, Volume 11, Issue 1, pp 95–104 | Cite as

Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b

  • Michael Borriss
  • Thierry Lombardot
  • Frank Oliver Glöckner
  • Dörte Becher
  • Dirk Albrecht
  • Thomas SchwederEmail author
Original Paper


Virion DNA of bacteriophage 11b (Φ11b), which infects a psychrophilic Flavobacterium isolate from Arctic sea-ice, was determined to consist of 36,012 bp. With 30.6% its GC content corresponds to that of host-genus species and is the lowest of all phages of Gram-negative bacteria sequenced so far. Similarities of several of 65 predicted ORFs, genome organization and phylogeny suggest an affiliation to ‘mesophilic’ nonmarine siphoviruses, e.g. to bacteriophages SPP1 and HK97. Early genes presumably encode an essential recombination factor (ERF), a single strand binding (SSB) protein, an endonuclease, and a DNA methylase. The late gene segment is likely to contain a terminase, portal, minor head, protease and a major capsid gene. Five ORFs exhibited similarities to Bacteroidetes species and seem to reflect the host specificity of the phage. Among PAGE-separated virion proteins that were identified by MALDI-ToF mass spectrometry are the portal, the major capsid, and a putative conserved tail protein. The Φ11b genome is the first to be described of a cultivated virus infecting a psychrophilic host as well as a Bacteroidetes bacterium.


Psychrophilic Flavobacterium bacteriophage Φ11b Genomics Proteome Low GC 



We thank Hansjörg Lehnherr for critical reading of the manuscript and Dr. Steffen Krüger for helpful comments during the sequencing and sequence assembly procedure. We are grateful for the support of Michael Hecker in the analysis of the phage proteome.

