Abstract
Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host-ranges relative to other cyanophages. It is currently unknown whether broad host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH7803, WH8102 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early-gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage–cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Anantharaman V, Aravind L . (2003). New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol 4: R81.
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C et al. (2006). The marine viromes of four oceanic regions. PLoS Biol 4: e368.
Avrani S, Lindell D . (2015). Convergent evolution toward an improved growth rate and a reduced resistance range in Prochlorococcus strains resistant to phage. Proc Natl Acad Sci USA 112: E2191–E2200.
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D . (2011). Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 474: 604–608.
Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, Wang K et al. (2007). Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 73: 7629–7641.
Breitbart M . (2012). Marine viruses: truth or dare. Ann Rev Mar Sci 4: 425–448.
Bullard JH, Purdom E, Hansen KD, Dudoit S . (2010). Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94.
Clokie MR, Mann NH . (2006). Marine cyanophages and light. Environ Microbiol 8: 2074–2082.
Clokie MR, Shan J, Bailey S, Jia Y, Krisch HM, West S et al. (2006). Transcription of a ‘photosynthetic’ T4-type phage during infection of a marine cyanobacterium. Environ Microbiol 8: 827–835.
Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, Delong EF et al. (2006). Genomic islands and the ecology and evolution of Prochlorococcus. Science 311: 1768–1770.
Comeau AM, Chan AM, Suttle CA . (2006). Genetic richness of vibriophages isolated in a coastal environment. Environ Microbiol 8: 1164–1176.
Dekel-Bird NP, Sabehi G, Mosevitzky B, Lindell D . (2015). Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea. Environ Microbiol 17: 1286–1299.
Desplats C, Dez C, Tétart F, Eleaume H, Krisch HM . (2002). Snapshot of the genome of the pseudo-T-even bacteriophage RB49. J Bacteriol 184: 2789–2804.
Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP et al. (2008). Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol 9: R90.
Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R . (2013). Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet 9: e1003602.
Elena SF, Agudelo-Romero P, Lalić J . (2009). The evolution of viruses in multi-host fitness landscapes. Open Virol J 3: 1–6.
Enav H, Béjà O, Mandel-Gutfreund Y . (2012). Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts. ISME J 6: 619–628.
Fuhrman JA . (1999). Marine viruses and their biogeochemical and ecological effects. Nature 399: 541–548.
Fuller NJ, Marie D, Partensky F, Vaulot D, Post AF, Scanlan DJ . (2003). Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl Environ Microbiol 69: 2430–2443.
Goldsmith DB, Crosti G, Dwivedi B, McDaniel LD, Varsani A, Suttle CA et al. (2011). Development of phoH as a novel signature gene for assessing marine phage diversity. Appl Environ Microbiol 77: 7730–7739.
Guttman B, Raya R, Kutter E . (2005) Basic phage biology. In: Kutter E, Sulakvelidze A (eds). Bacteriophages Biology and Application. CRC Press: Boca Raton, FL, USA, pp 29–66.
Herrero A, Muro-Pastor AM, Flores E . (2001). Nitrogen control in cyanobacteria. J Bacteriol 183: 411–425.
Holtzendorff J, Partensky F, Jacquet S, Bruyant F, Marie D, Garczarek L et al. (2001). Diel expression of cell cycle-related genes in synchronized cultures of Prochlorococcus sp. strain PCC 9511. J Bacteriol 183: 915–920.
Horvitz HR . (1974a). Bacteriophage T4 mutants deficient in alteration and modification of the Escherichia coli RNA polymerase. J Mol Biol 90: 739–750.
Horvitz HR . (1974b). Control by bacteriophage T4 of two sequential phosphorylations of the alpha subunit of Escherichia coli RNA polymerase. J Mol Biol 90: 727–738.
Jabbar MA, Snyder L . (1984). Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4. J Virol 51: 522–529.
Koch T, Raudonikiene A, Wilkens K, Rüger W . (1995). Overexpression, purification, and characterization of the ADP-ribosyltransferase (gpAlt) of bacteriophage T4: ADP-ribosylation of E. coli RNA polymerase modulates T4 ‘early’ transcription. Gene Expr 4: 253–264.
