Phage Biology

E M KUTTER, E THOMAS, J. CUSHING, M MUELLER, P LIPPINCOTT, B ANDERSON, AND J NEITZEL; F ZUCKER AND T HUNKAPILLAR The Evergreen State Coll., Olympia, WA; Univ. of WA, Seattle, WA

We still have no specific functional clues for almost half of T4's 270 probable protein-encoding genes. Only about 40 enzymes have clear database matches, so we are also using other approaches to look at functionality. For example, 13 T4 proteins are predicted to be integral membrane proteins (cf. Boyd et al 1998, Protein Science 7:201-205). These include imm, ac and t, as expected, and several interesting clusters of small ORFs. However, surprisingly, rII A and B, ndd and gp46 probably are not "integral membrane proteins". Most of the clear homologies involve enzymes of nucleic acid metabolism; there are still virtually no indications as to the origins of the large number of host-lethal proteins responsible for the transition from host to phage metabolism, or of the phage structural proteins. The latter have been shown by Krisch et al. to be shared among phage of T4 morphotype infecting the whole range of gram-negative bacteria. With the exception of tail-fiber genes and exchange among T-even-type phages, there is no evidence for acquisition of any genes since well before the split between Hemophilis and E. coli; in some cases, the divergence predates the separation of eubacteria and eucaryotes. We are working on a system to integrate and manipulate results from numerous runs of such programs as BLAST, FASTA and Smith-Waterman using various parameters, queries and databases and applying it to try to tease out meaning from weak T4 homologies.

We are also trying to better understand phage-host interactions in nature, and finding surprising complexities. For example, in contrast to the total shutoff of host replication, transcription and translation seen when T4 infects exponential-phase bacteria, we find that infection of nutrient-starved cells leads to a sort of state of hibernation. When nutrients are then added, both host and phage proteins are made, with the host syntheses gradually shutting off as the cell prepares a small burst of phage. We have also tested nearly 100 phages of the T-even morphotype against a range of hosts: the ECOR collection, pig pathogens, O157, Shigella. Anywhere from 1 to 43 phages infect each, with surprisingly complex patterns of infectivity; the mean is about 20 phages/strain. The implications of these various findings for medical antibacterial applications will be discussed. T-even-like phages also infect bacteria such as Pseudomonas and Vibrio, and form important components of the therapeutic cocktails used for decades for phage therapy in Eastern Europe, particularly through the Bacteriophage Institute, Tbilisi, Georgia, our collaborators in these explorations.

Written October 16, 1998.

Contact the Site Manager

Last Updated: May 29, 2008

The Evergreen State College

2700 Evergreen Parkway NW

Olympia, Washington 98505

(360) 867-6000