)
- Michelle Davison
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA.
| | - Eric Hall
- SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, 333 Campus Drive Mudd Building, Room 121, Stanford, CA, 94305-4401, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA
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60
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López-Bueno A, Rastrojo A, Peiró R, Arenas M, Alcamí A. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Mol Ecol 2015. [DOI: 10.1111/mec.13321] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- A. López-Bueno
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Rastrojo
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - R. Peiró
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - M. Arenas
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Alcamí
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
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61
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Puxty RJ, Perez-Sepulveda B, Rihtman B, Evans DJ, Millard AD, Scanlan DJ. Spontaneous Deletion of an "ORFanage" Region Facilitates Host Adaptation in a "Photosynthetic" Cyanophage. PLoS One 2015; 10:e0132642. [PMID: 26177354 PMCID: PMC4503421 DOI: 10.1371/journal.pone.0132642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/16/2015] [Indexed: 01/29/2023] Open
Abstract
Viruses have been suggested to be the largest source of genetic diversity on Earth. Genome sequencing and metagenomic surveys reveal that novel genes with unknown functions are abundant in viral genomes. Yet few observations exist for the processes and frequency by which these genes are gained and lost. The surface waters of marine environments are dominated by marine picocyanobacteria and their co-existing viruses (cyanophages). Recent genome sequencing of cyanophages has revealed a vast array of genes that have been acquired from their cyanobacterial hosts. Here, we re-sequenced the cyanophage S-PM2 genome after 10 years of near continuous passage through its marine Synechococcus host. During this time a spontaneous mutant (S-PM2d) lacking 13% of the S-PM2 ORFs became dominant in the cyanophage population. These ORFs are found at one loci and are not homologous to any proteins in any other sequenced organism (ORFans). We demonstrate a fitness cost to S-PM2WT associated with possession of these ORFs under standard laboratory growth. Metagenomic surveys reveal these ORFs are present in various aquatic environments, are likely of cyanophage origin and appear to be enriched in environments from the extremes of salinity (freshwater and hypersaline). We posit that these ORFs contribute to the flexible gene content of cyanophages and offer a distinct fitness advantage in freshwater and hypersaline environments.
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Affiliation(s)
- Richard J. Puxty
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Blanca Perez-Sepulveda
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - David J. Evans
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - Andrew D. Millard
- Warwick Medical School, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, United Kingdom
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62
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Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ 2015; 3:e985. [PMID: 26038737 PMCID: PMC4451026 DOI: 10.7717/peerj.985] [Citation(s) in RCA: 691] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023] Open
Abstract
Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.
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Affiliation(s)
- Simon Roux
- Ecology and Evolutionary Biology, University of Arizona , USA
| | - Francois Enault
- Clermont Université, Université Blaise Pascal, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand , France ; CNRS UMR 6023, LMGE , Aubière , France
| | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona , USA
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63
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Gene acquisition convergence between entomopoxviruses and baculoviruses. Viruses 2015; 7:1960-74. [PMID: 25871928 PMCID: PMC4411684 DOI: 10.3390/v7041960] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/25/2015] [Accepted: 04/08/2015] [Indexed: 12/30/2022] Open
Abstract
Organisms from diverse phylogenetic origins can thrive within the same ecological niches. They might be induced to evolve convergent adaptations in response to a similar landscape of selective pressures. Their genomes should bear the signature of this process. The study of unrelated virus lineages infecting the same host panels guarantees a clear identification of phyletically independent convergent adaptation. Here, we investigate the evolutionary history of genes in the accessory genome shared by unrelated insect large dsDNA viruses: the entomopoxviruses (EPVs, Poxviridae) and the baculoviruses (BVs). EPVs and BVs have overlapping ecological niches and have independently evolved similar infection processes. They are, in theory, subjected to the same selective pressures from their host’s immune responses. Their accessory genomes might, therefore, bear analogous genomic signatures of convergent adaption and could point out key genomic mechanisms of adaptation hitherto undetected in viruses. We uncovered 32 homologous, yet independent acquisitions of genes originating from insect hosts, different eukaryotes, bacteria and viruses. We showed different evolutionary levels of gene acquisition convergence in these viruses, underlining a continuous evolutionary process. We found both recent and ancient gene acquisitions possibly involved to the adaptation to both specific and distantly related hosts. Multidirectional and multipartite gene exchange networks appear to constantly drive exogenous gene assimilations, bringing key adaptive innovations and shaping the life histories of large DNA viruses. This evolutionary process might lead to genome level adaptive convergence.
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64
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Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus. J Virol 2015; 89:5812-21. [PMID: 25787287 DOI: 10.1128/jvi.00246-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/06/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCE Marine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.
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65
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Abstract
Oxygenic photosynthesis is the principal converter of sunlight into chemical energy on Earth. Cyanobacteria and plants provide the oxygen, food, fuel, fibers, and platform chemicals for life on Earth. The conversion of solar energy into chemical energy is catalyzed by two multisubunit membrane protein complexes, photosystem I (PSI) and photosystem II (PSII). Light is absorbed by the pigment cofactors, and excitation energy is transferred among the antennae pigments and converted into chemical energy at very high efficiency. Oxygenic photosynthesis has existed for more than three billion years, during which its molecular machinery was perfected to minimize wasteful reactions. Light excitation transfer and singlet trapping won over fluorescence, radiation-less decay, and triplet formation. Photosynthetic reaction centers operate in organisms ranging from bacteria to higher plants. They are all evolutionarily linked. The crystal structure determination of photosynthetic protein complexes sheds light on the various partial reactions and explains how they are protected against wasteful pathways and why their function is robust. This review discusses the efficiency of photosynthetic solar energy conversion.
