Bacteriophage Protein–Protein Interactions

Häuser, Roman; Blasche, Sonja; Dokland, Terje; Haggård‐Ljungquist, Elisabeth; Brunn, Albrecht von; Salas, Margarita; Casjens, Sherwood; Molineux, Ian J.; Uetz, Peter

doi:10.1016/b978-0-12-394438-2.00006-2

Cited by 64 publications

(59 citation statements)

References 421 publications

(319 reference statements)

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“…The other detected, known interaction appears between gpN and NusA, a well-known interaction involved in the antitermination of lambda transcription (15). We did not find the five previously known interactions involving transcription factors, namely, those among CI, CII, gpQ, and RNA polymerase or sigma-70 (15). Multiple proteins may be required to stabilize such proteins in a quaternary structure, a condition our Y2H assay did not capture.…”

Section: Discussioncontrasting

confidence: 55%

“…Such interactions are hard to detect with a highthroughput approach since they are probably weak, short, and transient, although we did find one protease, ClpP, to interact with gpO. The other detected, known interaction appears between gpN and NusA, a well-known interaction involved in the antitermination of lambda transcription (15). We did not find the five previously known interactions involving transcription factors, namely, those among CI, CII, gpQ, and RNA polymerase or sigma-70 (15).…”

Section: Discussionmentioning

confidence: 68%

“…Given our limited knowledge about lambda-host interactions, we identified 62 mostly new high confidence interactions (15). Although we were initially disappointed by finding few known PPIs, we can explain many of the false negatives in retrospect.…”

Section: Discussionmentioning

confidence: 97%

“…However, this conclusion is not supported by results from other phages. For instance, whereas lambda has nine interactions involving proteases, no such interactions appear to occur in phage T7 (15). Similarly, whereas a genetic screen of E. coli mutants identified 57 host genes required for lambda infection, a similar screen with T7 identified only 11, 9 (82%) of which are involved in LPS biosynthesis (20).…”

Section: Discussionmentioning

confidence: 99%

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

Blasche

Wuchty

Rajagopala

et al. 2013

J Virol

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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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Section: Discussioncontrasting

confidence: 55%

Section: Discussionmentioning

confidence: 68%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

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

Blasche

Wuchty

Rajagopala

et al. 2013

J Virol

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“…Bacteriophage P22 is a dsDNA virus with a scaffolding protein-mediated assembly pathway, which is similar to that of herpesvirus. Therefore, P22 provides a good simple model system for studying the capsid assembly of dsDNA viruses (3,4).…”

mentioning

confidence: 99%

A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly

D'Lima

Teschke

2015

J Virol

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Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as "molecular staples" at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging. Double-stranded DNA (dsDNA) viruses, such as the tailed phages and herpesviruses, have coat proteins that lack sequence homology but possess a common HK97 fold (1, 2). Herpesviruses infect vertebrate hosts and in humans are responsible for a wide spectrum of diseases causing conditions ranging from cold sores and genital sores to chicken pox and shingles. Thus, understanding the assembly of herpesviruses is crucial for identification of novel drug targets. Bacteriophage P22 is a dsDNA virus with a scaffolding protein-mediated assembly pathway, which is similar to that of herpesvirus. Therefore, P22 provides a good simple model system for studying the capsid assembly of dsDNA viruses (3, 4).In bacteriophage P22, capsid assembly involves interaction of 415 coat protein monomers with ϳ100 molecules of scaffolding protein (5-9). This results in the formation of an intermediate structure called the procapsid (10), into which ejection proteins (11, 12) as well as a portal complex are coassembled (13). DNA gets packaged through the portal complex (5), scaffolding protein exits, and the capsid expands in volume (14). The addition of plug, tail needle, and tailspike proteins results in a mature infectious virion (15).Some coat proteins having the HK97 fold are embellished with extra domains (Fig. 1) (16). P22 coat protein is one of these, as it has a nonconserved accessory domain inserted between the A and P domains (10,17,18). This domain, referred to as the insertion domain (I domain) (19), plays an important role in the folding of coat protein by acting as an intramolecular chaperone (20). The I domain is also involved in determination of capsid size (21) and is hypothesized to stabilize procapsids by forming intersubunit interactions between adjacent capsomers (10,19,20). A recent nuclear magnetic resonance (NMR) solution structure of the isolated I domain revealed a large flexible loop, referred to...

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Bacteriophage‐receptor binding proteins for multiplex detection of Staphylococcus and Enterococcus in blood

Santos

Cunha

Macedo

et al. 2020

Biotech & Bioengineering

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Healthcare-associated infections (HCAIs) affect hundreds of millions of patients, representing a significant burden for public health. They are usually associated to multidrug resistant bacteria, which increases their incidence and severity. Bloodstream infections are among the most frequent and life-threatening HCAIs, with Enterococcus and Staphylococcus among the most common isolated pathogens. The correct and fast identification of the etiological agents is crucial for clinical decisionmaking, allowing to rapidly select the appropriate antimicrobial and to prevent from overuse and misuse of antibiotics and the consequent increase in antimicrobial resistance. Conventional culture methods are still the gold standard to identify these pathogens, however, are time-consuming and may lead to erroneous diagnosis, which compromises an efficient treatment. (Bacterio)phage receptor binding proteins (RBPs) are the structures responsible for the high specificity conferred to phages against bacteria and thus are very attractive biorecognition elements with high potential for specific detection and identification of pathogens. Taking into account all these facts, we have designed and developed a new, fast, accurate, reliable and unskilled diagnostic method based on newly identified phage RBPs and spectrofluorometric techniques that allows the multiplex detection of Enterococcus and Staphylococcus in blood samples in less than 1.5 hr after an enrichment step.

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Bacteriophage Protein–Protein Interactions

Cited by 64 publications

References 421 publications

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

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

A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly

Bacteriophage‐receptor binding proteins for multiplex detection of Staphylococcus and Enterococcus in blood

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