Use of mariner transposases for one-step delivery and integration of DNA in prokaryotes and eukaryotes by transfection.

Delivery of DNA to cells and its subsequent integration into the host genome is a fundamental task in molecular biology, biotechnology and gene therapy. Here we describe an IP-free one-step method that enables stable genome integration into either prokaryotic or eukaryotic cells. A synthetic mariner transposon is generated by flanking a DNA sequence with short inverted repeats.

Design and synthesis of novel prostaglandin E ethanolamide and glycerol ester probes for the putative prostamide receptor(s).

Novel prostaglandin-ethanolamide (PGE-EA) and glycerol ester (2-PGE-G) analogs were designed and synthesized to aid in the characterization of a putative prostamide receptor. Our design incorporates the electrophilic isothiocyanato and the photoactivatable azido groups at the terminal tail position of the prototype. Stereoselective Wittig and Horner-Wadsworth-Emmons reactions install the head and the tail moieties of the PGE skeleton.

Novel tail and head group prostamide probes.

We report the design and synthesis of novel prostaglandin-ethanolamide (PGE2-EA) analogs containing head and tail group modifications to aid in the characterization of a putative prostamide receptor(s). Our synthetic approach utilizes Horner-Wadsworth-Emmons and Wittig reactions to construct the head and the tail moieties of the key PGE2 precursor, which leads to the final products through a peptide coupling, Swern oxidation and HF/pyridine assisted desilylation. The synthesized analogs were shown not to interact significantly with endocannabinoid proteins and recombinant EP1, EP3 and EP4 receptors and suggest a yet to be identified prostamide receptor as their site(s) of action.

Efficient meltwater drainage through supraglacial streams and rivers on the southwest Greenland ice sheet.

Thermally incised meltwater channels that flow each summer across melt-prone surfaces of the Greenland ice sheet have received little direct study. We use high-resolution WorldView-1/2 satellite mapping and in situ measurements to characterize supraglacial water storage, drainage pattern, and discharge across 6,812 km(2) of southwest Greenland in July 2012, after a record melt event. Efficient surface drainage was routed through 523 high-order stream/river channel networks, all of which terminated in moulins before reaching the ice edge.

Biochemical characterization and comparison of two closely related active mariner transposases.

Most DNA transposons move from one genomic location to another by a cut-and-paste mechanism and are useful tools for genomic manipulations. Short inverted repeat (IR) DNA sequences marking each end of the transposon are recognized by a DNA transposase (encoded by the transposon itself). This enzyme cleaves the transposon ends and integrates them at a new genomic location.

Retrotransposons.

June 27, 1970 was a significant day for our understanding of both the flow of information in biological systems and the evolution of eukaryotic genomes as this was the day that Nature published back-to-back papers reporting the discovery of an enzyme that copies RNA into DNA. This soon became known as reverse transcriptase and the RNA tumour viruses in which it was detected were renamed retroviruses. The realisation that retroviruses can convert their genomic RNA into DNA provided a route by which they could integrate into the chromosomes of infected cells as Howard Temin and his colleagues had proposed some years earlier.

RNA:RNA interaction can enhance RNA localization in Drosophila oocytes.

RNA localization is a key mechanism for targeting proteins to particular subcellular domains. Sequences necessary and sufficient for localization have been identified, but little is known about factors that affect its kinetics. Transcripts of gurken and the I factor, a non-LTR retrotransposon, colocalize at the nucleus in the dorso-antero corner of the Drosophila oocyte directed by localization signals, the GLS and ILS.

Oogenesis: active heterochromatin.

The genome of Drosophila is protected from DNA damage during oogenesis by a mechanism involving short RNAs. Surprisingly transcription of these RNAs requires that their DNA is associated with a histone modification usually associated with gene silencing.

Formation of polycyclic lactones through a ruthenium-catalyzed ring-closing metathesis/hetero-Pauson-Khand reaction sequence.

Processes that form multiple carbon-carbon bonds in one operation can generate molecular complexity quickly and therefore be used to shorten syntheses of desirable molecules. We selected the hetero-Pauson-Khand (HPK) cycloaddition and ring-closing metathesis (RCM) as two unique carbon-carbon bond-forming reactions that could be united in a tandem ruthenium-catalyzed process. In doing so, complex polycyclic products can be obtained in one reaction vessel from acyclic precursors using a single ruthenium additive that can catalyze sequentially two mechanistically distinct transformations.

Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote.

A key step in cut-and-paste DNA transposition is the pairing of transposon ends before the element is excised and inserted at a new site in its host genome. Crystallographic analyses of the paired-end complex (PEC) formed from precleaved transposon ends and the transposase of the eukaryotic element Mos1 reveals two parallel ends bound to a dimeric enzyme. The complex has a trans arrangement, with each transposon end recognized by the DNA binding region of one transposase monomer and by the active site of the other monomer.

Genome dynamics: transposition and the single cell.