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Affiliation(s)
- Nathan Nelson
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
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66
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Voorhies AA, Eisenlord SD, Marcus DN, Duhaime MB, Biddanda BA, Cavalcoli JD, Dick GJ. Ecological and genetic interactions between cyanobacteria and viruses in a low-oxygen mat community inferred through metagenomics and metatranscriptomics. Environ Microbiol 2015; 18:358-71. [DOI: 10.1111/1462-2920.12756] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/15/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Alexander A. Voorhies
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
| | - Sarah D. Eisenlord
- School of Natural Resources and Environment; University of Michigan; Ann Arbor MI 48109 USA
| | - Daniel N. Marcus
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
| | - Bopaiah A. Biddanda
- Annis Water Resources Institute; Grand Valley State University; Muskegon MI 49441 USA
| | - James D. Cavalcoli
- Department of Computational Medicine and Bioinformatics; University of Michigan; Ann Arbor MI 48109 USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
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Dang VT, Sullivan MB. Emerging methods to study bacteriophage infection at the single-cell level. Front Microbiol 2014; 5:724. [PMID: 25566233 PMCID: PMC4274963 DOI: 10.3389/fmicb.2014.00724] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/02/2014] [Indexed: 11/26/2022] Open
Abstract
Bacteria and their viruses (phages) are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage–host infection dynamics in nature. Here we review emerging methods to study phage–host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. These methods leverage ever-increasing sequence data to identify virus signals from single-cell amplified genome datasets or to produce primers/probes to target particular phage–bacteria pairs (digital PCR and phageFISH), even in complex communities. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage–host interaction outcomes (e.g., lytic, chronic, lysogenic) in model systems. Together these techniques enable quantitative, spatiotemporal studies of phage–bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage–host pairings in nature.
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Affiliation(s)
- Vinh T Dang
- Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA ; Department of Molecular and Cellular Biology, University of Arizona Tucson, AZ, USA
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Hevroni G, Enav H, Rohwer F, Béjà O. Diversity of viral photosystem-I psaA genes. ISME JOURNAL 2014; 9:1892-8. [PMID: 25535938 PMCID: PMC4511924 DOI: 10.1038/ismej.2014.244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 12/23/2022]
Abstract
Marine photosynthesis is one of the major contributors to the global carbon cycle and the world's oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJF→C→A→B→K→E→D and psaD→C→A→B. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaC→A arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaC→A arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought.
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Affiliation(s)
- Gur Hevroni
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hagay Enav
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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69
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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70
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Anderson RE, Sogin ML, Baross JA. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics. PLoS One 2014; 9:e109696. [PMID: 25279954 PMCID: PMC4184897 DOI: 10.1371/journal.pone.0109696] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
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Affiliation(s)
- Rika E. Anderson
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Mitchell L. Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - John A. Baross
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, Washington, United States of America
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71
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Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife 2014; 3:e03125. [PMID: 25171894 PMCID: PMC4164917 DOI: 10.7554/elife.03125] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022] Open
Abstract
Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus-host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.
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Affiliation(s)
- Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Monica Torres Beltran
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Patrick Schwientek
- U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
| | | | - Tanja Woyke
- U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, Canada
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
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72
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Jachiet PA, Colson P, Lopez P, Bapteste E. Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genome Biol Evol 2014; 6:2195-205. [PMID: 25104113 PMCID: PMC4202312 DOI: 10.1093/gbe/evu168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
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Affiliation(s)
- Pierre-Alain Jachiet
- UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France
| | - Philippe Colson
- URMITE UMR CNRS 6236 IRD 198, Facultés de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Philippe Lopez
- UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France
| | - Eric Bapteste
- UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France
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73
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Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome. ISME JOURNAL 2014; 9:472-84. [PMID: 25093636 DOI: 10.1038/ismej.2014.143] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 06/22/2014] [Accepted: 06/24/2014] [Indexed: 11/09/2022]
Abstract
Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established 'core' (180 PCs; one-third new to science) and 'flexible' (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron-sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.
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Affiliation(s)
- Bonnie L Hurwitz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Jennifer R Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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74
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Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 2014; 513:242-5. [PMID: 25043051 DOI: 10.1038/nature13459] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/07/2014] [Indexed: 11/09/2022]
Abstract
Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial diversity is only now being mapped at scales relevant to nature, while the viral diversity associated with any particular host remains little researched. Here we quantify host-associated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 10(7) Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater sample alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.
