The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli

Abstract

dAlthough most of the 73 open reading frames (ORFs) in bacteriophage have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its host Escherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between the E. coli transcriptional network and lambda proteins. Targeted host proteins and genes required for lambda infection are enriched among highly connected proteins, suggesting that bacteriophages resemble interaction patterns of human viruses. Lambda tail proteins interact with both bacterial fimbrial proteins and E. coli proteins homologous to other phage proteins. Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast twohybrid screens. More than 60 years ago, Esther Lederberg discovered phage lambda (1). Since this seminal discovery, lambda has become a model organism, contributing to our current understanding of the ways genes work and viruses take control of their hosts. However, phage lambda is still far from being completely understood given that the function of several genes in its 48.5-kb genome remain only vaguely defined. For instance, 14 of 73 predicted lambda proteins are still largely uncharacterized (2).Some of the best-characterized aspects of lambda biology are the genetic switch that determines whether a phage lyses the cell or integrates into its host genome as a prophage and the mechanism of transcriptional antitermination (3). Also, lambda continues to provide new insights into its gene regulatory circuits (4, 5), with recent studies of its DNA packaging motor as the vanguard of nanomotor research (6).Key to lambda biology is a detailed understanding of the phage's proteins, including their interactions. We recently analyzed 95 protein-protein interactions (PPIs) between ϳ70 lambda proteins, capturing 16 of 33 previously published interactions (2). Although protein interactions are reasonably well characterized within the virus particle, host-phage interactions remain incompletely known during the replication and recombination stages of the lambda life cycle in the host cell. In addition, the molecular details of virion assembly are still largely mysterious. Altogether, about 30 host-lambda interactions have been discovered in the past 50 years (Table 1).To improve our understanding of lambda PPIs, we have cloned 68 lambda open reading frames (ORFs) (2) and performed screens against a pooled Escherichia coli library using a multivector yeast two-hybrid (Y2H) strategy. Among a total of 631 raw interactions, we found 244 reproducible interactions. Furthermore, we confirmed 162 interactions in an additional round of retesting, allowing us to obtain an o...

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