Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease

Xu, Shuai; Gupta, Y. K.

doi:10.1093/nar/gks1043

Cited by 37 publications

(55 citation statements)

References 75 publications

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“…Also, lambda gpFI, an endonuclease, interacts with lambda terminase (16). Many phages encode an HNH protein (endonuclease) located adjacent to the phage DNA-packaging enzyme terminase, suggesting roles in phage DNA packaging and maturation (33). It is important and interesting that all of the phages, including mycobacteriophage Giles, harboring hnh genes are cos phages with linear DNA containing cohesive ends.…”

Section: Discussionmentioning

confidence: 99%

The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins

et al. 2015

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Mycobacteriophages are viruses that infect mycobacterial hosts and are prevalent in the environment. Nearly 700 mycobacteriophage genomes have been completely sequenced, revealing considerable diversity and genetic novelty. Here, we have determined the protein complement of mycobacteriophage Giles by mass spectrometry and mapped its genome-wide protein interactome to help elucidate the roles of its 77 predicted proteins, 50% of which have no known function. About 22,000 individual yeast twohybrid (Y2H) tests with four different Y2H vectors, followed by filtering and retest screens, resulted in 324 reproducible proteinprotein interactions, including 171 (136 nonredundant) high-confidence interactions. The complete set of high-confidence interactions among Giles proteins reveals new mechanistic details and predicts functions for unknown proteins. The Giles interactome is the first for any mycobacteriophage and one of just five known phage interactomes so far. Our results will help in understanding mycobacteriophage biology and aid in development of new genetic and therapeutic tools to understand Mycobacterium tuberculosis. IMPORTANCEMycobacterium tuberculosis causes over 9 million new cases of tuberculosis each year. Mycobacteriophages, viruses of mycobacterial hosts, hold considerable potential to understand phage diversity, evolution, and mycobacterial biology, aiding in the development of therapeutic tools to control mycobacterial infections. The mycobacteriophage Giles protein-protein interaction network allows us to predict functions for unknown proteins and shed light on major biological processes in phage biology. For example, Giles gp76, a protein of unknown function, is found to associate with phage packaging and maturation. The functions of mycobacteriophage-derived proteins may suggest novel therapeutic approaches for tuberculosis. Our ORFeome clone set of Giles proteins and the interactome data will be useful resources for phage interactomics.T he continuous emergence of bacterial pathogens resistant to antibiotics is an increasing medical problem (1). Mycobacterium tuberculosis is prominent among these pathogens, with over 9 million new cases of tuberculosis reported each year. There is an urgent need for alternate ways to control M. tuberculosis infections, and one potential strategy involves using mycobacteriophages for prophylaxis or therapy (2). The emergence of extensively drug-resistant (XDR) and totally drug-resistant (TDR) strains of M. tuberculosis, both of which are especially difficult to control (3), has spurred renewed interest in the therapeutic use of bacteriophages.Mycobacteriophages are known to infect many different species of both fast-and slow-growing mycobacteria, including M. tuberculosis and Mycobacterium smegmatis (4, 5). Over the past decade, thousands of mycobacteriophages have been isolated, and hundreds have been completely sequenced (http://phagesdb.org/). Mycobacteriophage genomes are highly mosaic due to horizontal genetic exchange (6-8) but can be grouped into 2...

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Section: Discussionmentioning

confidence: 99%

The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins

et al. 2015

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“…A recent study has reported that many phages, infecting both Gram-positive and -negative bacteria, encode an HNH protein adjacent to the genes encoding the TerS, TerL, and portal proteins (20). Interestingly, all of the characterized phages carrying an hnh gene are cos phages.…”

Section: Geobacter Metallireducens Pseudomonas Alcaligenes Pacimentioning

confidence: 99%

Staphylococcal pathogenicity island DNA packaging system involving cos -site packaging and phage-encoded HNH endonucleases

Quiles-Puchalt

Carpena

Alonso

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Staphylococcal pathogenicity islands (SaPIs) are the prototypical members of a widespread family of chromosomally located mobile genetic elements that contribute substantially to intra-and interspecies gene transfer, host adaptation, and virulence. The key feature of their mobility is the induction of SaPI excision and replication by certain helper phages and their efficient encapsidation into phagelike infectious particles. Most SaPIs use the headful packaging mechanism and encode small terminase subunit (TerS) homologs that recognize the SaPI-specific pac site and determine SaPI packaging specificity. Several of the known SaPIs do not encode a recognizable TerS homolog but are nevertheless packaged efficiently by helper phages and transferred at high frequencies. In this report, we have characterized one of the non-terS-coding SaPIs, SaPIbov5, and found that it uses two different, undescribed packaging strategies. SaPIbov5 is packaged in full-sized phage-like particles either by typical pac-type helper phages, or by cos-type phages-i.e., it has both pac and cos sites-a configuration that has not hitherto been described for any mobile element, phages included-and uses the two different phage-coded TerSs. To our knowledge, this is the first example of SaPI packaging by a cos phage, and in this, it resembles the P4 plasmid of Escherichia coli. Cos-site packaging in Staphylococcus aureus is additionally unique in that it requires the HNH nuclease, carried only by cos phages, in addition to the large terminase subunit, for cos-site cleavage and melting.interference | horizontal gene transfer | PICIs | molecular parasitism

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“…The frequent juxtaposition of HNH and phage terminase genes (10,20) suggests a unique role for HNH proteins in the endonuclease and/or packaging activities of the terminases. To address this issue, we investigated the function of E. coli phage HK97 gp74, a 119-residue protein containing an HNH motif.…”

mentioning

confidence: 99%

HNH proteins are a widespread component of phage DNA packaging machines

Kala

Cumby

Sadowski³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

116

106

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The genome packaging reactions of tailed bacteriophages and herpes viruses require the activity of a terminase enzyme, which is comprised of large and small subunits. Phage genomes are replicated as linear concatemers composed of multiple copies of the genome joined end to end. As the terminase enzyme packages the genome into the phage capsid, it cleaves the DNA into single genome-length units. In this work, we show that the phage HK97 HNH protein, gp74, is required for the specific endonuclease activity of HK97 terminase and is essential for phage head morphogenesis. HNH proteins are a very common family of proteins generally associated with nuclease activity that are found in all kingdoms of life. We show that the activity of gp74 in terminase-mediated cleavage of the phage cos site relies on the presence of an HNH motif active-site residue, and that the large subunit of HK97 terminase physically interacts with gp74. Bioinformatic analysis reveals that the role of HNH proteins in terminase function is widespread among long-tailed phages and is uniquely required for the activity of the Terminase_1 family of large terminase proteins.bacteriophage HK97 | HNH endonuclease | molecular chaperone

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Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease

Cited by 37 publications

References 75 publications

The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins

The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins

Staphylococcal pathogenicity island DNA packaging system involving cos -site packaging and phage-encoded HNH endonucleases

HNH proteins are a widespread component of phage DNA packaging machines

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