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Affiliation(s)
- Li Deng
- 1] Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA [2] Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg 85764, Germany. [3]
| | - J Cesar Ignacio-Espinoza
- 1] Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85719, USA [2]
| | - Ann C Gregory
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA
| | - Joshua S Weitz
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA [2] School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences &Institute for Molecular Bioscience, The University of Queensland, St Lucia QLB 4072, Australia
| | - Matthew B Sullivan
- 1] Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA [2] Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85719, USA
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75
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Rosenwasser S, Mausz MA, Schatz D, Sheyn U, Malitsky S, Aharoni A, Weinstock E, Tzfadia O, Ben-Dor S, Feldmesser E, Pohnert G, Vardi A. Rewiring Host Lipid Metabolism by Large Viruses Determines the Fate of Emiliania huxleyi, a Bloom-Forming Alga in the Ocean. THE PLANT CELL 2014; 26:2689-2707. [PMID: 24920329 PMCID: PMC4114960 DOI: 10.1105/tpc.114.125641] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/07/2014] [Accepted: 05/26/2014] [Indexed: 05/21/2023]
Abstract
Marine viruses are major ecological and evolutionary drivers of microbial food webs regulating the fate of carbon in the ocean. We combined transcriptomic and metabolomic analyses to explore the cellular pathways mediating the interaction between the bloom-forming coccolithophore Emiliania huxleyi and its specific coccolithoviruses (E. huxleyi virus [EhV]). We show that EhV induces profound transcriptome remodeling targeted toward fatty acid synthesis to support viral assembly. A metabolic shift toward production of viral-derived sphingolipids was detected during infection and coincided with downregulation of host de novo sphingolipid genes and induction of the viral-encoded homologous pathway. The depletion of host-specific sterols during lytic infection and their detection in purified virions revealed their novel role in viral life cycle. We identify an essential function of the mevalonate-isoprenoid branch of sterol biosynthesis during infection and propose its downregulation as an antiviral mechanism. We demonstrate how viral replication depends on the hijacking of host lipid metabolism during the chemical "arms race" in the ocean.
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Affiliation(s)
- Shilo Rosenwasser
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michaela A Mausz
- Institute of Inorganic and Analytical Chemistry/Bioorganic Analytics, Friedrich Schiller University Jena, 07743 Jena, Germany Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Daniella Schatz
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Sheyn
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Weinstock
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Oren Tzfadia
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ester Feldmesser
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry/Bioorganic Analytics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Assaf Vardi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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76
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Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A 2014; 111:7795-800. [PMID: 24821787 DOI: 10.1073/pnas.1400295111] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.
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77
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Enav H, Mandel-Gutfreund Y, Béjà O. Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis. MICROBIOME 2014; 2:9. [PMID: 24666644 PMCID: PMC4022391 DOI: 10.1186/2049-2618-2-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/13/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Viral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. While many individual auxiliary genes were observed in viral genomes and metagenomes, there is great importance in investigating the abundance of auxiliary genes and metabolic functions in the marine environment towards a better understanding of their role in promoting viral reproduction. RESULTS In this study, we searched for enriched viral auxiliary genes and mapped them to metabolic pathways. To initially identify enriched auxiliary genes, we analyzed metagenomic microbial reads from the Global Ocean Survey (GOS) dataset that were characterized as viral, as well as marine virome and microbiome datasets from the Line Islands. Viral-enriched genes were mapped to a "global metabolism network" that comprises all KEGG metabolic pathways. Our analysis of the viral-enriched pathways revealed that purine and pyrimidine metabolism pathways are among the most enriched pathways. Moreover, many other viral-enriched metabolic pathways were found to be closely associated with the purine and pyrimidine metabolism pathways. Furthermore, we observed that sequential reactions are promoted in pathways having a high proportion of enriched genes. In addition, these enriched genes were found to be of modular nature, participating in several pathways. CONCLUSIONS Our naïve metagenomic analyses strongly support the well-established notion that viral auxiliary genes promote viral replication via both degradation of host DNA and RNA as well as a shift of the host metabolism towards nucleotide biosynthesis, clearly indicating that comparative metagenomics can be used to understand different environments and systems without prior knowledge of pathways involved.
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Affiliation(s)
- Hagay Enav
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | | | - Oded Béjà
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
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78
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The evolutionary divergence of psbA gene in Synechococcus and their myoviruses in the East China Sea. PLoS One 2014; 9:e86644. [PMID: 24466184 PMCID: PMC3900582 DOI: 10.1371/journal.pone.0086644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/11/2013] [Indexed: 11/19/2022] Open
Abstract
Marine Synechococcus is a principal component of the picophytoplankton and makes an important contribution to primary productivity in the ocean. Synechophages, infecting Synechococcus, are believed to have significant influences on the distribution and abundance of their hosts. Extensive previous ecological studies on cyanobacteria and viruses have been carried out in the East China Sea (ECS). Here we investigate the diversity and divergence of Synechococcus and their myoviruses (Synechomyoviruses) based on their shared photosynthesis psbA gene. Synechococcus is dominated by subclades 5.1A I, 5.1A II and 5.1A IV in the ECS, and clades I and II are the dominant groups in the Synechomyoviruses. As two phylogenetically independent clades, there is much higher diversity of the Synechomyoviruses than Synechococcus. Obvious partitioning characteristics of GC and GC3 (the GC content at the third codon position) contents are obtained among different picophytoplankton populations and their phages. The GC3 content causes the psbA gene in Synechococcus to have a higher GC content, while the opposite is true in the Synechomyoviruses. Analyzing more than one-time difference of the codon usage frequency of psbA sequences, the third position nucleotides of preferred codons for Synechococcus are all G and C, while most Synechomyoviral sequences (72.7%) have A and T at the third position of their preferred codons. This work shed light on the ecology and evolution of phage-host interactions in the environment.
