Transposition of ISHp608, member of an unusual family of bacterial insertion sequences

Ton‐Hoang, Bao; Guynet, Catherine; Ronning, Donald R.; Cointin-Marty, Brigitte; Dyda, Fred; Chandler, Michaël

doi:10.1038/sj.emboj.7600787

Cited by 74 publications

(118 citation statements)

References 39 publications

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“…The IS200/IS605 family (242-244) (He et al, this volume) is divided into three major groups based on the presence or absence of two reading frames, tnpA (encoding a Y1 Tpase) and tnpB (whose exact role is unknown) (245). The IS200 group includes tnpA only, the IS1341 (246) group carries only tnpB (and as such its status as an autonomous TE remains questionable), while the third group, IS605, carries both tnpA and tnpB.…”

Section: Is200/is605 (I) Generalmentioning

confidence: 99%

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: Is200/is605 (I) Generalmentioning

confidence: 99%

Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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“…Similar to dUTPases, only a single metal ion is involved in the catalytic reaction of several enzymes, such as nucleases with the ββα-Me structural motifs, [71][72] or HUH motifs (where H's denote two histidine residues separated by a hydrophobic residue, U). 69,[73][74] An analogous role of the single metal ion in one-metal ion catalysis has been proposed to metal ion B in two-metal ion catalysis based on structural data. 8 An additional emerging role for metal ion B is to take on a more symmetrical coordination near the transition state region, and thereby to facilitate catalysis.…”

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confidence: 99%

Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction

et al. 2015

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Most enzymes present a catalytic mechanism where one or more proton transfer events occur coupled tightly together with the enzymatic chemical reaction. We show here that inactivating mutations decouple this proton transfer step from the phosphate cleavage reaction in dUTPase. Homotrimeric dUTPase enzymes catalyze the hydrolysis of dUTP to dUMP and pyrophosphate, using largely similar structural and functional groups as most AAA+ enzymes. dUTPases typically use a single Mg 2+ ion as a cofactor in the active site that is formed by direct protein-protein contacts including all three protomers. Here we focus on the C-terminal arm structural motif, which has sequence and functional similarities to P-loop motifs, and is required for catalysis. In this work, we have studied the functional roles of the C-terminal arm in ligand binding and catalysis by using QM/MM (quantum mechanics/molecular mechanics) calculations in conjunction with site-directed mutagenesis experiments. We also present a new method to assess the metal ion coordination symmetry during the catalytic reaction. Using this new implementation, we identified that the coordination symmetry follows a consistent pattern in the three systems studied, reaching the most symmetrical state near the transition states. We found that the phosphate cleavage proceeds with a concerted bimolecular (A N D N ) mechanism with a loose dissociative transition state, and that it is coupled with a proton transfer step involving a unanimously conserved Asp residue. We show that the main mechanistic effect of the lack of the C-terminal arm is to decouple the phosphate cleavage from the subsequent proton transfer step, resulting in a highbarrier altered reaction pathway.

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“…The IS200/IS605 family is widely distributed, with 153 distinct members spread over 45 genera and 61 species of eubacteria and archaea (27). Transposition occurs by exact excision from a single DNA strand (21,(28)(29)(30)(31)(32). Imperfect palindromic sequences flanking the ends of the TE form unique structures that are recognized by transposase protein TnpA, which can act as a homodimer to excise the TE.…”

Section: Significancementioning

confidence: 99%

Real-time transposable element activity in individual live cells

Kim

Lee

Sherer

et al. 2016

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

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The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time. We find that TE activity depends upon the TE's orientation in the genome and the amount of transposase protein in the cell. We also find that TE activity is highly variable throughout the lifetime of the cell. Upon entering stationary phase, TE activity increases in cells hereditarily predisposed to TE activity. These direct observations demonstrate that real-time live-cell imaging of evolution at the molecular and individual event level is a powerful tool for the exploration of genome plasticity in stressed cells.transposable elements | evolution | quantitative biology A transposable element (TE) is a mobile genetic element that propagates within its host genome by self-catalyzed copying or excision followed by genomic reintegration (1). TEs exist in all domains of life, and the activity of TEs necessarily generates mutations in the host genome. Consequently, TEs are major contributors to disease (2-8), development (9, 10), and evolution (11, 12); they are also used as molecular tools in synthetic biology and bioengineering (13).Despite their ubiquity and importance, surprisingly little is known about the behavior and dynamics of TE activity in living cells. TE propagation rates can be inferred from comparative phylogenetic analyses of related organisms (14-20) or endpoint analyses of TE abundance within populations (11,(21)(22)(23). By making assumptions about the mechanisms of TE proliferation, models can be constructed to describe the distribution of TEs within genomes over evolutionary time scales, and sequenced genomes can be analyzed and fit to TE proliferation models to infer phylogeny of TE copies and estimate their rates of propagation (24). However, most sequencing techniques require bulk sampling of cells to provide genetic material, and sequencing is therefore generally an average over many cells. As a result, without extremely deep or single-cell sequencing techniques, most current methods are sufficient to detect only those TE events that have occurred in the germ line and therefore appear in every somatic cell in the body (25).TE rates can also be estimated by measuring relative abundances in populations that have been allowed to mutate over laboratory time scales. One of the first examples of this approach was that by Paquin and Williamson (23) to study the effects of temperature on the rate of integration of Ty retrotransposons in Saccharomyces cerevisiae after growth for 6-8 generations, resulting in yeast re...

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Transposition of ISHp608, member of an unusual family of bacterial insertion sequences

Cited by 74 publications

References 39 publications

Everyman's Guide to Bacterial Insertion Sequences

Everyman's Guide to Bacterial Insertion Sequences

Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction

Real-time transposable element activity in individual live cells

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