Supplementary material

792_2006_14_MOESM1_ESM.pdf (47 kb)
Supplementary material


  1. Ackermann H-W, Abedon ST (2001) Bacteriophage names. The Bacteriophage Ecology Group. (Online.)
  2. Alonso JC, Luder G, Stiege AC, Chai S, Weise F, Trautner TA (1997) The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 204:201–212PubMedCrossRefGoogle Scholar
  3. Andrade MA, Ponting CP, Gibson TJ, Bork P (2000) Homology-based method for identification of protein repeats using statistical significance estimates. J Mol Biol 298:521–537PubMedCrossRefGoogle Scholar
  4. Arai M, Mitsuke H, Ikeda M, Xia J-X, Kikuchi T, Satake M, Shimizu T (2004) ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res 32:390–393CrossRefGoogle Scholar
  5. Badger JH, Olsen GJ (1999) CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 16:512–524PubMedGoogle Scholar
  6. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795PubMedCrossRefGoogle Scholar
  7. Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS (1995) Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci USA 92:8259–8263PubMedCrossRefGoogle Scholar
  8. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148CrossRefGoogle Scholar
  9. Blum H, Beier H, Gross HJ (1987) Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 8:93–99CrossRefGoogle Scholar
  10. Borriss M, Helmke E, Hanschke R, Schweder T (2003) Isolation and characterisation of marine psychrophillic phage-host systems from Arctic sea ice. Extremophiles 7:377–384PubMedCrossRefGoogle Scholar
  11. Bujnicki JM (2002) Sequence permutations in the molecular evolution of DNA methyltransferases. BMC Evol Biol 2:3PubMedCrossRefGoogle Scholar
  12. Büttner K, Bernhardt J, Scharf C, Schmid R, Mäder U, Eymann C, Antelmann H, Völker A, Völker U, Hecker M (2001) A comprehensive two-dimensional map of cytosolic proteins of Bacillus subtilis. Electrophoresis 22:2908–2935PubMedCrossRefGoogle Scholar
  13. Bradford D, Hugenholtz P, Seviour EM, Cunningham MA, Stratton H, Seviour RJ, Blackall LL (1996) 16S rRNA analysis of isolates obtained from gram-negative filamentous bacteria micromanipulated from activated sludge. Syst Appl Microbiol 19:334–343Google Scholar
  14. Brinkmeyer R, Knittel K, Jurgens J, Weyland H, Amann R, Helmke E (2003) Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl Environ Microbiol 69: 6610–6599PubMedCrossRefGoogle Scholar
  15. Camacho AG, A. Gual A, Lurz R, Tavares P, Alonso JC (2003) Bacillus subtilis bacteriophage SPP1 DNA packaging motor requires terminase and portal proteins. J Biol Chem 278:23251–23239PubMedCrossRefGoogle Scholar
  16. Casjens SR, Gilcrease EB, Winn-Stapley DA, Schicklmaier P, Schmieger H, Pedulla ML, Ford ME, Houtz JM, Hatfull GF, Hendrix RW (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J Bacteriol 187:1091–1104PubMedCrossRefGoogle Scholar
  17. Chai S, Bravo A, Luder G, Nedlin A, Trautner TA, Alonso JC (1992) Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1 to 6. The products of gene 1 and gene 2 are required for pac cleavage. J Mol Biol 224:87–102PubMedCrossRefGoogle Scholar
  18. Clarke GD, Beiko RG, Ragan MA, Charlebois RL (2002) Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 184:2072–2080PubMedCrossRefGoogle Scholar
  19. Combet C, Blanchet C, Geourjon C, Deléage G (2000) NPS@: Network Protein Sequence Analysis TIBS 25:147–150Google Scholar
  20. Crutz-Le Coq AM, Cesselin B, Commissaire J, Anba J (2002) Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Microbiology 148:985–1001PubMedGoogle Scholar
  21. Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the Dense Alignment Surface method. Prot Eng 10:673–676CrossRefGoogle Scholar
  22. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641PubMedCrossRefGoogle Scholar
  23. Desiere F, Lucchini S, Canchaya C, Ventura M, Brussow H (2002) Comparative genomics of phages and prophages in lactic acid bacteria. Antonie Van Leeuwenhoek 82:73–91PubMedCrossRefGoogle Scholar
  24. Duda RL, Martincic K, Hendrix RW (1995) Genetic basis of bacteriophage HK97 prohead assembly. J Mol Biol 247:636–647PubMedCrossRefGoogle Scholar
  25. Engelke DR, Hoener PA, Collins FS (1988) Direct sequencing of enzymatically amplified human genomic DNA. Proc Natl Acad Sci USA 85:544–548PubMedCrossRefGoogle Scholar
  26. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FSL (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21:617–623PubMedCrossRefGoogle Scholar
  27. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In Walker JM (eds) The proteomics protocols handbook. Humana Press, pp 571–607Google Scholar
  28. Gruber M, Soding J, Lupas AN (2005) REPPER–repeats and their periodicities in fibrous proteins. Nucleic Acids Res 33:239–243CrossRefGoogle Scholar
  29. Gual A, Camacho AG Alonso JC (2000) Functional analysis of the terminase large subunit, G2P, of Bacillus subtilis bacteriophage SPP1. J Biol Chem 275:35311–35299PubMedCrossRefGoogle Scholar
