Host-Derived Viral Transporter Protein for Nitrogen Uptake in Infected
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Host-derived viral transporter protein for nitrogen PNAS PLUS uptake in infected marine phytoplankton Adam Moniera,b,1, Aurelie´ Chambouveta,c,2, David S. Milnera,2, Victoria Attaha, Ramon´ Terradod, Connie Lovejoyb,e, Herve´ Moreauf, Alyson E. Santorog, Evelyne´ Derellef, and Thomas A. Richardsa,1 aLiving Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom; bQuebec´ Ocean,´ Universite´ Laval, Quebec,´ QC, Canada G1V 0A6; cLaboratoire des Sciences de l’Environnement Marin, CNRS UMR 6539, Institut Universitaire Europeen´ de la Mer, Universite´ de Bretagne Occidentale, 29280 Plouzane,´ France; dDepartment of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089-0371; eTakuvik International Laboratory (CNRS Unite´ Mixte Internationale 3376), Departement´ de Biologie and Institut de Biologie Integrative´ et des Systemes,` Universite´ Laval, Quebec,´ QC, Canada G1V 0A6; fCNRS UMR 7232, Sorbonne Universites,´ Observatoire Oceanologique´ de Banyuls, 66650 Banyuls-sur-mer, France; and gDepartment of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106 Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved July 10, 2017 (received for review May 18, 2017) Phytoplankton community structure is shaped by both bottom– In addition to bottom–up nutrient limitation, phytoplankton up factors, such as nutrient availability, and top–down processes, community structures are influenced by top–down controls (13). such as predation. Here we show that marine viruses can blur For phytoplankton communities these include predation by graz- these distinctions, being able to amend how host cells acquire ers and viral infection (e.g., ref. 14). Marine viruses are the nutrients from their environment while also predating and lysing most abundant biological entities in the oceans; they are esti- their algal hosts. Viral genomes often encode genes derived from mated to induce 1023 infections daily (15) and are thought to their host. These genes may allow the virus to manipulate host control phytoplankton abundance, biomass, and species com- metabolism to improve viral fitness. We identify in the genome of position through taxon-specific infections (16, 17). There is a a phytoplankton virus, which infects the small green alga Ostre- growing appreciation of the role of viruses in oceanic nutrient ococcus tauri, a host-derived ammonium transporter. This gene is cycles, based on lytic infections leading to the release of dissolved transcribed during infection and when expressed in yeast mutants and particulate organic matter, which is then recycled by other SCIENCES the viral protein is located to the plasma membrane and res- microorganisms (15, 18). This virus-mediated process, referred ENVIRONMENTAL cues growth when cultured with ammonium as the sole nitro- to as the viral shunt, was suggested as a mechanism that main- gen source. We also show that viral infection alters the nature tains availability of organic matter in the euphotic zone by lysing of nitrogen compound uptake of host cells, by both increas- cells before they sink (15, 18). However, the influence of viruses ing substrate affinity and allowing the host to access diverse on oceanic ecosystems extends beyond top–down host mortality. nitrogen sources. This is important because the availability of Genomic and metagenomic analyses show that marine viruses— nitrogen often limits phytoplankton growth. Collectively, these either phages or eukaryotic viruses—harbor host-derived genes data show that a virus can acquire genes encoding nutrient encoding a diverse range of putative functions (19–21), includ- transporters from a host genome and that expression of the ing whole biochemical pathways (22). These “auxiliary metabolic viral gene can alter the nutrient uptake behavior of host cells. genes” (AMGs) may allow the virus to manipulate the host via These results have implications for understanding how viruses metabolic reprogramming during infection and have been exper- manipulate the physiology and ecology of phytoplankton, influ- imentally shown to alter the central carbon metabolism and pig- ence marine nutrient cycles, and act as vectors for horizontal ment biosynthesis of cyanobacteria (23, 24) and to “reprogram” gene transfer. Significance Phycodnaviridae j NCLDV j prasinophytes j Mamiellophyceae j lateral gene transfer Viruses often carry genes acquired from their host. In the present work, we show that a virus of a marine alga carries hytoplankton underpin the biogeochemistry of the surface a gene encoding a transporter protein that mediates nutri- oceans and drive the marine carbon and nitrogen