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A subset of nuclear receptor coregulators act as coupling proteins during synthesis and maturation of RNA transcripts

Author(s) : Auboeuf D, Dowhan D, Dutertre M, Martin N, Berget S, O'Malley B,
Journal : Mol Cell Biol

Detection of human immunodeficiency virus type 1 Nef and CD4 physical interaction in living human cells by using bioluminescence resonance energy transfer.

Author(s) : Cluet D, Bertsch C, Beyer C, Gloeckler L, Erhardt M, Gut J, Galzi J, Aubertin A,
Journal : J Virol
CD4 down-regulation by human immunodeficiency virus type 1 (HIV-1) Nef protein is a key function for virus virulence. This activity may be mediated by a direct Nef-CD4 interaction. We investigated the formation, in situ, of such a complex between proteins using bioluminescence resonance energy transfer technology and co-immunoprecipitations. Our data clearly demonstrate that Nef and CD4 interact in intact human cells. Moreover, our results clearly indicate that the dileucinemotif of the CD4 cytoplasmic domain, critical for the Nef-induced CD4 down-regulation, is not implicated in the Nef/CD4 complex formation in the cellular context.

FAST DB: a website resource for the study of the expression regulation of human gene products

Author(s) : de la Grange P, Dutertre M, Martin N, Auboeuf D,
Journal : Nucleic Acids Res

Fate of premalignant clones during the asymptomatic phase preceding lymphoid malignancy

Author(s) : Moul?s V, Pomier C, Sibon D, Gabet A, Reichert M, Kerkhofs P, Willems L, Mortreux F, Wattel E,
Journal : Cancer Res

HPRT mutations, TCR gene rearrangements, and HTLV-1 integration sites define in vivo T-cell clonal lineages

Author(s) : Allegretta M, Ardell S, Sullivan L, Jacobson S, Mortreux F, Wattel E, Albertini R,
Journal : Environ Mol Mutagen

Human papillomavirus type 18 E6 protein binds the cellular PDZ protein TIP-2/GIPC, which is involved in transforming growth factor beta signaling and triggers its degradation by the proteasome.

Author(s) : Favre-Bonvin A, Reynaud C, Kretz-Remy C, Jalinot P,
Journal : J Virol
Several viral proteins expressed by DNA or RNA transforming viruses have the particular property of binding via their C-terminal end to various cellular proteins with PDZ domains. This study is focused on the PDZ protein TIP-2/GIPC, which was originally identified in two-hybrid screens performed with two different baits: the human T-cell leukemia virus type 1 Tax oncoprotein and the regulator of G signaling RGS-GAIP. Further studies have shown that TIP-2/GIPC isalso able to associate with the cytoplasmic domains of various transmembrane proteins. In this report we show that TIP-2/GIPC interacts with the E6 protein of human papillomavirus type 18 (HPV-18). This event triggers polyubiquitination and proteasome-mediated degradation of the cellular protein. In agreement with this observation, silencing of E6 by RNA interference in HeLa cells causes an increase in the intracellular TIP-2/GIPC level. This PDZ protein has been previously found to be involved in transforming growth factor beta (TGF-beta) signaling by favoring expression of the TGF-beta type III receptor at the cell membrane. In line with this activity of TIP-2/GIPC, we observed that depletion of this protein in HeLa cells hampers induction of the Id3 gene by TGF-beta treatment and also diminishes the antiproliferative effect of this cytokine. Conversely, silencing of E6 increases the expression of Id3 and blocks proliferation of HeLa cells. These results support the notion that HPV-18 E6 renders cells less sensitive to the cytostatic effect of TGF-beta by lowering the intracellular amount of TIP-2/GIPC.

Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software.

Author(s) : Soula H, Robardet C, Perrin F, Gripon S, Beslon G, Gandrillon O,
Journal : BMC Bioinformatics
BACKGROUND: There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal. RESULTS: We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. Weobserved that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization ofreal life multi-protein structures. CONCLUSION: The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures.A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells.

Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability.