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Abstract
Viruses have been considered for a long time as by-products of biological evolution. This view is changing now as a result of several recent discoveries. Viral ecologists have shown that viral particles are the most abundant biological entities on our planet, whereas metagenomic analyses have revealed an unexpected abundance and diversity of viral genes in the biosphere. Comparative genomics have highlighted the uniqueness of viral sequences, in contradiction with the traditional view of viruses as pickpockets of cellular genes. On the contrary, cellular genomes, especially eukaryotic ones, turned out to be full of genes derived from viruses or related elements (plasmids, transposons, retroelements and so on). The discovery of unusual viruses infecting archaea has shown that the viral world is much more diverse than previously thought, ruining the traditional dichotomy between bacteriophages and viruses. Finally, the discovery of giant viruses has blurred the traditional image of viruses as small entities. Furthermore, essential clues on virus history have been obtained in the last ten years. In particular, structural analyses of capsid proteins have uncovered deeply rooted homologies between viruses infecting different cellular domains, suggesting that viruses originated before the last universal common ancestor (LUCA). These studies have shown that several lineages of viruses originated independently, i.e., viruses are polyphyletic. From the time of LUCA, viruses have coevolved with their hosts, and viral lineages can be viewed as lianas wrapping around the trunk, branches and leaves of the tree of life. Although viruses are very diverse, with genomes encoding from one to more than one thousand proteins, they can all be simply defined as organisms producing virions. Virions themselves can be defined as infectious particles made of at least one protein associated with the viral nucleic acid, endowed with the capability to protect the viral genome and ensure its delivery to the infected cell. These definitions, which clearly distinguish viruses from plasmids, suggest that infectious RNA molecules that only encode an RNA replicase presently classified among viruses by the ICTV (International Committee for the Taxonomy of Viruses) into families of Endornaviridae and Hypoviridae are in fact RNA plasmids. Since a viral genome should encode for at least one structural protein, these definitions also imply that viruses originated after the emergence of the ribosome in an RNA-protein cellular world. Although virions are the hallmarks of viruses, viruses and virions should not be confused. The infection transforms the ribocell (cell encoding ribosomes and dividing by binary fission) into a virocell (cell producing virions) or ribovirocell (cell that produces virions but can still divide by binary fission). In the ribovirocell, two different organisms, defined by their distinct evolutionary histories, coexist in symbiosis in the same cell. The virocells or ribovirocells are the living forms of the virus, which can be in fine considered to be a living organism. In the virocell, the metabolism is reorganized for the production of virions, while the ability to capture and store free energy is retained, as in other cellular organisms. In the virocell, viral genomes replicate, recombine and evolve, leading to the emergence of new viral proteins and potentially novel functions. Some of these new functions can be later on transferred to the cell, explaining how viruses can play a major (often underestimated) role in the evolution of cellular organisms. The virocell concept thus helps to understand recent hypotheses suggesting that viruses played a critical role in major evolutionary transitions, such as the origin of DNA genomes or else the origin of the eukaryotic nucleus. Finally, it is more and more recognized that viruses are the major source of variation and selection in living organisms (both viruses and cells), the two pillars of darwinism. One can thus conclude that the continuous interaction between viruses and cells, all along the history of life, has been, and still is, a major engine of biological evolution.
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Affiliation(s)
- Patrick Forterre
- Université Paris-Sud, Institut de Génétique Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France - Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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80
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Roux S, Krupovic M, Debroas D, Forterre P, Enault F. Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. Open Biol 2013; 3:130160. [PMID: 24335607 PMCID: PMC3877843 DOI: 10.1098/rsob.130160] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/19/2013] [Indexed: 11/12/2022] Open
Abstract
Although the importance of viruses in natural ecosystems is widely acknowledged, the functional potential of viral communities is yet to be determined. Viral genomes are traditionally believed to carry only those genes that are directly pertinent to the viral life cycle, though this view was challenged by the discovery of metabolism genes in several phage genomes. Metagenomic approaches extended these analyses to a community scale, and several studies concluded that microbial and viral communities encompass similar functional potentials. However, these conclusions could originate from the presence of cellular DNA within viral metagenomes. We developed a computational method to estimate the proportion and origin of cellular sequences in a set of 67 published viromes. A quarter of the datasets were found to contain a substantial amount of sequences originating from cellular genomes. When considering only viromes with no cellular DNA detected, the functional potential of viral and microbial communities was found to be fundamentally different-a conclusion more consistent with the actual picture drawn from known viruses. Yet a significant number of cellular metabolism genes was still retrieved in these viromes, suggesting that the presence of auxiliary genes involved in various metabolic pathways within viral genomes is a general trend in the virosphere.
