Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms
António Pagarete
Equipe EPPO-Evolution du Plancton et PaléoOcéans, CNRS-UMR7144, Université Pierre et Marie Curie, Station Biologique, Roscoff, France
Plymouth Marine Laboratory, The Hoe, Plymouth, UK
Search for more papers by this authorGildas Le Corguillé
CNRS/UMPC, FR2424, Service Informatique et Génomique, Station Biologique, Roscoff, France
Search for more papers by this authorBela Tiwari
NERC Environmental Bioinformatics Centre, Centre for Ecology and Hydrology, Wallingford, UK
Search for more papers by this authorHiroyuki Ogata
Structural and Genomic Information Laboratory, CNRS-UPR2589, Mediterranean Institute of Microbiology (IFR-88), Aix-Marseille University, Marseille, France
Search for more papers by this authorColomban de Vargas
Equipe EPPO-Evolution du Plancton et PaléoOcéans, CNRS-UMR7144, Université Pierre et Marie Curie, Station Biologique, Roscoff, France
Search for more papers by this authorWilliam H. Wilson
Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME, USA
Search for more papers by this authorCorresponding Author
Michael J. Allen
Plymouth Marine Laboratory, The Hoe, Plymouth, UK
Correspondence: Michael J. Allen, Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK. Tel.: +44 1752 633472; fax: +44 1752 633101; e-mail: [email protected]Search for more papers by this authorAntónio Pagarete
Equipe EPPO-Evolution du Plancton et PaléoOcéans, CNRS-UMR7144, Université Pierre et Marie Curie, Station Biologique, Roscoff, France
Plymouth Marine Laboratory, The Hoe, Plymouth, UK
Search for more papers by this authorGildas Le Corguillé
CNRS/UMPC, FR2424, Service Informatique et Génomique, Station Biologique, Roscoff, France
Search for more papers by this authorBela Tiwari
NERC Environmental Bioinformatics Centre, Centre for Ecology and Hydrology, Wallingford, UK
Search for more papers by this authorHiroyuki Ogata
Structural and Genomic Information Laboratory, CNRS-UPR2589, Mediterranean Institute of Microbiology (IFR-88), Aix-Marseille University, Marseille, France
Search for more papers by this authorColomban de Vargas
Equipe EPPO-Evolution du Plancton et PaléoOcéans, CNRS-UMR7144, Université Pierre et Marie Curie, Station Biologique, Roscoff, France
Search for more papers by this authorWilliam H. Wilson
Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME, USA
Search for more papers by this authorCorresponding Author
Michael J. Allen
Plymouth Marine Laboratory, The Hoe, Plymouth, UK
Correspondence: Michael J. Allen, Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK. Tel.: +44 1752 633472; fax: +44 1752 633101; e-mail: [email protected]Search for more papers by this authorAbstract
Lytic viruses have been implicated in the massive cellular lysis observed during algal blooms, through which they assume a prominent role in oceanic carbon and nutrient flows. Despite their impact on biogeochemical cycling, the transcriptional dynamics of these important oceanic events is still poorly understood. Here, we employ an oligonucleotide microarray to monitor host (Emiliania huxleyi) and virus (coccolithovirus) transcriptomic features during the course of E. huxleyi blooms induced in seawater-based mesocosm enclosures. Host bloom development and subsequent coccolithovirus infection was associated with a major shift in transcriptional profile. In addition to the expected metabolic requirements typically associated with viral infection (amino acid and nucleotide metabolism, as well as transcription- and replication-associated functions), the results strongly suggest that the manipulation of lipid metabolism plays a fundamental role during host–virus interaction. The results herein reveal the scale, so far massively underestimated, of the transcriptional domination that occurs during coccolithovirus infection in the natural environment.
Supporting Information
| Filename | Description |
|---|---|
| fem1191-sup-0001-FigureS1.TIFimage/TIF, 99.7 MB | Fig. S1. E. huxleyi and coccolithovirus concentrations in Enclosures 1 to 6 as determined by flow cytometry. |
| fem1191-sup-0002-FigureS2.tifimage/tif, 168.4 KB | Fig. S2. Hierarchical clustering of all transcription profiles through the use of Non-negative Matrix Factorization (Brunet et al., 2004). |
| fem1191-sup-0003-FigureS3.TIFimage/TIF, 1,003.2 KB | Fig. S3. Non-negative Matrix Factorization (Brunet et al., 2004) of transcription profiles from Enclosures 2 and 3 including four daily time points (6, 12, 18, and 24 h). |
| fem1191-sup-0004-FigureS4a.TIFimage/TIF, 3.2 MB | Fig. S4. Comparison microarray fluorescence signal vs. qPCR relative expression of host and virus genes, respectively. |
| fem1191-sup-0005-FigureS4b.TIFimage/TIF, 3.8 MB | |
| fem1191-sup-0006-FigureS4c.TIFimage/TIF, 3.2 MB | |
| fem1191-sup-0007-FigureS4d.TIFimage/TIF, 2.5 MB | |
| fem1191-sup-0008-FigureS4e.TIFimage/TIF, 4.7 MB | |
| fem1191-sup-0009-FigureS5.tifimage/TIF, 15.8 KB | Fig. S5. Sequence alignment showing the homologous regions (dots) between the coccolithovirus serine palmitoyltransferase gene sequence and the E. huxleyi microarray probe ‘B.Read.TopHits.Contig12834_4576_46’. |
| fem1191-sup-0010-TableS1.docWord document, 33.5 KB | Table S1. E. huxleyi and coccolithovirus qPCR primer sequences used in this study |
| fem1191-sup-0011-TableS2.docWord document, 67.5 KB | Table S2. Sample cluster obtained after different distance metrics (Euclidean distance, Manhattan distance, Pearson Correlation, Pearson Uncentered) and Non-negative Matrix Factorization |
| fem1191-sup-0012-TableS3.docWord document, 48 KB | Table S3. List of E. huxleyi probes that presented too high nucleotide alignment similarity to EhV genomic sequences, and hence were removed from analysis |
| fem1191-sup-0013-TableS4.docWord document, 84 KB | Table S4. List of EhV and E. huxleyi probes that presented significant up-regulation from Cluster 1 to Cluster 2. KOG refers to the NCBI's list of EuKaryotic Orthologous Groups of proteins |
| fem1191-sup-0014-DataS1.rtfWord document, 103.3 KB | Data S1 Supplementary Methods |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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