  30. Heger A, Holm L (2000) Rapid automatic detection and alignment of repeats in protein sequences. Proteins 41:224–237PubMedCrossRefGoogle Scholar
  31. Hirokawa T, Seah BC, Mitaku S (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14:378–379PubMedCrossRefGoogle Scholar
  32. Jiang SC, Kellogg CA, Paul JH (1998) Characterization of marine temperate phage-host systems isolated from Mamala Bay, Oahu, Hawaii. Appl Environ Microbiol 64:535–542PubMedGoogle Scholar
  33. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202PubMedCrossRefGoogle Scholar
  34. Juncker AS, Willenbrock H, von Heijne G, Nielsen H, Brunak S, Krogh A (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12:1652–1662PubMedCrossRefGoogle Scholar
  35. Kirchman DL (2002) The ecology of cytophaga–flavobacteria in aquatic environments. FEMS Microbiol Ecol 39:91–100PubMedGoogle Scholar
  36. Kisand V, Cuadros R, Wikner J (2002) Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern Baltic Sea. Appl Environ Microbiol 68:379–388PubMedCrossRefGoogle Scholar
  37. Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29:3742–3756PubMedCrossRefGoogle Scholar
  38. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580PubMedCrossRefGoogle Scholar
  39. Kwan T, Liu J, Dubow M, Gros P Pelletier J (2005) The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci USA 102:5174–5179PubMedCrossRefGoogle Scholar
  40. Leader DP (2004) BugView: a browser for comparing genomes. Bioinformatics 20:129–130PubMedCrossRefGoogle Scholar
  41. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964PubMedCrossRefGoogle Scholar
  42. Lupas A, Van Dyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164CrossRefGoogle Scholar
  43. Magrini V, Salmi D, Thomas D, Herbert S, Hartzell P, Youderian P (1997) Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox. J Bacteriol 179:4254–4263PubMedGoogle Scholar
  44. McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32:20–25CrossRefGoogle Scholar
  45. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A (2003) GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195PubMedCrossRefGoogle Scholar
  46. Proux C, van Sinderen D, Suarez J, Garcia P, Ladero V, Fitzgerald GF, Desiere F, Brussow H (2002) The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J Bacteriol 184:6026–6036PubMedCrossRefGoogle Scholar
  47. Rao DN, Eberle H, Bickle TA (1989) Characterization and mutations of the bacteriophage P1 mod gene encoding the recognition subunit of the EcoP1 restriction and modification system. J Bacteriol 171:2347–2352PubMedGoogle Scholar
  48. Roberts MD, Martin NL, Kropinski AM (2004) The genome and proteome of coliphage T1. Virology 318:245–266PubMedCrossRefGoogle Scholar
  49. Smith MC, Burns RN, Wilson SE, Gregory MA (1999) The complete genome sequence of the Streptomyces temperate phage phiC31: evolutionary relationships to other viruses. Nucleic Acids Res 27:2145–2155PubMedCrossRefGoogle Scholar
  50. Teeling H., Lombardot T, Bauer M, Ludwig W, Glöckner FO (2004) Evaluation of the phylogenetic position of the planctomycete ‘Rhodopirellula baltica’ SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int J Syst Evol Microbiol 54:791–801PubMedCrossRefGoogle Scholar
  51. Tusnady GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:849–850PubMedCrossRefGoogle Scholar
  52. Van Sinderen D, Karsens H, Kok J, Terpstra P, Ruiters MH, Venema G, Nauta A (1996) Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Mol Microbiol 19:1343–1355PubMedCrossRefGoogle Scholar
  53. Wikoff WR, Liljas L, Duda RL, Tsuruta H, Hendrix RW, Johnson JE (2000) Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289:2129–2133PubMedCrossRefGoogle Scholar
  54. Wolf E, Kim PS, Berger B (1997) MultiCoil: a program for predicting two- and three-stranded coiled coils. Protein Sci 6:1179–1189PubMedCrossRefGoogle Scholar
  55. Young R, Wang I-N, Roof WD (2000) Phages will out: strategies of host cell lysis. Trends Microbiol 8:120–128PubMedCrossRefGoogle Scholar
  56. Zimmer M, Sattelberger E, Inman RB, Calendar R, Loessner MJ (2003) Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed +1 translational frameshifting in structural protein synthesis. Mol Microbiol 50:303–317PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Michael Borriss
    • 1
  • Thierry Lombardot
    • 2
  • Frank Oliver Glöckner
    • 2
  • Dörte Becher
    • 3
  • Dirk Albrecht
    • 3
  • Thomas Schweder
    • 1
    • 4
    Email author
  1. 1.Institute of Marine BiotechnologyGreifswaldGermany
  2. 2.Max-Planck-Institute for Marine MicrobiologyBremenGermany
  3. 3.Institute of MicrobiologyErnst-Moritz-Arndt-UniversityGreifswaldGermany
  4. 4.Institute of PharmacyErnst-Moritz-Arndt-UniversityGreifswaldGermany

Personalised recommendations