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Affiliation(s)
- Simon Roux
- Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS UMR 6023, LMGE, Aubière, France
| | - Mart Krupovic
- Département de Microbiologie, Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France
| | - Didier Debroas
- Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS UMR 6023, LMGE, Aubière, France
| | - Patrick Forterre
- Département de Microbiologie, Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France
- Laboratoire de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut de Génétique et Microbiologie, Université Paris Sud, CNRS UMR 8621, Orsay, France
| | - François Enault
- Laboratoire ‘Microorganismes: Génome et Environnement’, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS UMR 6023, LMGE, Aubière, France
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81
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Schönknecht G, Weber APM, Lercher MJ. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays 2013; 36:9-20. [DOI: 10.1002/bies.201300095] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
- Cluster of Excellence on Plant Sciences (CEPLAS); Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | - Martin J. Lercher
- Cluster of Excellence on Plant Sciences (CEPLAS); Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
- Institute for Computer Science; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
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82
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Nelson N. Evolution of photosystem I and the control of global enthalpy in an oxidizing world. PHOTOSYNTHESIS RESEARCH 2013; 116:145-151. [PMID: 23954951 DOI: 10.1007/s11120-013-9902-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/26/2013] [Indexed: 05/28/2023]
Abstract
Life on earth is governed by light, chemical reactions, and the second law of thermodynamics, which defines the tendency for increasing entropy as an expression of disorder or randomness. Life is an expression of increasing order, and a constant influx of energy and loss of entropic wastes are required to maintain or increase order in living organisms. Most of the energy for life comes from sunlight and, thus, photosynthesis underlies the survival of all life forms. Oxygenic photosynthesis determines not only the global amount of enthalpy in living systems, but also the composition of the Earth's atmosphere and surface. Photosynthesis was established on the Earth more than 3.5 billion years ago. The primordial reaction center has been suggested to comprise a homodimeric unit resembling the core complex of the current reaction centers in Chlorobi, Heliobacteria, and Acidobacteria. Here, an evolutionary scenario based on the known structures of the current reaction centers is proposed.
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Affiliation(s)
- Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel,
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83
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Affiliation(s)
- Valerian V Dolja
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
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84
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McDaniel LD, Rosario K, Breitbart M, Paul JH. Comparative metagenomics: natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences. Environ Microbiol 2013; 16:570-85. [PMID: 23879711 DOI: 10.1111/1462-2920.12184] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/20/2013] [Accepted: 06/06/2013] [Indexed: 01/31/2023]
Abstract
To understand the similarities and differences between a free living viral population and its co-occurring temperate population, metagenomes of each type were prepared from the same seawater sample from Tampa Bay, FL. Libraries were prepared from extracted DNA of the ambient viruses and induced prophages from the co-occurring, viral-reduced microbial assemblage. Duplicate libraries were also prepared using the same DNA amplified by multiple displacement amplification. A non-viral-reduced, induced, amplified viral dataset from the same site in 2005 was reanalysed for temporal comparison. The induced viral metagenome was higher in identifiable virus sequences and differed from the other three datasets based on principal component, rarefaction, trinucleotide composition and contig spectrum analyses. This study indicated that induced prophages are unique and have lower overall community diversity than ambient viral populations from the same site. Both of the amplified contemporary metagenomes were enriched in single-stranded DNA (ssDNA) viral sequences. Six and 16 complete, circular ssDNA viral genomes were assembled from the amplified induced and ambient libraries, respectively, mostly similar to circoviruses. The amplified ambient metagenome contained genomes similar to an RNA-DNA hybrid virus recently identified in a hot spring and to an ssDNA virus infecting the diatom Chaetoceros.
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Affiliation(s)
- Lauren D McDaniel
- College of Marine Science, University of South Florida, 140 7th Avenue South, St Petersburg, FL, 33701, USA
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85
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Sousa FL, Shavit-Grievink L, Allen JF, Martin WF. Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome Biol Evol 2013; 5:200-16. [PMID: 23258841 PMCID: PMC3595025 DOI: 10.1093/gbe/evs127] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII). The two main competing theories in the foreground of current thinking on this issue are that either 1) RCI and RCII are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theories) or 2) the two RC types are related via gene duplication in an ancestral, anoxygenic but protocyanobacterial phototroph that possessed both RC types before making the transition to using water as an electron donor. To distinguish between these possibilities, we studied the evolution of the core (bacterio)chlorophyll biosynthetic pathway from protoporphyrin IX (Proto IX) up to (bacterio)chlorophyllide a. The results show no dichotomy of chlorophyll biosynthesis genes into RCI- and RCII-specific chlorophyll biosynthetic clades, thereby excluding models of fusion at the origin of cyanobacteria and supporting the selective-loss hypothesis. By considering the cofactor demands of the pathway and the source genes from which several steps in chlorophyll biosynthesis are derived, we infer that the cell that first synthesized chlorophyll was a cobalamin-dependent, heme-synthesizing, diazotrophic anaerobe.
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Affiliation(s)
- Filipa L Sousa
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany.
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86
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Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB. Structure and function of a cyanophage-encoded peptide deformylase. THE ISME JOURNAL 2013; 7:1150-60. [PMID: 23407310 PMCID: PMC3660681 DOI: 10.1038/ismej.2013.4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 12/01/2012] [Accepted: 12/07/2012] [Indexed: 12/19/2022]
Abstract
Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal α-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.