Ciliate development requires assembly of functional genes from segments separated by intervening sequences now shown to have properties of transposons. This may be a relic of a time when transposition drove genome evolution, leading to the differentiation of the germline micronucleus and somatic macronucleus.

A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons.

mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein-dependent transport of gurken/TGF-alpha mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein.

RNA interference: endogenous siRNAs derived from transposable elements.

The Piwi-interacting RNA interference pathway plays an important role in suppressing transposable elements in the Drosophila germline. Now, deep sequencing of short RNAs from somatic tissue and cell culture has identified a novel class of endogenous siRNAs that may have a similar role in the soma.

Molecular dissection of Penelope transposable element regulatory machinery.

Penelope-like elements (PLEs) represent a new class of retroelements identified in more than 80 species belonging to at least 10 animal phyla. Penelope isolated from Drosophila virilis is the only known transpositionally active representative of this class. Although the size and structure of the Penelope major transcript has been previously described in both D.

Crystallization of a Mos1 transposase-inverted-repeat DNA complex: biochemical and preliminary crystallographic analyses.

A complex formed between Mos1 transposase and its inverted-repeat DNA has been crystallized. The crystals diffract to 3.25 A resolution and exhibit monoclinic (P2(1)) symmetry, with unit-cell parameters a = 120.

Live imaging of Drosophila gonad formation reveals roles for Six4 in regulating germline and somatic cell migration.

Background: Movement of cells, either as amoeboid individuals or in organised groups, is a key feature of organ formation. Both modes of migration occur during Drosophila embryonic gonad development, which therefore provides a paradigm for understanding the contribution of these processes to organ morphogenesis. Gonads of Drosophila are formed from three distinct cell types: primordial germ cells (PGCs), somatic gonadal precursors (SGPs), and in males, male-specific somatic gonadal precursors (msSGPs).

Preparation of aliphatic ketones through a ruthenium-catalyzed tandem cross-metathesis/allylic alcohol isomerization.

Grubbs' 2nd generation and Hoveyda-Grubbs' ruthenium alkylidenes are shown to be effective catalysts for cross-metatheses of allylic alcohols with cyclic and acyclic olefins, as well as isomerization of the resulting allylic alcohols to alkyl ketones. The net result of this new tandem methodology is a single-flask process that provides highly functionalized, ketone-containing products from simple allylic alcohol precursors. [reaction: see text]

D-six4 plays a key role in patterning cell identities deriving from the Drosophila mesoderm.

Patterning of the Drosophila embryonic mesoderm requires the regulation of cell type-specific factors in response to dorsoventral and anteroposterior axis information. For the dorsoventral axis, the homeodomain gene, tinman, is a key patterning mediator for dorsal mesodermal fates like the heart. However, equivalent mediators for more ventral fates are unknown.

Mechanism of Mos1 transposition: insights from structural analysis.

We present the crystal structure of the catalytic domain of Mos1 transposase, a member of the Tc1/mariner family of transposases. The structure comprises an RNase H-like core, bringing together an aspartic acid triad to form the active site, capped by N- and C-terminal alpha-helices. We have solved structures with either one Mg2+ or two Mn2+ ions in the active site, consistent with a two-metal mechanism for catalysis.

gurken and the I factor retrotransposon RNAs share common localization signals and machinery.

Drosophila gurken mRNA is localized by dynein-mediated transport to a crescent near the oocyte nucleus, thus targeting the TGFalpha signal and forming the primary embryonic axes. Here, we show that gurken and the I factor, a non-LTR retrotransposon, share a small consensus RNA stem loop of defined secondary structure, which forms a conserved signal for dynein-mediated RNA transport to the oocyte nucleus. Furthermore, gurken and the I factor compete in vivo for the same localization machinery.

Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.

Penelope-like elements are a class of retroelement that have now been identified in >50 species belonging to at least 10 animal phyla. The Penelope element isolated from Drosophila virilis is the only transpositionally active representative of this class isolated so far. The single ORF of Penelope and its relatives contains regions homologous to a reverse transcriptase of atypical structure and to the GIY-YIG, or Uri, an endonuclease (EN) domain not previously found in retroelements.

Expression, purification and preliminary crystallographic studies of a single-point mutant of Mos1 mariner transposase.

A soluble single-point mutant of full-length Mos1 mariner transposase (MW = 40.7 kDa) has been overexpressed in Escherichia coli, purified to 95% homogeneity and crystallized. This provides the first example of the crystallization of a eukaryotic transposase.

Excision of the Drosophila mariner transposon Mos1. Comparison with bacterial transposition and V(D)J recombination.

It has been proposed that the modern immune system has evolved from a transposon in an ancient vertebrate. While much is known about the mechanism by which bacterial transposable elements catalyze double-strand breaks at their ends, less is known about how eukaryotic transposable elements carry out these reactions. We have examined the mechanism by which mariner, a eukaryotic transposable element, performs DNA cleavage.