Interaction of yeast eIF4G with spliceosome components Implications in pre-mRNA processing events

International audienceAs evidenced from mammalian cells the eukaryotic translation initiation factor eIF4G has a putative role in nuclear RNA metabolism. Here we investigate whether this role is conserved in the yeast Saccharomyces cerevisiae. Using a combination of in vitro and in vivo methods, we show that, similar to mammalian eIF4G, yeast eIF4G homologues, Tif4631p and Tif4632p, are present both in the nucleus and the cytoplasm. We show that both eIF4G proteins interact efficiently in vitro with UsnRNP components of the splicing machinery. More specifically, Tif4631p and Tif4632p interact efficiently with U1 snRNA in vitro. In addition, Tif4631p and Tif4632p associate with protein components of the splicing machinery, namely Snu71p and Prp11p. To further delineate these interactions, we map the regions of Tif4631p and Tif4632p that are important for the interaction with Prp11p and Snu71p and we show that addition of these regions to splicing reactions in vitro has a dominant inhibitory effect. The observed interactions implicate eIF4G in aspects of pre-mRNA processing. In support of this hypothesis, deletion of one of the eIF4G isoforms results in accumulation of un-spliced precursors for a number of endogenous genes, in vivo. In conclusion these observations are suggestive of the involvement of yeast eIF4G in pre-mRNA metabolism

Resampling-based confidence regions and multiple tests for a correlated random vector

We derive non-asymptotic confidence regions for the mean of a random vector whose coordinates have an unknown dependence structure. The random vector is supposed to be either Gaussian or to have a symmetric bounded distribution, and we observe $n$ i.i.d copies of it. The confidence regions are built using a data-dependent threshold based on a weighted bootstrap procedure. We consider two approaches, the first based on a concentration approach and the second on a direct boostrapped quantile approach. The first one allows to deal with a very large class of resampling weights while our results for the second are restricted to Rademacher weights. However, the second method seems more accurate in practice. Our results are motivated by multiple testing problems, and we show on simulations that our procedures are better than the Bonferroni procedure (union bound) as soon as the observed vector has sufficiently correlated coordinates.Comment: submitted to COL

Marine benthic flora and fauna of Gourdon Bay and the Dampier Peninsula in the Kimberley region of North-Western Australia

Surveys undertaken to characterise the marine benthic habitats along the Dampier Peninsula and further south at Gourdon Bay in the Kimberley region of Western Australia were augmented with epibenthic sled sampling of soft and hard bottom habitats. This paper describes the species collected, their biomass and relative abundance for the main groups of marine macrophytes and invertebrates. Five localities were surveyed; Gourdon Bay, Quondong Point to Coulomb Point, Carnot Bay to Beagle Bay, Perpendicular Head and Packer Island. Sampling was limited to fifteen epibenthic dredge operations from a range of habitat types and was designed to target the most common habitat types and to obtain species identifications of the most important species and those which typified different habitat types. Surveys covered a total of 1,350 m 2 of seabed in depths between 11 and 23m. We identified 415 taxa comprising: 1 seagrass, 43 algae, 52 sponges, 30 ascidians, 10 hydroids, 14 scleractinian corals, 52 other cnidarians, 69 crustaceans, 73 molluscs and 71 echinoderms. Despite the limited nature of the sampling, a significant number of new species, range extensions and new records for Western Australia and Australia were recorded. Within the algae, one range extension (Halimeda cf. cuneata f. digitata not previously recorded in Western Australia) and one possible new species of Areschougia were recorded. Two range extensions were present in the ascidians; the solitary ascidian Polycarpa cf. intonata has previously only been recorded in Queensland and Cnemidocarpa cf. radicosa only in temperate Australian waters. There were several range extensions for the crustacea, for example, the sponge crab, Tumidodromia dormia, has only been recorded in Queensland. One species of holothurian of the genus Phyllophorus could not be identified from the literature available and may represent a new species. Similarly, a small species of the echinoid Gymnechinus could possibly be a new species. The collections of hydroids, hard corals, crinoids and molluscs contained no new species or range extensions. There was difficulty in identification of some groups to species level due to the status of the current taxonomic literature (e.g. Cnidaria, Porifera and ascidians) and there may be a number of new species among the material collected. Among the anthozoa, there is at least one new species of Chromonephthea and potentially 10 range extensions to Western Australia. Sinularia cf. acuta and Chromonephthea curvata are both new records for Australia with both previously recorded in Indonesia only. Among the better known taxa (e.g. molluscs, echinoderms, corals), most of the taxa identified to species level have been recorded to occur throughout north-western Australia, however the diversity recorded in this study is less than other parts of the Kimberley and this is almost certainly a result of the small overall area sampled and the single method of collection utilised. The most important species on soft bottom habitats in terms of biomass was the heart urchin Breynia desorii (up to 326 g.m -2). Sponges were the dominant fauna by biomass (up to 620 g.m -2) on hard bottom habitats and biomass was dominated a by a few large cup and massive sponge species (e.g. Pione velans and two unidentified Spheciospongia). The biomass of other filter feeders, especially ascidians (e.g. Aplidium cf. crateriferum), soft corals (e.g. Chromonephthea spp.), gorgonians (e.g. Junceella fragilis and Dichotella gemmacea) was also high, indicating the importance of these groups in characterising hard bottom habitats. Although low in biomass, crinoids such as Comaster multifidus and Comatula pectinata were abundant in samples that included a high biomass of other filter feeders

