Protein tyrosine phosphatases in the human genome

Tyrosine phosphorylation is catalyzed by protein tyrosine kinases, which are represented by 90 genes in the human genome. Here, we present the set of 107 genes in the human genome that encode members of the four protein tyrosine phosphatase (PTP) families. The four families of PTPases, their substrates, structure, function, regulation, and the role of these enzymes in human disease will be discussed.     

A model for dynamic regulation of choline acetyltransferase by phosphorylation

Choline acetyltransferase (ChAT) synthesizes the neurotransmitter acetylcholine (ACh) and is a phenotypic marker for cholinergic neurons. Cholinergic neurons in brain are involved in cognitive function, attentional processing and motor control, and decreased ChAT activity is found in several neurological disorders including Alzheimer's disease. Dysregulation of ChAT and cholinergic communication is also associated with some spontaneous point-mutations in ChAT that alter its substrate binding kinetics, or by disruption of signaling pathways that could regulate protein kinases for which ChAT is a substrate. It has been identified recently that the catalytic activity and subcellular distribution of ChAT, and its interaction with other cellular proteins, can be modified by phosphorylation of the enzyme by protein kinase-C and Ca2+/calmodulin-dependent protein kinase II; these kinases appear also to mediate some of the effects of beta-amyloid peptides on cholinergic neuron functions, including the effects on ChAT. This review outlines a new model for the regulation of cholinergic transmission at the level of the presynaptic terminal that is mediated by hierarchically-regulated, multi-site phosphorylation of ChAT.     

Silencing the morphogenesis of rotavirus

The morphogenesis of rotaviruses follows a unique pathway in which immature double-layered particles (DLPs) assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum (ER), acquiring during this process a transient lipid membrane which is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the nonstructural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles (TLPs). In this work, we have characterized the role of NSP4 and VP7 in rotavirus morphogenesis by silencing the expression of both glycoproteins through RNA interference. Silencing the expression of either NSP4 or VP7 reduced the yield of viral progeny by 75 to 80%, although the underlying mechanism of this reduction was different in each case. Blocking the synthesis of NSP4 affected the intracellular accumulation and the cellular distribution of several viral proteins, and little or no virus particles (neither DLPs nor TLPs) were assembled. VP7 silencing, in contrast, did not affect the expression or distribution of other viral proteins, but in its absence, enveloped particles accumulated within the lumen of the ER, and no mature infectious virus was produced. Altogether, these results indicate that during a viral infection, NSP4 serves as a receptor for DLPs on the ER membrane and drives the budding of these particles into the ER lumen, while VP7 is required for removing the lipid envelope during the final step of virus morphogenesis.     

Proteome of Methanosarcina acetivorans Part II: comparison of protein levels in acetate- and methanol-grown cells

Methanosarcina acetivorans is an archaeon isolated from marine sediments which utilizes a diversity of substrates for growth and methanogenesis. Part I of a two-part investigation has profiled proteins of this microorganism cultured with both methanol and acetate as growth substrates, utilizing two-dimensional gel electrophoresis and MALDI-TOF-TOF mass spectrometry. In this report, Part II, the analyses were extended to identify 34 proteins found to be present in different amounts between methanol- and acetate-grown M. acetivorans. Among these proteins are enzymes which function in pathways for methanogenesis from either acetate or methanol. Several of the 34 proteins were determined to have redundant functions based on annotations of the genomic sequence. Enzymes which function in ATP synthesis and steps common to both methanogenic pathways were elevated in acetate- versus methanol-grown cells, whereas enzymes that have a more general function in protein synthesis were in greater amounts in methanol- compared to acetate-grown cells. Several group I chaperonins were present in greater amounts in methanol- versus acetate-grown cells, whereas lower amounts of several stress related proteins were found in methanol- versus acetate-grown cells. The potential physiological basis for these novel patterns of protein synthesis are discussed.     

