Journal ArticleDOI
Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution
Debbie Lindell,Jacob D. Jaffe,Maureen L. Coleman,Matthias E. Futschik,Ilka M. Axmann,Trent Rector,Gregory Carl Kettler,Matthew B. Sullivan,Robert G. Steen,Wolfgang R. Hess,George M. Church,Sallie W. Chisholm +11 more
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It is hypothesized that phage have evolved to use upregulated host genes, leading to their stable incorporation into phage genomes and their subsequent transfer back to hosts in genome islands, and activation of host genes during infection may be directing the co-evolution of gene content in both host and phages genomes.Abstract:
It's known that interactions between bacteria and their viruses (or phages) can result in a degree of co-evolution of host and phage. A picture of just how close that relationship can become is given by whole-genome expression profiling of the marine cyanobacterium Prochlorococcus and its T7-like cyanophage during infection. A number of host genes are expressed in a coordinated fashion during phage infection, and the phage seem to have evolved to make good use of the gene products. These cyanobacteria are ubiquitous in the oceans and dominant in their particular niche. It seems likely that evolutionary cooperation between host and phage contributes to the success of both partners. Phages have a major impact on the evolution of their bacterial hosts. Providing the first whole genome expression profiling of the marine cyanobacterium Prochlorococcus and its T7-like cyanophage during lytic infection reveals potential mechanistic features of this co-evolutionary process. Interactions between bacterial hosts and their viruses (phages) lead to reciprocal genome evolution through a dynamic co-evolutionary process1,2,3,4,5. Phage-mediated transfer of host genes—often located in genome islands—has had a major impact on microbial evolution1,4,6. Furthermore, phage genomes have clearly been shaped by the acquisition of genes from their hosts2,3,5. Here we investigate whole-genome expression of a host and phage, the marine cyanobacterium Prochlorococcus MED4 and the T7-like cyanophage P-SSP7, during lytic infection, to gain insight into these co-evolutionary processes. Although most of the phage genome was linearly transcribed over the course of infection, four phage-encoded bacterial metabolism genes formed part of the same expression cluster, even though they are physically separated on the genome. These genes—encoding photosystem II D1 (psbA), high-light inducible protein (hli), transaldolase (talC) and ribonucleotide reductase (nrd)—are transcribed together with phage DNA replication genes and seem to make up a functional unit involved in energy and deoxynucleotide production for phage replication in resource-poor oceans. Also unique to this system was the upregulation of numerous genes in the host during infection. These may be host stress response genes and/or genes induced by the phage. Many of these host genes are located in genome islands and have homologues in cyanophage genomes. We hypothesize that phage have evolved to use upregulated host genes, leading to their stable incorporation into phage genomes and their subsequent transfer back to hosts in genome islands. Thus activation of host genes during infection may be directing the co-evolution of gene content in both host and phage genomes.read more
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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
TL;DR: Pplacer as discussed by the authors is a software package for phylogenetic placement and subsequent visualization, which can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, and is easy to run in parallel.
Journal ArticleDOI
Phages in nature.
TL;DR: The roles of phages in different host systems are described and how modeling, microscopy, isolation, genomic and metagenomic based approaches have come together recently to provide unparalleled insights into these small but vital constituents of the microbial world are shown.
Posted Content
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
TL;DR: Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.
Journal ArticleDOI
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Simon Roux,Jennifer R. Brum,Bas E. Dutilh,Bas E. Dutilh,Bas E. Dutilh,Shinichi Sunagawa,Melissa B. Duhaime,Alexander Loy,Bonnie T. Poulos,Natalie Solonenko,Elena Lara,Elena Lara,Julie Poulain,Stephane Pesant,Stefanie Kandels-Lewis,Céline Dimier,Céline Dimier,Céline Dimier,Marc Picheral,Marc Picheral,Sarah Searson,Sarah Searson,Corinne Cruaud,Adriana Alberti,Carlos M. Duarte,Carlos M. Duarte,Josep M. Gasol,Dolors Vaqué,Peer Bork,Silvia G. Acinas,Patrick Wincker,Patrick Wincker,Mathew B. Sullivan +32 more
TL;DR: A global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts is presented to present a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
Journal Article
Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
TL;DR: Reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains, which is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between understanding of these organisms in the lab and the wild.
References
More filters
Journal ArticleDOI
Bioconductor: open software development for computational biology and bioinformatics
Robert Gentleman,Vincent J. Carey,Douglas M. Bates,Benjamin M. Bolstad,Marcel Dettling,Sandrine Dudoit,Byron Ellis,Laurent Gautier,Yongchao Ge,Jeff Gentry,Kurt Hornik,Torsten Hothorn,Wolfgang Huber,Stefano Maria Iacus,Rafael A. Irizarry,Friedrich Leisch,Cheng Li,Martin Maechler,A. J. Rossini,Günther Sawitzki,Colin A. Smith,Gordon K. Smyth,Luke Tierney,Jean Yang,Jianhua Zhang +24 more
TL;DR: Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
Journal ArticleDOI
Statistical significance for genomewide studies
John D. Storey,Robert Tibshirani +1 more
TL;DR: This work proposes an approach to measuring statistical significance in genomewide studies based on the concept of the false discovery rate, which offers a sensible balance between the number of true and false positives that is automatically calibrated and easily interpreted.
Journal ArticleDOI
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
TL;DR: The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.
Journal ArticleDOI
Summaries of Affymetrix GeneChip probe level data
Rafael A. Irizarry,Benjamin M. Bolstad,Francois Collin,Leslie Cope,Bridget G. Hobbs,Terence P. Speed,Terence P. Speed +6 more
TL;DR: It is found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models.
Journal ArticleDOI
affy---analysis of Affymetrix GeneChip data at the probe level
TL;DR: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix that provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data.