Breaking and joining single-stranded DNA: the HUH endonuclease superfamily

Chandler, Michaël; Cruz, Fernando de la; Dyda, Fred; Hickman, A.B.; Moncalián, Gabriel; Ton‐Hoang, Bao

doi:10.1038/nrmicro3067

Cited by 239 publications

(334 citation statements)

References 122 publications

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“…More recently, a group of related elements, ISCR (IS with a "common region") was described (reviewed in references 55 and 56). Although there has been no formal demonstration that these actually transpose, the CR is an orf that resembles the IS91 family HUH Tpases (41). The major feature of ISCR elements is that they are associated with a diverse variety of antibiotic resistance genes and, particularly in the case of Pseudomonas ISCR, with aromatic degradation pathways, both upstream and downstream of the Tpase orf.…”

Section: Is Related To Icementioning

confidence: 99%

“…ASMscience.org/MicrobiolSpectrum IS5 IS903 950-1,150 9 GG Y 1 DDE ISL2 850-1,200 2-3 1 ISH1 900-1,150 8 -GC 1 IS5 1,000-1,500 4 Ga/g 1 IS1031 850-1,050 3 GAa/g 1 IS427 800-1, (41). They are limited to two prokaryotic (IS91 and IS200/ IS605; He et al, this volume) and one eukaryotic (helitron; Thomas and Pritham this volume) TE family.…”

Section: Dedd Transposasesmentioning

confidence: 99%

“…There are two major HUH Tpase families: Y1 and Y2 enzymes (41) according to whether they carry one or two Y residues involved in catalysis. One (Y1) is associated with the IS200/IS605 family.…”

Section: Is With Huh Transposasesmentioning

confidence: 99%

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Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

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Section: Is Related To Icementioning

confidence: 99%

Section: Dedd Transposasesmentioning

confidence: 99%

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Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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“…Thus, relaxases offer a potentially superior alternative to existing methods for protein conjugation to DNA nanostructures, due to their sequence specificity, orthogonality and also their natural capacity to form covalent bonds with standard oligonucleotides. Relaxases belong to the HUH protein superfamily,13 and the three‐dimensional structure of some relaxases is known 14. Their overall shape resembles a left hand, where the β‐sheet “palm” holds the HUH motif (histidine–hydrophobic amino acid–histidine) responsible for metal coordination, and the α‐helix “thumb” contains the catalytic tyrosine.…”

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confidence: 99%

Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases

et al. 2016

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DNA‐binding proteins are promising reagents for the sequence‐specific modification of DNA‐based nanostructures. Here, we investigate the utility of a series of relaxase proteins—TrwC, TraI, and MobA—for nanofunctionalization. Relaxases are involved in the conjugative transfer of plasmids between bacteria, and bind to their DNA target sites via a covalent phosphotyrosine linkage. We study the binding of the relaxases to two standard DNA origami structures—rodlike six‐helix bundles and flat rectangular origami sheets. We find highly orthogonal binding of the proteins with binding yields of 40–50 % per binding site, which is comparable to other functionalization methods. The yields differ for the two origami structures and also depend on the position of the binding sites. Due to their specificity for a single‐stranded DNA target, their orthogonality, and their binding properties, relaxases are a uniquely useful addition to the toolbox available for the modification of DNA nanostructures with proteins.

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“…The requirement of site-specific nicking of the AAVS1 trs site suggests that some of the steps resemble the terminal resolution reaction during AAV DNA replication. This process is a variation of the mechanism used by DNA relaxases during DNA conjugation (20,24,25). The first step in site-specific integration is the assembly of a Rep78/ Rep68-DNA complex guided by the recognition of GCTC repeats through the N-terminal origin-binding domain (OBD).…”

Section: Adeno-associated Virus (Aav)mentioning

confidence: 99%