In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to <it>Plasmodium falciparum </it>infection. During its complex life cycle in the Anopheles vector and human host, the parasite requires the coordinated and modulated expression of diverse sets of genes involved in epigenetic, transcriptional and post-transcriptional regulation. However, despite the availability of the complete sequence of the <it>Plasmodium falciparum </it>genome, we are still quite ignorant about <it>Plasmodium </it>mechanisms of transcriptional gene regulation. This is due to the poor prediction of nuclear proteins, cognate DNA motifs and structures involved in transcription.</p> <p>Results</p> <p>A comprehensive directory of proteins reported to be potentially involved in <it>Plasmodium </it>transcriptional machinery was built from all <it>in silico </it>reports and databanks. The transcription-associated proteins were clustered in three main sets of factors: general transcription factors, chromatin-related proteins (structuring, remodelling and histone modifying enzymes), and specific transcription factors. Only a few of these factors have been molecularly analysed. Furthermore, from transcriptome and proteome data we modelled expression patterns of transcripts and corresponding proteins during the intra-erythrocytic cycle. Finally, an interactome of these proteins based either on <it>in silico </it>or on 2-yeast-hybrid experimental approaches is discussed.</p> <p>Conclusion</p> <p>This is the first attempt to build a comprehensive directory of potential transcription-associated proteins in <it>Plasmodium</it>. In addition, all complete transcriptome, proteome and interactome raw data were re-analysed, compared and discussed for a better comprehension of the complex biological processes of <it>Plasmodium falciparum </it>transcriptional regulation during the erythrocytic development.</p

A natural antisense RNA derived from the HIV-1 env gene encodes a protein which is recognized by circulating antibodies of HIV+ individuals

AbstractA naturally occurring antisense RNA, transcribed in the opposite direction and complementary to the envelope transcript,was identified in various cell lines chronically infected with HIV-1. In T cells, the antisense transcript is constitutively expressed and enhanced by activation with phorbol myristate acetate. The open reading frame corresponding to the antisense transcript, when expressed in vitro, encodes a protein with an apparent molecular mass of 19 kDa. Antibodies against this protein have been detected in several sera of HIV+ individuals and not in any of the noninfected control sera. These results indicate, for the first time, that expression of an antisense open reading frame most likely accompanies the HIV infection cycle in humans

Detection, characterization and regulation of antisense transcripts in HIV-1

© 2007 Landry et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Temperature Shift and Host Cell Contact Up-Regulate Sporozoite Expression of Plasmodium falciparum Genes Involved in Hepatocyte Infection

Plasmodium sporozoites are deposited in the skin by Anopheles mosquitoes. They then find their way to the liver, where they specifically invade hepatocytes in which they develop to yield merozoites infective to red blood cells. Relatively little is known of the molecular interactions during these initial obligatory phases of the infection. Recent data suggested that many of the inoculated sporozoites invade hepatocytes an hour or more after the infective bite. We hypothesised that this pre-invasive period in the mammalian host prepares sporozoites for successful hepatocyte infection. Therefore, the genes whose expression becomes modified prior to hepatocyte invasion would be those likely to code for proteins implicated in the subsequent events of invasion and development. We have used P. falciparum sporozoites and their natural host cells, primary human hepatocytes, in in vitro co-culture system as a model for the pre-invasive period. We first established that under co-culture conditions, sporozoites maintain infectivity for an hour or more, in contrast to a drastic loss in infectivity when hepatocytes were not included. Thus, a differential transcriptome of salivary gland sporozoites versus sporozoites co-cultured with hepatocytes was established using a pan-genomic P. falciparum microarray. The expression of 532 genes was found to have been up-regulated following co-culture. A fifth of these genes had no orthologues in the genomes of Plasmodium species used in rodent models of malaria. Quantitative RT-PCR analysis of a selection of 21 genes confirmed the reliability of the microarray data. Time-course analysis further indicated two patterns of up-regulation following sporozoite co-culture, one transient and the other sustained, suggesting roles in hepatocyte invasion and liver stage development, respectively. This was supported by functional studies of four hitherto uncharacterized proteins of which two were shown to be sporozoite surface proteins involved in hepatocyte invasion, while the other two were predominantly expressed during hepatic parasite development. The genome-wide up-regulation of expression observed supports the hypothesis that the shift from the mosquito to the mammalian host contributes to activate quiescent salivary gland sporozoites into a state of readiness for the hepatic stages. Functional studies on four of the up-regulated genes validated our approach as one means to determine the repertoire of proteins implicated during the early events of the Plasmodium infection, and in this case that of P. falciparum, the species responsible for the severest forms of malaria

Etude de la régulation transcriptionnelle des gènes lors du cycle érythrocytaire de Plasmodium falciparum (implication des acteurs de la régulation transcriptionnelle dans les évènements clefs du cycle érythrocytaire)

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Do natural antisense transcripts make sense in eukaryotes?