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Affiliation(s)
- Jeremy A Frank
- Department of Biology, San Diego State University, San Diego, CA 92182-7720, USA.
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87
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Mazor Y, Greenberg I, Toporik H, Beja O, Nelson N. The evolution of photosystem I in light of phage-encoded reaction centres. Philos Trans R Soc Lond B Biol Sci 2013; 367:3400-5. [PMID: 23148266 DOI: 10.1098/rstb.2012.0057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent structural determinations and metagenomic studies shed light on the evolution of photosystem I (PSI) from the homodimeric reaction centre of primitive bacteria to plant PSI at the top of the evolutionary development. The evolutionary scenario of over 3.5 billion years reveals an increase in the complexity of PSI. This phenomenon of ever-increasing complexity is common to all evolutionary processes that in their advanced stages are highly dependent on fine-tuning of regulatory processes. On the other hand, the recently discovered virus-encoded PSI complexes contain a minimal number of subunits. This may reflect the unique selection scenarios associated with viral replication. It may be beneficial for future engineering of productive processes to utilize 'primitive' complexes that disregard the cellular regulatory processes and to avoid those regulatory constraints when our goal is to divert the process from its original route. In this article, we discuss the evolutionary forces that act on viral reaction centres and the role of the virus-carried photosynthetic genes in the evolution of photosynthesis.
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Affiliation(s)
- Yuval Mazor
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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88
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Muniesa M, Allué-Guardia A, Martínez-Castillo A. Bacteriophage-driven emergence of novel pathogens. Future Virol 2013. [DOI: 10.2217/fvl.13.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Maite Muniesa
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain.
| | - Anna Allué-Guardia
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
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89
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Bhattacharya D, Price DC, Bicep C, Bapteste E, Sarwade M, Rajah VD, Yoon HS. Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly. JOURNAL OF PHYCOLOGY 2013; 49:207-212. [PMID: 27008402 DOI: 10.1111/jpy.12028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/27/2012] [Indexed: 06/05/2023]
Abstract
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
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Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Dana C Price
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Cedric Bicep
- Unité Mixte de Recherche, Centre National de la Recherche Scientifique 7138, Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, 75005, France
| | - Eric Bapteste
- Unité Mixte de Recherche, Centre National de la Recherche Scientifique 7138, Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, 75005, France
| | - Mihir Sarwade
- Department of Ecology, Evolution Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Veeran D Rajah
- Department of Ecology, Evolution Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea
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90
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Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environ Microbiol 2013; 15:1356-76. [DOI: 10.1111/1462-2920.12053] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 11/13/2012] [Indexed: 11/30/2022]
Affiliation(s)
- S. J. Labrie
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
| | - K. Frois-Moniz
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
| | - M. S. Osburne
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
| | - L. Kelly
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
| | - S. E. Roggensack
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
| | - M. B. Sullivan
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
| | | | - Q. Zeng
- Broad Institute; Cambridge; MA; USA
| | | | | | - S. W. Chisholm
- Department of Civil and Environmental Engineering; Massachusetts Institute of Technology; Cambridge; MA; USA
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91
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Mazor Y, Nataf D, Toporik H, Nelson N. Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803. eLife 2013; 3:e01496. [PMID: 24473073 PMCID: PMC3903132 DOI: 10.7554/elife.01496] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Oxygenic photosynthesis supports virtually all life forms on earth. Light energy is converted by two photosystems—photosystem I (PSI) and photosystem II (PSII). Globally, nearly 50% of photosynthesis takes place in the Ocean, where single cell cyanobacteria and algae reside together with their viruses. An operon encoding PSI was identified in cyanobacterial marine viruses. We generated a PSI that mimics the salient features of the viral complex, named PSIPsaJF. PSIPsaJF is promiscuous for its electron donors and can accept electrons from respiratory cytochromes. We solved the structure of PSIPsaJF and a monomeric PSI, with subunit composition similar to the viral PSI, providing for the first time a detailed description of the reaction center and antenna system from mesophilic cyanobacteria, including red chlorophylls and cofactors of the electron transport chain. Our finding extends the understanding of PSI structure, function and evolution and suggests a unique function for the viral PSI. DOI:http://dx.doi.org/10.7554/eLife.01496.001 Photosynthesis—the process by which plants and other organisms harness the energy in sunlight—is the source of almost all oxygen, food and fuel on earth. Oxygenic photosynthesis in living cells involves a series of reactions catalyzed by large protein complexes, various other soluble chemicals, and the transfer of electrons from so-called donors to acceptors. The energy in the sunlight is captured by two membrane-embedded protein complexes—photosystem I, which is the most powerful electron donor in nature, and photosystem II—and converted into chemical energy. Almost half of the world’s photosynthesis occurs in the oceans, and is performed by single-celled cyanobacteria and algae. Interestingly, some of the genes that encode photosynthetic enzymes in cyanobacteria are also found in the genomes of viruses that infect these bacteria. It is thought that these viruses can alter photosynthetic pathways in their hosts, but the interactions between these viruses and their hosts are not fully understood. Now, Mazor et al. have created a photosystem I complex that mimics the viral version of this complex, and have gone on to solve its three-dimensional structure. This mimetic virus-encoded complex was shown to be a ‘promiscuous’ electron acceptor: this means that, unlike most electron acceptors, it can accept electrons from more than one electron donor. Further, Mazor et al. solved the structure of photosystem I from Synechocystis, a cyanobacterium that lives in fresh water; and found some surprising differences between it and the only other published structure for photosystem I from a cyanobacterium (which was from a species that lives in hot water springs). These included differences in components involved in the electron transfer chain—a series of chemical reactions in which electrons are passed from donor to acceptor molecules—that were thought to be highly conserved. Other differences in the structures allowed Mazor et al. to identify the location of a unique chlorophyll pigment group in the Synechocystis photosystem I. Since Synechocystis is commonly used as a model to study photosynthesis, an improved understanding of its photosystem I should lead to further improvements in our knowledge of photosynthesis. DOI:http://dx.doi.org/10.7554/eLife.01496.002
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Affiliation(s)
- Yuval Mazor
- Department of Biochemistry and Molecular Biology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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92
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Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin WF. Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol 2013; 5:31-44. [PMID: 23221676 PMCID: PMC3595030 DOI: 10.1093/gbe/evs117] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2012] [Indexed: 01/12/2023] Open
Abstract
Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.
