Unusual Target Site Disruption by the Rare-Cutting HNH Restriction Endonuclease PacI

Shen, Betty; Heiter, Daniel F.; Chan, Siu-Hong; Wang, Hua; Xu, Shuang-yong; Morgan, Richard D.; Wilson, Geoffrey G.; Stoddard, Barry

doi:10.1016/j.str.2010.03.009

Cited by 41 publications

(63 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Examples of this group of enzymes are the N 6 -adenine MTases Dam and CcrM (cell cycle-regulated MTase) and the C-5-cytosine MTase Dcm (17)(18)(19). Interestingly, unlike the vast majority of REases, which are accompanied by MTases to protect the genomic DNA from selfdigestion, some of the rare-cutting REases, viz., R.PacI and R.PmeI, seem to be solitary enzymes with no cognate MTase (http: //rebase.neb.com/rebase/rebase.html) (20). It appears that genome protection in these organisms is dependent on the underrepresentation of the recognition sequences in the genome (20).…”

Section: Introductionmentioning

confidence: 99%

“…Interestingly, unlike the vast majority of REases, which are accompanied by MTases to protect the genomic DNA from selfdigestion, some of the rare-cutting REases, viz., R.PacI and R.PmeI, seem to be solitary enzymes with no cognate MTase (http: //rebase.neb.com/rebase/rebase.html) (20). It appears that genome protection in these organisms is dependent on the underrepresentation of the recognition sequences in the genome (20). However, the biological significance of "solitary REases" is not known.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Vasu

Nagaraja

2013

Microbiol Mol Biol Rev

522

462

View full text Add to dashboard Cite

SUMMARY Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Vasu

Nagaraja

2013

Microbiol Mol Biol Rev

522

462

View full text Add to dashboard Cite

show abstract

“…The HNH motif is ∼35 aa long, and is characterized by the presence of two highly conserved His residues and one Asn residue. These HNH motifs, as defined by the large (∼7,400-member) HNH Pfam (11) protein sequence family (PF01844), are often found in proteins that possess endonuclease activity, such as site-specific homing endonucleases (12,13), colicins (14,15), S pyocins (16), and restriction enzymes (17)(18)(19). HNH motifcontaining proteins comprised of primarily an HNH motif as found in E. coli colicins, usually possess nonspecific endonuclease activity.…”

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.

120

106

View full text Add to dashboard Cite

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

show abstract

“…This superfamily includes a number of specific enzymes (e.g. the I-HmuI [76] and I-PpoI [74] group I. homing endonucleases or Eco31I [77] HphI [78], KpnI [79,80], MnlI [81], Hpy99I [82], PacI [83] restriction endonucleases) the RNA guided Cas9 nuclease [84,85] and nonspecific enzymes (e.g. Nuclease A [86], Serratia nuclease [74], Vvn [87], CAD -caspase-activated DNase [88] and bacterial toxins -colicins [89] and pyocins [90]).…”

Section: Hnh Nucleasesmentioning

confidence: 99%

“…The nucleases such as e.g. the IHmuI HNH homing endonuclease [76], PacI restriction endonuclease [83], T4 endonuclease VII [93], Cas9 nuclease [84,85] contain Mg 2+ in the active site bound to the conserved second asparagine residue from HNN motif (Fig. 1).…”

Section: Structure Of the Hnh Motifmentioning

confidence: 99%

Rescue of the activity of HNH nuclease mutants - towards controlled enzymes for gene therapy

Gyurcsik

2016

CPPS

View full text Add to dashboard Cite

Artificial nucleases are designed for in vivo gene engineering, as the DNA cleavage performed at a specific target site enhances the effectiveness of the cell's DNA repair machinery. The therapeutic potential of the above phenomenon stems from the knowledge that (i) the shifted reading frame can be restored by non-homologous end-joining, or (ii) a DNA of erroneous sequence -causing a genetic disease -can be corrected by homologous recombination in the presence of a suitable DNA template. Besides the advantageous properties of the nowadays applied zinc finger nucleases, TALE nucleases and the CRISPR/Cas9 system, they possess a residual citotoxicity. This is related to offtarget cleavages, which could be prevented by the strict regulation of the enzymes. The studies on enzymes acting naturally in a controlled manner are beneficial to get better insight into their mechanism. Such enzymes or their appropriate domains may be the most promising alternatives to the presently applied ones. As an example, the DNA cleavage of the inactive HNH nuclease mutants is inducible in a multiple way. This property may be used for establishing a control mechanism and thus, in combination with specific DNA-binding domains they are good candidates for the catalytic site of artificial nucleases. Here we collect the results on the properties of the HNH nucleases that allow for their redesign into enzymes with possible therapeutic applications.

show abstract

Unusual Target Site Disruption by the Rare-Cutting HNH Restriction Endonuclease PacI

Cited by 41 publications

References 39 publications

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

HNH proteins are a widespread component of phage DNA packaging machines

Rescue of the activity of HNH nuclease mutants - towards controlled enzymes for gene therapy

Contact Info

Product

Resources

About