International audienceThe existence of naturally occurring antisense RNAs has been illustrated, in eukaryotes, by an increasing number of reports. The following review presents the major findings in this field, with a special focus on the regulation of gene expression exerted by endogenous complementary transcripts. A large variety of eukaryotic organisms, contains antisense transcripts. Moreover, the great diversity of genetic loci encoding overlapping sense and antisense RNAs suggests that such transcripts may be involved in numerous biological functions, such as control of development, adaptative response, viral infection. The regulation of gene expression by endogenous antisense RNAs seems of general importance in eukaryotes as already established in prokaryotes: it is likely to be involved in the control of various biological functions and to play a role in the development of pathological situations. Several experimental evidences for coupled, balanced or unbalanced expression of sense and antisense RNAs suggest that antisense transcripts may govern the expression of their sense counterparts. Furthermore, documented examples indicate that this control may be exerted at many levels of gene expression (transcription, maturation, transport, stability and translation). This review also addresses the underlying molecular mechanisms of antisense regulation and presents the current mechanistic hypotheses

Etude de l'implication des facteurs High Mobility Group Box de Plasmodium dans l'établissement du neuropaludisme à l'aide d'un modèle expérimental murin

L une des caractéristiques du neuropaludisme (NP), complication mortelle d une infection à P. falciparum, est la production de cytokines pro-inflammatoires. Les protéines nucléaires High Mobility Group B (HMGB), très conservées chez les mammifères, sont caractérisées par une double vie de facteurs architecturaux impliqués dans la régulation transcriptionnelle et de cytokines pro-inflammatoires. Deux facteurs HMGB annotés chez P. falciparum par le groupe, possèdent les fonctions nucléaires des HMGB de mammifères et sont des facteurs potentiels d activation des monocytes/macrophages. Pour étudier leur rôle dans le NP, plusieurs approches expérimentales ont été menées à l aide de modèles murins d étude du NP expérimental (NPE). L immunisation par PbHMGB1 de souris C57BL/6, sensibles au NPE, infectées par P. berghei ANKA diminue l inflammation dans le cerveau, ayant pour conséquence la survie des souris. L inactivation du gène pbhmgb2 chez PbANKA diminue l incidence du NPE chez les C57BL/6, conséquence de la diminution de la sévérité des lésions cérébrales et de l inflammation. La primo-infection de C57BL/6 par PbNK65 KOhmgb2 protège les souris contre la réinfection par les deux souches sauvage PbNK65 et PbANKA. Enfin, l administration des protéines PbHMGB1/-B2 à des BALB/c (résistantes au NPE) infectées par PbANKA induit la mort de celles-ci par NPE et, l administration de PbHMGB2 à des C57BL/6 infectées par PbANKA KOhmgb2 rétablit l incidence du NPE. Par ces approches, nous avons montré l implication des facteurs HMGB de Plasmodium dans le NPE, qui pourraient servir de cibles thérapeutiques pour l élaboration de nouvelles stratégies de lutte contre le NP.PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes

Abstract Background With the availability of complete genome sequences of both human and non-human Plasmodium parasites, it is now possible to use comparative genomics to look for orthology across Plasmodium species and for species specific genes. This comparative analyses could provide important clues for the development of new strategies to prevent and treat malaria in humans, however, the number of functionally annotated proteins is still low for all Plasmodium species. In the context of genomes that are hard to annotate because of sequence divergence, such as Plasmodium, domain co-occurrence becomes particularly important to trust predictions. In particular, domain architecture prediction can be used to improve the performance of existing annotation methods since homologous proteins might share their architectural context. Results Plasmobase is a unique database designed for the comparative study of Plasmodium genomes. Domain architecture reconstruction in Plasmobase relies on DAMA, the state-of-the-art method in architecture prediction, while domain annotation is realised with CLADE, a novel annotation tool based on a multi-source strategy. Plasmobase significantly increases the Pfam domain coverage of all Plasmodium genomes, it proposes new domain architectures as well as new domain families that have never been reported before for these genomes. It proposes a visualization of domain architectures and allows for an easy comparison among architectures within Plasmodium species and with other species, described in UniProt. Conclusions Plasmobase is a valuable new resource for domain annotation in Plasmodium genomes. Its graphical presentation of protein sequences, based on domain architectures, will hopefully be of interest for comparative genomic studies. It should help to discover species-specific genes, possibly underlying important phenotypic differences between parasites, and orthologous gene families for deciphering the biology of these complex and important Apicomplexan organisms. In conclusion, Plasmobase is a flexible and rich site where any biologist can find something of his/her own interest. Availability Plasmobase is accessible at http://genome.lcqb.upmc.fr/plasmobase/

Real-Time Study of Interactions between a Composite DNA Regulatory Region (HIV-1 LTR NRE) and Several Transcription Factors of Nuclear Extracts

International audienceHere we describe the first real-time study of nuclear protein interaction with a composite DNA regulatory region. We studied the interplay between the three target sites of the negative regulatory element (NRE) of HIV-1 LTR, comprising a noncanonical GATA site overlapping two negative regulatory regions, USF and NFIL-6, and their corresponding transcription factors in nuclear extracts. By bandshift analysis, no GATA binding activity could be detected between LTR NRE and different nuclear extracts, although evidenced by in vitro footprinting. Additionally, the LTR NRE and a USF oligonucleotide showed identical retarded complexes. BIAcore study of these interactions revealed the binding of huGATA-3, as well as USF, to the immobilized LTR NRE oligonucleotide. Competition analyses , performed with GATA, USF, and NFIL-6 oligonu-cleotides, clearly showed that this regulatory region could bind both huGATA-3 and USF factors. Finally, the presence of USF and huGATA-3 proteins in the complexes formed with LTR NRE was ascertained using specific anti-huGATA-3 and anti-USF2 polyclonal antibodies