Author(s) : Loppin B, Lepetit D, Dorus S, Couble P, Karr T,
Journal : Curr Biol
BACKGROUND: Although evolutionary novelty by gene duplication is well established, the origin and maintenance of essential genes that provide entirelynew functions (neofunctionalization) is still largely unknown. Drosophila is a good model for the search of genes that are young enough to allow deciphering the molecular details of their evolutionary history. Recent years have seen increased interest in genes specifically required for male fertility because they often evolve rapidly. A special class of genes affecting male fertility, the paternal effect genes, have also become a focus of study to geneticists and reproductive biologists interested in fertilization and sperm-egg interactions. RESULTS: Using molecular genetics and the annotated Drosophila melanogaster genome, we identified CG14251 as the Drosophila paternal effect gene, ms(3)K81 (K81). This assignment was subsequently confirmed by P-element rescue of K81. A search for orthologous K81 sequences revealed that the distribution of K81 is surprisingly restricted to the 9 species comprising the melanogaster subgroup. Phylogenetic analyses indicate that K81 arose through duplication, most likely retroposition,of a ubiquitously expressed gene before the radiation of the melanogaster subgroup, followed by a period of rapid divergence and acquisition of a criticalmale germline-specific function. Interestingly, K81 has adopted the expression profile of a flanking gene suggesting that transcriptional coregulation may havebeen important in the neofunctionalization of K81. CONCLUSION: We present a detailed case history of the origin and evolution of a new essential gene and, in so doing, provide the first molecular identification of a Drosophila paternal effect gene, ms(3)K81 (K81).

Photoreceptor differentiation in Drosophila: from immature neurons to functional photoreceptors.

Author(s) : Mollereau B, Domingos P,
Journal : Dev Dyn
How a pool of equipotent cells acquires a multitude of distinct fates is a majorquestion in developmental biology. The study of photoreceptor (PR) cell differentiation in Drosophila has been used to address this question. PR differentiation is a process that extends over a period of 5 days: It begins in the larval eye imaginal disc when PRs are recruited and commit to particular PR fates, and it culminates in the pupal eye disc with the morphogenesis of the rhabdomeres and the initiation of rhodopsin expression. Several models for PR specification agree that the Ras and Notch signaling pathways are important for the specification of different PR subtypes (Freeman [1997] Development 124:261-270; Cooper and Bray [2000] Curr. Biol. 10:1507-1510; Tomlinson and Struhl [2001] Mol. Cell. 7:487-495). In the first part of this review, we briefly describe the different signaling pathways and transcription factors required forthe specification and differentiation of the different PR subtypes in the larvaleye disc. In the second part, we review the roles of several transcription factors, which are required for the terminal photoreceptor differentiation and rhodopsin expression.

Reduced cell turnover in lymphocytic monkeys infected by human T-lymphotropic virus type 1

Author(s) : Debacq C, H?raud J, Asquith B, Bangham C, Merien F, Moules V, Mortreux F, Wattel E, Burny A, Kettmann R, Kazanji M, Willems L,
Journal : Oncogene

Role of conformational heterogeneity in domain swapping and adapter function of the Cks proteins.