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Affiliation(s)
- Tal Dagan
- Institute of Genomic Microbiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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93
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Zhu B, Tabor S, Raytcheva DA, Hernandez A, King JA, Richardson CC. The RNA polymerase of marine cyanophage Syn5. J Biol Chem 2012; 288:3545-52. [PMID: 23258537 DOI: 10.1074/jbc.m112.442350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A single subunit DNA-dependent RNA polymerase was identified and purified to apparent homogeneity from cyanophage Syn5 that infects the marine cyanobacteria Synechococcus. Syn5 is homologous to bacteriophage T7 that infects Escherichia coli. Using the purified enzyme its promoter has been identified by examining transcription of segments of Syn5 DNA and sequencing the 5'-termini of the transcripts. Only two Syn5 RNAP promoters, having the sequence 5'-ATTGGGCACCCGTAA-3', are found within the Syn5 genome. One promoter is located within the Syn5 RNA polymerase gene and the other is located close to the right genetic end of the genome. The purified enzyme and its promoter have enabled a determination of the requirements for transcription. Unlike the salt-sensitive bacteriophage T7 RNA polymerase, this marine RNA polymerase requires 160 mm potassium for maximal activity. The optimal temperature for Syn5 RNA polymerase is 24 °C, much lower than that for T7 RNA polymerase. Magnesium is required as a cofactor although some activity is observed with ferrous ions. Syn5 RNA polymerase is more efficient in utilizing low concentrations of ribonucleotides than T7 RNA polymerase.
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Affiliation(s)
- Bin Zhu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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94
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Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids. Appl Environ Microbiol 2012; 79:688-95. [PMID: 23160125 DOI: 10.1128/aem.02742-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cellular metagenomes are primarily used for investigating microbial community structure and function. However, cloned fosmids from such metagenomes capture phage genome fragments that can be used as a source of phage genomes. We show that fosmid cloning from cellular metagenomes and sequencing at a high coverage is a credible alternative to constructing metaviriomes and allows capturing and assembling novel, complete phage genomes. It is likely that phages recovered from cellular metagenomes are those replicating within cells during sample collection and represent "active" phages, naturally amplifying their genomic DNA and increasing chances for cloning. We describe five sets of siphoviral contigs (MEDS1, MEDS2, MEDS3, MEDS4, and MEDS5), obtained by sequencing fosmids from the cellular metagenome of the deep chlorophyll maximum in the Mediterranean. Three of these represent complete siphoviral genomes and two represent partial ones. This is the first set of phage genomes assembled directly from cellular metagenomic fosmid libraries. They exhibit low sequence similarities to one another and to known siphoviruses but are remarkably similar in overall genome architecture. We present evidence suggesting they infect picocyanobacteria, likely Synechococcus. Four of these sets also define a novel branch in the phylogenetic tree of phage large subunit terminases. Moreover, some of these siphoviral groups are globally distributed and abundant in the oceans, comparable to some known myoviruses and podoviruses. This suggests that, as more siphoviral genomes become available, we will be better able to assess the abundance and influence of this diverse and polyphyletic group in the marine habitat.
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95
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Ashkenazi S, Snir R, Ofran Y. Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins. ACTA ACUST UNITED AC 2012; 28:3203-10. [PMID: 23080118 DOI: 10.1093/bioinformatics/bts608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Assessing the false positive rate of function prediction methods is difficult, as it is hard to establish that a protein does not have a certain function. To determine to what extent proteins with similar sequences have a common function, we focused on photosynthesis-related proteins. A protein that comes from a non-photosynthetic organism is, undoubtedly, not involved in photosynthesis. RESULTS We show that function diverges very rapidly: 70% of the close homologs of photosynthetic proteins come from non-photosynthetic organisms. Therefore, high sequence similarity, in most cases, is not tantamount to similar function. However, we found that many functionally similar proteins often share short sequence elements, which may correspond to a functional site and could reveal functional similarities more accurately than sequence similarity. CONCLUSIONS These results shed light on the way biological function is conserved in evolution and may help improve large-scale analysis of protein function.