Continuous fermentation of undetoxified dilute acid lignocellulose hydrolysate by Saccharomyces cerevisiae ATCC 96581 using cell recirculation

Saccharomyces cerevisiae ATCC 96581 was cultivated in a chemostat reactor with undetoxified dilute acid softwood hydrolysate as the only carbon and energy source. The effects of nutrient addition, dilution rate, cell recirculation, and microaerobicity were investigated. Fermentation of unsupplemented dilute acid lignocellulose hydrolysate at D = 0.10 h(-1) in an anaerobic continuous reactor led to washout. Addition of ammonium sulfate or yeast extract was insufficient for obtaining steady state. In contrast, dilute acid lignocellulose hydrolysate supplemented with complete mineral medium, except for the carbon and energy source, was fermentable under anaerobic steady-state conditions at dilution rates up to 0.14 h(-1). Under these conditions, washout occurred at D = 0.15 h(-1). This was preceded by a drop in fermentative capacity and a very high specific ethanol production rate. Growth at all different dilution rates tested resulted in residual sugar in the chemostat. Cell recirculation (90%), achieved by cross-flow filtration, increased the sugar conversion rate from 92% to 99% at D = 0.10 h(-1). Nutrient addition clearly improved the long-term ethanol productivity in the recirculation cultures. Application of microaerobic conditions on the nutrient-supplemented recirculation cultures resulted in a higher production of biomass, a higher cellular protein content, and improved fermentative capacity, which further improves the robustness of fermentation of undetoxified lignocellulose hydrolysate.     

The Human β-Defensin-1 and α-Defensins Are Encoded by Adjacent Genes: Two Peptide Families with Differing Disulfide Topology Share a Common Ancestry

We cloned a novel human β-defensin gene and determined its full-length cDNA sequence. The entire gene spanned more than 7 kb and included a large 6962-bp intron. The 362-bp cDNA encoded a prepropeptide that corresponded precisely to the recently identified human β-defensin HBD-1, an antimicrobial peptide implicated in the resistance of epithelial surfaces to microbial colonization. By two-color fluorescencein situhybridization on both metaphase chromosome and released chromatin fiber, HBD-1 gene (DEFB1 in HUGO/GDB nomenclature) mapped to chromosomal region 8p23.1–p23.2 in close proximity (within 100–150 kb) to the gene for the human neutrophil α-defensin HNP-1 (DEFA1). Thus, despite a complete lack of DNA sequence similarity and despite differences in their disulfide-pairing pattern, the α- and β-families appear to have evolved from a common premammalian defensin gene.     

Biodegradation of polychlorinated biphenyls by plant cells

The PCB biodegradative ability of plant cells cultivated in vitro in media containing a mixture of PCB congeners, Delor 103, is demonstrated. For experiments we used submerged cultures of Armoracia rusticana, Solanum aviculare, Atropa bella-donna, transformed hairy root or embryogenic cultures of Solanum nigrum. Transformation of PCB was followed by gas chromatography after cultivations of the above-mentioned cultures with Delor 103 (10 mg 100 ml⁻¹). The overall PCB metabolizing capability and also degradation of individual congeners greatly differed from strain to strain. The highest capability to metabolize PCB was assayed with differentiated cultures of Solanum nigrum. Beside the capability of PCB degradation, total peroxidase activity in the medium and the cell extract was also followed. Differentiated or hairy root cultures exhibiting higher degradation abilities of PCB also showed increase of peroxidase activities.     

Regulation of S-layer protein synthesis of Bacillus stearothermophilus PV72 through variation of continuous cultivation conditions

The crystalline cell surface layer (S-layer) of Bacillus stearothermophilus PV72 shows hexagonal lattice symmetry and is composed of a single protein species with a molecular weight of 130000. For investigating the regulation of S-layer protein synthesis, Bacillus stearothermophilus PV72 was grown in continuous culture on synthetic PVIII- medium with glucose as carbon source at constant dilution rate of 0.3 h⁻¹ at 57 ° C under different conditions and limitations. A complete outer S-layer and an S-layer protein pool sufficient for formation of about 70% inner S-layer was produced under carbon-limited growth. The inner S-layer results from an S-layer protein pool stored in the peptidoglycan-containing layer of whole cells which can emerge and assemble on the inner face of the rigid cell wall layer during the cell wall preparation procedure. Under oxygen-limited growth, only a complete outer S-layer but no S-layer protein pool was synthesized. Reduction of the methionine concentration of PVIII-medium from 100 to 10 mg l⁻¹ led to a clear decrease in S-layer protein production and to an incomplete outer S-layer. During growth in the presence of excess glucose, S-layer protein synthesis was replaced by that of an exopolysaccharide matrix. After changing to carbon limitation again, the original level of S-layer protein synthesis was achieved after only four volume exchanges. Feeding of casein hydrolysate or aromatic or basic amino acids to the continuous culture induced an irreversible loss of S-layer protein synthesis after from five to ten volume exchanges. In contrast, addition of Gly, Ala, Val, Leu, Ile, Glu, Gln, Asp, Asn, Ser and Thr in different mixtures could significantly stimulate S-layer protein production.