cycles P ent uptake. We confirm that the viral transporter protein is (1). Nutrients fuel cyanobacteria and eukaryotic single-celled expressed during infection and show that the protein func- algae with the elements essential for organic matter biosynthe- tions to take up sources of nitrogen. This is important because sis, especially nitrogen (N) and phosphorus (P); hence nutrient acquisition of nutrients often determines the ecological suc- availability exerts a bottom–up control on phytoplankton cell cess of phytoplankton populations. This work demonstrates growth and oceanic productivity (2, 3). In particular, N and P are how a virus can amend host–viral dynamics by modulating found in low concentrations over much of the open ocean, lim- acquisition of nutrients from the environment. iting phytoplankton growth rates. Nutrient limitation, including colimitation by several nutrients, results in competition among Author contributions: A.M., D.S.M., and T.A.R. designed research; A.M., A.C., D.S.M., V.A., phytoplankton. In oligotrophic environments, and transiently R.T., and E.D. performed research; H.M. and E.D. contributed new reagents/analytic tools; nutrient-depleted environments, phytoplankton species have A.M. analyzed data; and A.M., C.L., A.E.S., and T.A.R. wrote the paper. evolved a range of strategies to optimize nutrient acquisition (4). The authors declare no conflict of interest. The genetic repertoire of N and P transporters shows evidence This article is a PNAS Direct Submission. of gene duplication, differential loss, and horizontal gene trans- Freely available online through the PNAS open access option. fer (HGT) in phytoplankton genomes as well as contrasting gene Data deposition: The sequence reported in this paper has been deposited in the GenBank expression levels (5–9), suggesting that the evolution of these database (accession no. KX254356). Phylogenetic and experimental data are available at genes has been driven by adaptation to environmental limita- the Zenodo data repository, zenodo.org/record/61901. + − tion. Ammonium (NH4 ) and nitrate (NO3 ) are commonly avail- 1To whom correspondence may be addressed. Email: [email protected] or t.a. able N sources for marine phytoplankton (10, 11) and, as such, [email protected]. the gene repertoires of cyanobacterial and eukaryotic phyto- 2A.C. and D.S.M. contributed equally to this work. plankton are configured toward utilization of these two forms of This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. inorganic N sources (12). 1073/pnas.1708097114/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1708097114 PNAS Early Edition j 1 of 10 Downloaded by guest on September 25, 2021 lipid biosynthesis of eukaryotic algal cells (25–27). AMGs are of 22 conserved protein sequences (46) with a sampling of 7,668 thought to modulate host function to improve fitness of the sites. In the resulting ML phylogeny, OtV6 branched at the base virus and, in some cases, temporarily the host. For example, it of all other Ostreococcus viruses (Fig. 1); both the basal posi- was hypothesized that virally encoded putative phosphate trans- tion of OtV6 and the clustering of all other Ostreococcus viruses porters increase accumulation of P in host cells (28, 29), which in a single clade were strongly supported (100% bootstrap sup- may in turn increase virus fitness given that P-depleted phyto- port). This intermediate phylogenetic position was also found in plankton cells limit viral proliferation (e.g., refs. 30 and 31). a ML phylogenetic tree of the viral DNA polymerase B (915 Given the evidence of HGT for genes involved in both N and sites; SI Appendix, Fig. S2) a gene commonly used as a marker P metabolisms (7, 9, 32), the presence of host-derived phosphate for NCLDV phylogenetic and diversity analyses (48–50). transporters in phytoplankton viral genomes (29), and the impor- The phylogenies of both the viral core protein set and DNA tance of nutrient availability for phytoplankton and viral replica- polymerase B trees demonstrate that OtV6 is positioned almost tion (33), we hypothesize that functional N transporters would equidistant between the sampled members of the Ostreococcus also be found in genomes of phytoplankton viruses. Indeed, a virus and Micromonas virus clades. By comparing the amino acid recent analysis of marine viral metagenomes extended the cat- conservation levels of the 250 ORF sequences of OtV6 with alog of functions encoded by AMGs and reported the presence those of the other 11 Ostreococcus viruses and 3 Micromonas + of genes putatively encoding NH4 transporters in metagenomic viruses, we found that 20% of OtV6 ORFs were more similar assemblies which harbored phage genes (21).