Koerner JF, Snustad DP . (1979). Shutoff of host macromolecular synthesis after T-even bacteriophage infection. Microbiol Rev 43: 199–223.
Labrie SJ, Samson JE, Moineau S . (2010). Bacteriophage resistance mechanisms. Nat Rev Microbiol 8: 317–327.
Lavigne R, Lecoutere E, Wagemans J, Cenens W, Aertsen A, Schoofs L et al. (2013). A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19. MBio 4: e00061–13.
Limor-Waisberg K, Carmi A, Scherz A, Pilpel Y, Furman I . (2011). Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies. Nucleic Acids Res 39: 6016–6028.
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T et al. (2007). Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449: 83–86.
Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW . (2005). Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438: 86–89.
Lindell D, Padan E, Post AF . (1998). Regulation of ntcA expression and nitrite uptake in the marine Synechococcus sp. strain WH 7803. J Bacteriol 180: 1878–1886.
Mann NH, Clokie MR, Millard AD, Cook A, Wilson WH, Wheatley PJ et al. (2005). The genome of S-PM2, a ‘photosynthetic’ T4-type bacteriophage that infects marine Synechococcus strains. J Bacteriol 187: 3188–3200.
Mann NH, Cook A, Millard A, Bailey S, Clokie M . (2003). Marine ecosystems: bacterial photosynthesis genes in a virus. Nature 424: 741.
Marchand I, Nicholson AW, Dreyfus M . (2001). Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase. Mol Microbiol 42: 767–776.
Marston MF, Pierciey FJ, Shepard A, Gearin G, Qi J, Yandava C et al. (2012). Rapid diversification of coevolving marine Synechococcus and a virus. Proc Natl Acad Sci USA 109: 4544–4549.
Marston MF, Sallee JL . (2003). Genetic diversity and temporal variation in the cyanophage community infecting marine Synechococcus species in Rhode Island’s coastal waters. Appl Environ Microbiol 69: 4639–4647.
Martiny AC, Coleman ML, Chisholm SW . (2006). Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation. Proc Natl Acad Sci USA 103: 12552–12557.
Millard AD, Gierga G, Clokie MR, Evans DJ, Hess WR, Scanlan DJ . (2010). An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease. ISME J 4: 1121–1135.
Millard AD, Mann NH . (2006). A temporal and spatial investigation of cyanophage abundance in the Gulf of Aqaba, Red Sea. J Mar Biol Assoc UK 86: 507–515.
Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ . (2009). Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environ Microbiol 11: 2370–2387.
Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A et al. (2003a). Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol 185: 5220–5233.
Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W . (2003b). Bacteriophage T4 genome. Microbiol Mol Biol Rev 67: 86–156.
Mitschke J, Georg J, Scholz I, Sharma C, Dienst D, Bantscheff J et al. (2011). An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci USA 108: 1–6.
Moore LR, Coe A, Zinser ER, Saito MA, Sullivan MB, Lindell D et al. (2007). Culturing the marine cyanobacterium. Prochlorococcus Limnol Ocean Methods 5: 353–362.
Mosig G, Eiserling F . (2006) T4 and related phages: structure and development. In: Calendar R (ed). The Bacteriophages. Oxford University Press: New York, NY, USA, pp 225–267.
Mosig G, Yu S, Myung H, Haggård-Ljungquist E, Davenport L, Carlson K et al. (1997). A novel mechanism of virus-virus interactions: bacteriophage P2 Tin protein inhibits phage T4 DNA synthesis by poisoning the T4 single-stranded DNA binding protein, gp32. Virology 230: 72–81.
Muro-Pastor MI, Reyes JC, Florencio FJ . (2001). Cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate levels. J Biol Chem 276: 38320–38328.
Nolan JM, Petrov V, Bertrand C, Krisch HM, Karam JD . (2006). Genetic diversity among five T4-like bacteriophages. Virol J 3: 30.
Palenik BP, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P et al. (2003). The genome of a motile marine. Synechococcus Nature 424: 1037–1042.