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Affiliation(s)
- Shaul Ashkenazi
- The Goodman faculty of life sciences, Bar Ilan University, Ramat Gan 52900, Israel
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96
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Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, Brami D, Thiagarajan M, McCrow JP, Tovchigrechko A, Yooseph S, Venter JC. Metagenomic exploration of viruses throughout the Indian Ocean. PLoS One 2012; 7:e42047. [PMID: 23082107 PMCID: PMC3474794 DOI: 10.1371/journal.pone.0042047] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 07/02/2012] [Indexed: 11/20/2022] Open
Abstract
The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction (<0.1 µm). Phylogenetic approaches were also used to identify predicted proteins of viral origin in the larger fractions of data from all Indian Ocean samples, which were included in subsequent metagenomic analyses. Taxonomic profiling of viral sequences suggested that size fractionation of marine microbial communities enriches for specific groups of viruses within the different size classes and functional characterization further substantiated this observation. Functional analyses also revealed a relative enrichment for metabolic proteins of viral origin that potentially reflect the physiological condition of host cells in the Indian Ocean including those involved in nitrogen metabolism and oxidative phosphorylation. A novel classification method, MGTAXA, was used to assess virus-host relationships in the Indian Ocean by predicting the taxonomy of putative host genera, with Prochlorococcus, Acanthochlois and members of the SAR86 cluster comprising the most abundant predictions. This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions.
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Affiliation(s)
- Shannon J Williamson
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
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97
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Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology 2012; 434:181-6. [PMID: 23084423 DOI: 10.1016/j.virol.2012.09.036] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 11/21/2022]
Abstract
As new environments are studied, viruses consistently emerge as important and prominent players in natural and man-made ecosystems. However, much of what we know is built both upon the foundation of the culturable minority and using methods that are often insufficiently ground-truthed. Here, we review the modern culture-independent viral metagenomic sample-to-sequence pipeline and how next-generation sequencing techniques are drastically altering our ability to systematically and rigorously evaluate them. Together, a series of studies quantitatively evaluate existing and new methods that allow-even for ultra-low DNA samples-the generation of replicable, near-quantitative datasets that maximize inter-comparability and biological inference.
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98
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Finkel OM, Béjà O, Belkin S. Global abundance of microbial rhodopsins. ISME JOURNAL 2012; 7:448-51. [PMID: 23051692 DOI: 10.1038/ismej.2012.112] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Photochemical reaction centers and rhodopsins are the only phototrophic mechanisms known to have evolved on Earth. The minimal cost of bearing a rhodopsin-based phototrophic mechanism in comparison to maintaining a photochemical reaction center suggests that rhodopsin is the more abundant of the two. We tested this hypothesis by conducting a global abundance calculation of phototrophic mechanisms from 116 marine and terrestrial microbial metagenomes. On average, 48% of the cells from which these metagenomes were generated harbored a rhodopsin gene, exceeding the reaction center abundance by threefold. Evidence from metatranscriptomic data suggests that this genomic potential is realized to a substantial extent, at least for the small-sized (>0.8 μm) of microbial fractions.
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Affiliation(s)
- Omri M Finkel
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
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99
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Cassman N, Prieto-Davó A, Walsh K, Silva GGZ, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, DeLong EF, Dutilh BE, Rohwer F, Dinsdale EA. Oxygen minimum zones harbour novel viral communities with low diversity. Environ Microbiol 2012; 14:3043-65. [PMID: 23039259 DOI: 10.1111/j.1462-2920.2012.02891.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 08/23/2012] [Accepted: 09/02/2012] [Indexed: 01/03/2023]
Abstract
Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral diversity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences sampled within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and diversity across the oxygen gradient. The ecological significance of these changes was difficult to predict; however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.
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Affiliation(s)
- Noriko Cassman
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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100
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Yoshida-Takashima Y, Yoshida M, Ogata H, Nagasaki K, Hiroishi S, Yoshida T. Cyanophage infection in the bloom-forming cyanobacteria Microcystis aeruginosa in surface freshwater. Microbes Environ 2012; 27:350-5. [PMID: 23047146 PMCID: PMC4103541 DOI: 10.1264/jsme2.me12037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Host-like genes are often found in viral genomes. To date, multiple host-like genes involved in photosynthesis and the pentose phosphate pathway have been found in phages of marine cyanobacteria Synechococcus and Prochlorococcus. These gene products are predicted to redirect host metabolism to deoxynucleotide biosynthesis for phage replication while maintaining photosynthesis. A cyanophage, Ma-LMM01, infecting the toxic cyanobacterium Microcystis aeruginosa, was isolated from a eutrophic freshwater lake and assigned as a member of a new lineage of the Myoviridae family. The genome encodes a host-like NblA. Cyanobacterial NblA is known to be involved in the degradation of the major light harvesting complex, the phycobilisomes. Ma-LMM01 nblA gene showed an early expression pattern and was highly transcribed during phage infection. We speculate that the co-option of nblA into Microcystis phages provides a significant fitness advantage to phages by preventing photoinhibition during infection and possibly represents an important part of the co-evolutionary interactions between cyanobacteria and their phages.
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Affiliation(s)
- Yukari Yoshida-Takashima
- Subsurface Geobiology Advanced Research Team, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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