Author(s) : Seeliger M, Spichty M, Kelly S, Bycroft M, Freund S, Karplus M, Itzhaki L,
Journal : J Biol Chem
Cks proteins are adapter molecules that coordinate the assembly of multiprotein complexes. They share the ability to domain swap by exchanging a beta-strand, beta4. Here we use NMR spectroscopy and molecular dynamics simulations to investigate the dynamic properties of human Cks1 and its response on assembly with components of the SCF(Skp2) ubiquitin ligation machinery. In the NMR experiment with the free form of Cks1, a subset of residues displayed elevated R2 values and the cross-peaks of neighboring residues were missing from the spectrum, indicating a substantial conformational exchange contribution on the microsecond to millisecond time scale. Strikingly the region of greatest conformational variability was the beta4-strand that domain swaps to form the dimer. Binding of the ligand common to all Cks proteins, Cdk2, suppressed the conformational heterogeneity. This response was specific to Cdk2 binding; in contrast, binding of Skp2, a ligand unique to human Cks1, did not alter the dynamic behavior. Short time (<5 ns) molecular dynamics simulations indicate that residues of Cks1 that form the binding site for phosphorylated ligands are considerably more flexible in the free form of Cks1 than they are in the Cdk2-Cks1 complex. A cooperative interaction between Cdk2 and Cks1 is suggested,which reduces the configurational entropy of Cks1 and therefore facilitates phosphoprotein binding. Indications of an unusual dynamic behavior of strand beta4 in the free form of Cks1 were obtained from longer time scale (50 ns) dynamics simulations. A spontaneous reversible unzipping of hydrogen bonds between beta4 and beta2 was observed, suggesting an early intermediate structurefor unfolding and/or domain swapping. We propose that the dynamic properties of the beta-sheet and its modification upon ligand binding underlie the domain swapping ability and the adapter function of Cks proteins.

Serial analysis of gene expression in the silkworm, Bombyx mori.

Author(s) : Huang J, Miao X, Jin W, Couble P, Mita K, Zhang Y, Liu W, Zhuang L, Shen Y, Keime C, Gandrillon O, Brouilly P, Briolay J, Zhao G, Huang Y,
Journal : Genomics
The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmentallife cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, ofwhich 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, andadult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

Silencing of human Int-6 impairs mitosis progression and inhibits cyclin B-Cdk1 activation.

Author(s) : Morris C, Jalinot P,
Journal : Oncogene
The Int-6 protein has been originally identified as the product of a mouse gene being a frequent integration site of the mouse mammary tumour virus. Here, we show that reducing Int-6 expression by RNA interference in HeLa cells markedly alters mitosis progression. Defects in spindle formation, chromosome segregationand cytokinesis were observed. These abnormalities of mitosis completion are correlated with an inhibition of cyclin B-Cdk1 kinase activity, due to a prolonged inhibitory phosphorylated state of Cdk1. In line with this observation, the Wee1 tyrosine kinase that negatively controls Cdk1 was less efficiently inactivated during G2 in Int-6-depleted cells. These findings support the notionthat the oncogenic properties associated with alteration of Int-6 originate fromchromosomal instability.

Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta

Author(s) : Dowhan D, Hong E, Auboeuf D, Dennis A, Wilson M, Berget S, O'Malley B,
Journal : Mol Cell

The histone H3.3 chaperone HIRA is essential for chromatin assembly in the male pronucleus.

Author(s) : Loppin B, Bonnefoy E, Anselme C, Laurencon A, Karr T, Couble P,
Journal : Nature
In sexually reproducing animals, a crucial step in zygote formation is the decondensation of the fertilizing sperm nucleus into a DNA replication-competentmale pronucleus. Genome-wide nucleosome assembly on paternal DNA implies the replacement of sperm chromosomal proteins, such as protamines, by maternally provided histones. This fundamental process is specifically impaired in sesame (ssm), a unique Drosophila maternal effect mutant that prevents male pronucleus formation. Here we show that ssm is a point mutation in the Hira gene, thus demonstrating that the histone chaperone protein HIRA is required for nucleosomeassembly during sperm nucleus decondensation. In vertebrates, HIRA has recently been shown to be critical for a nucleosome assembly pathway independent of DNA synthesis that specifically involves the H3.3 histone variant. We also show thatnucleosomes containing H3.3, and not H3, are specifically assembled in paternal Drosophila chromatin before the first round of DNA replication. The exclusive marking of paternal chromosomes with H3.3 represents a primary epigenetic distinction between parental genomes in the zygote, and underlines an important consequence of the critical and highly specialized function of HIRA at fertilization.

Up-regulation of the ubiquitous alternative splicing factor Tra2beta causes inclusion of a germ cell-specific exon

Author(s) : Venables J, Bourgeois C, Dalgliesh C, Kister L, Stevenin J, Elliott D,
Journal : Hum Mol Genet