Palenik BP, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH et al. (2006). Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci USA 103: 13555–13559.
Pinto FL, Thapper A, Sontheim W, Lindblad P . (2009). Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria. BMC Mol Biol 10: 79–87.
Poranen MM, Ravantti JJ, Grahn AM, Gupta R, Auvinen P, Bamford DH . (2006). Global changes in cellular gene expression during bacteriophage PRD1 infection. J Virol 80: 8081–8088.
Puerta-Fernández E, Vioque A . (2011). Hfq is required for optimal nitrate assimilation in the Cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 193: 3546–3555.
Pène C, Uzan M . (2000). The bacteriophage T4 anti-sigma factor AsiA is not necessary for the inhibition of early promoters in vivo. Mol Microbiol 35: 1180–1191.
Ravantti JJ, Ruokoranta TM, Alapuranen AM, Bamford DH . (2008). Global transcriptional responses of Pseudomonas aeruginosa to phage PRR1 infection. J Virol 82: 2324–2329.
Riede I, Eschbach ML . (1986). Evidence that TraT interacts with OmpA of Escherichia coli. FEBS Lett 205: 241–245.
Rifat D, Wright NT, Varney KM, Weber DJ, Black LW . (2008). Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target. J Mol Biol 375: 720–734.
Rocap G, Distel DL, Waterbury JB, Chisholm SW . (2002). Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68: 1180–1191.
Roucourt B, Lavigne R . (2009). The role of interactions between phage and bacterial proteins within the infected cell: a diverse and puzzling interactome. Environ Microbiol 11: 2789–2805.
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S et al. (2007). The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, Lindell D . (2012). A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proc Natl Acad Sci USA 109: 2037–2042.
Salzberg SL, Delcher AL, Kasif S, White O . (1998). Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26: 544–548.
Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR et al. (2009). Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73: 249–299.
Scanlan DJ . (2003). Physiological diversity and niche adaptation in marine Synechococcus. Adv Microb Physiol 47: 1–64.
Smyth GK . (2005) Limma: linear models for microarray data. In: Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Statistics for Biology and Health, Springer-Verlag: New York, NY, USA, pp 397–420.
Staley JT, Gunsalus RP, Lory S, Perry JJ . (2007) Viruses. In: Microbial Life. Sinauer Associates, Inc.: Sunderland, MA, USA, pp 389–408.
Stazic D, Lindell D, Steglich C . (2011). Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection. Nucleic Acids Res 39: 4890–4899.
Stern A, Sorek R . (2011). The phage-host arms race: shaping the evolution of microbes. Bioessays 33: 43–51.
Stork T, Michel K-P, Pistorius EK, Dietz K-J . (2005). Bioinformatic analysis of the genomes of the cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 for the presence of peroxiredoxins and their transcript regulation under stress. J Exp Bot 56: 3193–3206.
Stuart RK, Brahamsha B, Busby K, Palenik B . (2013). Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress. ISME J 7: 1139–1149.
Su Z, Mao F, Dam P, Wu H, Olman V, Paulsen IT et al. (2006). Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res 34: 1050–1065.
Sullivan MB, Coleman ML, Weigele PR, Rohwer F, Chisholm SW . (2005). Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 3: e144.
Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR et al. (2010). Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol 12: 3035–3056.
Sullivan MB, Waterbury JB, Chisholm SW . (2003). Cyanophages infecting the oceanic cyanobacterium. Prochlorococcus Nature 424: 1047–1051.
Suttle CA, Chan AM . (1993). Marine cyanophages infecting oceanic and coastal strains of Synechococcus: abundance, morphology, cross-infectivity and growth characteristics. Mar Ecol Prog Ser 92: 99–109.
Suttle CA . (2005). Viruses in the sea. Nature 437: 356–361.
Tetu SG, Johnson DA, Varkey D, Phillippy K, Stuart RK, Dupont CL et al. (2013). Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Front Microbiol 4: 232.
Thompson AW, Huang K, Saito MA, Chisholm SW . (2011a). Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. ISME J 5: 1580–1594.
Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J et al. (2011b). Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc Natl Acad Sci USA 108: E757–E764.
Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R et al. (2006). Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol 2: 53.
Ueno H, Yonesaki T . (2004). Phage-induced change in the stability of mRNAs. Virology 329: 134–141.
Uzan M . (2009). RNA processing and decay in bacteriophage T4. Prog Mol Biol Transl Sci 85: 43–89.
Wang K, Chen F . (2008). Prevalence of highly host-specific cyanophages in the estuarine environment. Environ Microbiol 10: 300–312.
Waterbury JB, Valois FW . (1993). Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl Environ Microbiol 59: 3393–3399.
Weigele PR, Pope WH, Pedulla ML, Houtz JM, Smith AL, Conway JF et al. (2007). Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ Microbiol 9: 1675–1695.
Woolhouse ME, Taylor LH, Haydon DT . (2001). Population biology of multihost pathogens. Science 292: 1109–1112.
Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S, Becavin C et al. (2012a). Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8: 583.
Wurtzel O, Yoder-Himes DR, Han K, Dandekar AA, Edelheit S, Greenberg EP et al. (2012b). The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature. PLoS Pathog 8: e1002945.
Wyman M, Gregory RP, Carr NG . (1985). Novel role for phycoerythrin in a marine cyanobacterium, Synechococcus strain DC2. Science 230: 818–820.
Zinser ER, Coe A, Johnson ZI, Martiny AC, Fuller NJ, Scanlan DJ et al. (2006). Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method. Appl Environ Microbiol 72: 723–732.
Zwirglmaier K, Jardillier L, Ostrowski M, Mazard S, Garczarek L, Vaulot D et al. (2008). Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol 10: 147–161.
Acknowledgements
We thank Hila Sberro, Eyal Weinstock, Asaf Levy, Daniel Dar, Gil Amitai and Daniel Schwartz for comments and stimulating discussions. We also thank Omri Wurtzel for the transcriptome browser and computational infrastructures, Sarit Edelheit for the bisulfite libraries, Irina Pekarsky and Shay Kirzner for assistance with the infection experiments, Forest Rohwer for the water sample for P-TIM40 isolation, Nils Schurgers and Annegret Wilde for discussions and help annotating the pil genes. This research was funded, in part, by European Research Council Starting Grants 203406 (to DL) and 260432 (to RS), the ISF Morasha Program grant 1504/06 (to DL), the ISF grant 1303/12 and I-CORE grant 1796/12 (to RS), HFSP grant RGP0011/2013 (to RS), the Leona M and Harry B Helmsley Charitable Trust (to RS), the Abisch-Frenkel foundation, the Pasteur-Weizmann Program (to RS) and by a research grant from Mr Martin Kushner Schnur in honor of Fanny Kushner (to RS); and by grants from the Portuguese Fundação para a Ciência e a Tecnologia (PTDC/BIA-MIC/101036/2008 and PTDC/BIA-MIC/4418/2012 and IF/00881/2013) (to MF) and the Deutsche Forschungsgemeinschaft grant STE 1119/4–1 (to CS). The Gordon and Betty Moore Foundation Marine Microbial Genome Sequencing Project funded the sequencing of the Synechococcus WH8109 genome (to DL).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Additional information
Supplementary Information accompanies this paper on The ISME Journal website
Rights and permissions
About this article
Cite this article
Doron, S., Fedida, A., Hernández-Prieto, M. et al. Transcriptome dynamics of a broad host-range cyanophage and its hosts. ISME J 10, 1437–1455 (2016). https://doi.org/10.1038/ismej.2015.210
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/ismej.2015.210
This article is cited by
-
Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages
The ISME Journal (2022)
-
Protist impacts on marine cyanovirocell metabolism
ISME Communications (2022)
-
Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity
The ISME Journal (2021)
-
Frequency of mispackaging of Prochlorococcus DNA by cyanophage
The ISME Journal (2021)
-
Confocal microscopy reveals alterations of thylakoids in Limnospira fusiformis during prophage induction
Protoplasma (2021)