New species and new records of sponge-inhabiting barnacles (Cirripedia, balanidae, acastinae) from Australia

The subfamily Acastinae contains a diverse group of barnacles that are obligate symbionts of sponges and alcyonacean and antipatharian corals. Integrating morphological and genetic (COI) data to compare against known species, this paper reports on nine species of sponge-inhabiting barnacles of the subfamily Acastinae, including three undescribed species (Acasta caveata sp. nov., Euacasta acutaflava sp. nov., and E. excoriatrix sp. nov.) and three species previously not recorded in Australian waters (A. sandwichi, Pectinoacasta cancellorum, and P. sculpturata). The new species are distinguished from similar species by a suite of morphological characters as well as genetic distances. A lectotype for Pectinoacasta cancellorum is designated. Sponge hosts were identified for all specimens where possible and are represented by 19 species from eight families and five orders

Interaction of eukaryotic translation initiation factor 4G with the nuclear cap-binding complex provides a link between nuclear and cytoplasmic functions of the m7 guanosine cap

In eukaryotes the majority of mRNAs have an m7G cap that is added cotranscriptionally and that plays an important role in many aspects of mRNA metabolism. The nuclear cap-binding complex (CBC; consisting of CBP20 and CBP80) mediates the stimulatory functions of the cap in pre-mRNA splicing, 3' end formation, and U snRNA export. As little is known about how nuclear CBC mediates the effects of the cap in higher eukaryotes, we have characterized proteins that interact with CBC in HeLa cell nuclear extracts as potential mediators of its function. Using cross-linking and coimmunoprecipitation, we show that eukaryotic translation initiation factor 4G (eIF4G), in addition to its function in the cytoplasm, is a nuclear CBC-interacting protein. We demonstrate that eIF4G interacts with CBC in vitro and that, in addition to its cytoplasmic localization, there is a significant nuclear pool of eIF4G in mammalian cells in vivo. Immunoprecipitation experiments suggest that, in contrast to the cytoplasmic pool, much of the nuclear eIF4G is not associated with eIF4E (translation cap binding protein of eIF4F) but is associated with CBC. While eIF4G stably associates with spliceosomes in vitro and shows close association with spliceosomal snRNPs and splicing factors in vivo, depletion studies show that it does not participate directly in the splicing reaction. Taken together the data indicate that nuclear eIF4G may be recruited to pre-mRNAs via its interaction with CBC and accompanies the mRNA to the cytoplasm, facilitating the switching of CBC for eIF4F. This may provide a mechanism to couple nuclear and cytoplasmic functions of the mRNA cap structure

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. Thus, we suggest that a date/party dichotomy is not meaningful and it might be more useful to conceive of roles for protein-protein interactions rather than individual proteins. We find significant correlations between interaction centrality and the functional similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure

Activation of TRPV2 and BKCa channels by the LL-37 enantiomers stimulates calcium entry and migration of cancer cells.

International audienceExpression of the antimicrobial peptide hCAP18/LL-37 is associated to malignancy in various cancer forms, stimulating cell migration and metastasis. We report that LL-37 induces migration of three cancer cell lines by activating the TRPV2 calcium-permeable channel and recruiting it to pseudopodia through activation of the PI3K/AKT pathway. Ca2+ entry through TRPV2 cooperated with a K+ efflux through the BKCa channel. In a panel of human breast tumors, the expression of TRPV2 and LL-37 was found to be positively correlated. The D-enantiomer of LL-37 showed identical effects as the L-peptide, suggesting that no binding to a specific receptor was involved. LL-37 attached to caveolae and pseudopodia membranes and decreased membrane fluidity, suggesting that a modification of the physical properties of the lipid membrane bilayer was the underlying mechanism of its effects

Rhomboid family member 2 regulates cytoskeletal stress-associated Keratin 16.

Keratin 16 (K16) is a cytoskeletal scaffolding protein highly expressed at pressure-bearing sites of the mammalian footpad. It can be induced in hyperproliferative states such as wound healing, inflammation and cancer. Here we show that the inactive rhomboid protease RHBDF2 (iRHOM2) regulates thickening of the footpad epidermis through its interaction with K16. K16 expression is absent in the thinned footpads of irhom2-/- mice compared with irhom2+/+mice, due to reduced keratinocyte proliferation. Gain-of-function mutations in iRHOM2 underlie Tylosis with oesophageal cancer (TOC), characterized by palmoplantar thickening, upregulate K16 with robust downregulation of its type II keratin binding partner, K6. By orchestrating the remodelling and turnover of K16, and uncoupling it from K6, iRHOM2 regulates the epithelial response to physical stress. These findings contribute to our understanding of the molecular mechanisms underlying hyperproliferation of the palmoplantar epidermis in both physiological and disease states, and how this 'stress' keratin is regulated