Extremophiles

, Volume 17, Issue 1, pp 99–114

Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage–host interactions

Original Paper

DOI: 10.1007/s00792-012-0497-1

Cite this article as:
Colangelo-Lillis, J.R. & Deming, J.W. Extremophiles (2013) 17: 99. doi:10.1007/s00792-012-0497-1

Abstract

The 104 kb genome of cold-active bacteriophage 9A, which replicates in the marine psychrophilic gamma-proteobacterium Colwellia psychrerythraea strain 34H (between −12 and 8 °C), was sequenced and analyzed to investigate elements of molecular adaptation to low temperature and phage–host interactions in the cold. Most characterized ORFs indicated closest similarity to gamma-proteobacteria and their phages, though no single module provided definitive phylogenetic grouping. A subset of primary structural features linked to psychrophily suggested that the majority of annotated phage proteins were not psychrophilic; those that were, primarily serve phage-specific functions and may also contribute to 9A’s restricted temperature range for replication as compared to host. Comparative analyses suggest ribonucleotide reductase genes were acquired laterally from host. Neither restriction modification nor the CRISPR-Cas system appeared to be the predominant phage defense mechanism of Cp34H or other cold-adapted bacteria; we hypothesize that psychrophilic hosts rely more on the use of extracellular polymeric material to block cell surface receptors recognized by phages. The relative dearth of evidence for genome-specific defenses, genetic transfer events or auxiliary metabolic genes suggest that the 9A-Cp34H system may be less tightly coupled than are other genomically characterized marine phage–host systems, with possible implications for phage specificity under different environmental conditions.

Keywords

BacteriophagePsychrophilicColwelliaSiphoviridaeGenomeLateral gene transferPhage-defense strategiesEPS

Abbreviations

9A

Colwelliaphage 9A

11b

Flavobacteriophage 11b

AMG

Auxiliary metabolic gene

CDS

Coding sequence corresponding to sequence of amino acids in predicted protein including start and stop codons

ch

Conserved hypothetical protein

Cp34H

Colwellia psychrerythraea strain 34H

CRISPR

Clustered regularly interspaced short palindromic repeat

EPS

Extracellular polymeric substances

LGT

Lateral gene transfer

MPSP

Marine Phage Sequencing Project

MT

Methyltransferase

nr

NCBI Genbank non-redundant database

nrd

Ribonucleotide reductase

ORF

Open reading frame

ORFan

ORF with no known homolog

PHS

Phage–host system

pp

Predicted protein

RE

Restriction enzyme

RM

Restriction-modification system

SD

Standard deviation

Supplementary material

792_2012_497_MOESM1_ESM.pdf (297 kb)
Fig. S1. Colwelliaphage 9A ORF protein characters compared to mean character value for all 9A ORFs. Each subfigure shows deviation from 9A genome character mean as fraction of that mean for each ORF. Modules separated with vertical lines. * indicates ORF contained no Glutamic Acid (E) residues, but was graphed as though it contained 1. Only ORFs with a minimum of two protein characters values scored as psychrophilic, or one character scored as strongly psychrophilic are shown. Note varying scale of x-axes. See text for definition of character values binned as psychrophilic and strongly psychrophilic and Table S1 for gene abbreviations (PDF 297 kb)
792_2012_497_MOESM2_ESM.pdf (1.1 mb)
Table S1 (PDF 1113 kb)
792_2012_497_MOESM3_ESM.pdf (133 kb)
Table S2 (PDF 133 kb)
792_2012_497_MOESM4_ESM.pdf (59 kb)
Table S3 (PDF 60 kb)
792_2012_497_MOESM5_ESM.pdf (92 kb)
Table S4 (PDF 92 kb)

Copyright information

© Springer Japan 2012

Authors and Affiliations

  1. 1.School of Oceanography and Astrobiology ProgramUniversity of WashingtonSeattleUSA