Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.

Differential regulation of gene expression is essential for cell fate specification in metazoans. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step toward understanding complex biological systems. Here we present an in vivo spatiotemporal analysis for approximately 900 predicted C. elegans promoters (approximately 5% of the predicted protein-coding genes), each driving the expression of green fluorescent protein (GFP). Using a flow-cytometer adapted for nematode profiling, we generated 'chronograms', two-dimensional representations of fluorescence intensity along the body axis and throughout development from early larvae to adults. Automated comparison and clustering of the obtained in vivo expression patterns show that genes coexpressed in space and time tend to belong to common functional categories. Moreover, integration of this data set with C. elegans protein-protein interactome data sets enables prediction of anatomical and temporal interaction territories between protein partners.

Changes in the Activity of the Maturation-Promoting Factor Are Correlated with Those of a Major Cyclic AMP and Calcium-Independent Protein Kinase During the First Mitotic Cell Cycles in the Early Starfish Embryo: (cell cycle/maturation-promoting factor/protein kinase/protein synthesis/starfish).

Many studies suggest that MPF activation depends on protein phosphorylation or that MPF is itself a protein kinase. In the present report, cyclic variations of MPF activity have been correlated in vivo with changes in the extent of protein phosphorylation or in vitro with changes of a major protein kinase during the first cell cycles of fertilized starfish eggs. This cycling protein kinase neither requires cAMP nor Ca2+ . Neither colchicine nor aphidicoline, which inhibits cleavage and chromosome replication respectively, was found to suppress the synchronous and cyclic variations of both MPF and protein kinase activities. Protein synthesis was found to be required for both MPF and protein kinase activities to reappear after their simultaneous drop at the time of mitotic or meiotic cleavages. Production of either MPF or protein kinase activities is not the immediate result of protein synthesis since there is a delay at each cell cycle between the time when protein synthesis is required and the time when both MPF and protein kinase activities are produced. This suggests that both MPF and protein kinase activities might involve some post-translational modification of a precursor protein synthesized during the preceeding cell cycle.

The C-terminal domain of Plasmodium falciparum merozoite surface protein 3 self-assembles into alpha-helical coiled coil tetramer.

Proteins located on the surface of the pathogenic malaria parasite Plasmodium falciparum are objects of intensive studies due to their important role in the invasion of human cells and the accessibility to host antibodies thus making these proteins attractive vaccine candidates. One of these proteins, merozoite surface protein 3 (MSP3) represents a leading component among vaccine candidates; however, little is known about its structure and function. Our biophysical studies suggest that the 40 residue C-terminal domain of MSP3 protein self-assembles into a four-stranded alpha-helical coiled coil structure where alpha-helices are packed "side-by-side". A bioinformatics analysis provides an extended list of known and putative proteins from different species of Plasmodium which have such MSP3-like C-terminal domains. This finding allowed us to extend some conclusions of our studies to a larger group of the malaria surface proteins. Possible structural and functional roles of these highly conserved oligomerization domains in the intact merozoite surface proteins are discussed.

Initial activation of cyclin-B1-cdc2 kinase requires phosphorylation of cyclin B1.

At the G(2)/M transition of the cell cycle, the cdc25c phosphatase dephosphorylates inhibitory residues of cdc2, and cyclin-B-cdc2 kinase (MPF) is activated. Phosphorylation of cyclin B1 induces its nuclear accumulation, and, since cdc25c is also believed to accumulate and activate shortly before G(2)/M in the nucleus, it has been proposed that this induces cyclin-B1-cdc2 kinase activation. We demonstrate that cyclin B1 phosphorylation has another essential function in vivo: it is required for cdc25c and MPF activation, which does not require nuclear accumulation of cyclin B1, and occurs in the cytoplasm.

Human ORFeome version 1.1: a platform for reverse proteomics.

The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes. Here, we describe the generation of a first version of the human ORFeome using a newly improved Gateway recombinational cloning approach. Using the Mammalian Gene Collection (MGC) resource as a starting point, we report the successful cloning of 8076 human ORFs, representing at least 7263 human genes, as mini-pools of PCR-amplified products. These were assembled into the human ORFeome version 1.1 (hORFeome v1.1) collection. After assessing the overall quality of this version, we describe the use of hORFeome v1.1 for heterologous protein expression in two different expression systems at proteome scale. The hORFeome v1.1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome.