Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics

The biosynthesis of CoA from pantothenic acid (vitamin B5) is an essential universal pathway in prokaryotes and eukaryotes. The CoA biosynthetic genes in bacteria have all recently been identified, but their counterparts in humans and other eukaryotes remained mostly unknown. Using comparative genomics, we have identified human genes encoding the last four enzymatic steps in CoA biosynthesis: phosphopantothenoylcysteine synthetase (EC ), phosphopantothenoylcysteine decarboxylase (EC ), phosphopantetheine adenylyltransferase (EC ), and dephospho-CoA kinase (EC ). Biological functions of these human genes were verified using a complementation system in Escherichia coli based on transposon mutagenesis. The individual human enzymes were overexpressed in E. coli and purified, and the corresponding activities were experimentally verified. In addition, the entire pathway from phosphopantothenate to CoA was successfully reconstituted in vitro using a mixture of purified recombinant enzymes. Human recombinant bifunctional phosphopantetheine adenylyltransferase/dephospho-CoA kinase was kinetically characterized. This enzyme was previously suggested as a point of CoA biosynthesis regulation, and we have observed significant differences in mRNA levels of the corresponding human gene in normal and tumor cells by Northern blot analysis.     

Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?

Apicomplexan species constitute a diverse group of parasitic protozoa, which are responsible for a wide range of diseases in many organisms. Despite differences in the diseases they cause, these parasites share an underlying biology, from the genetic controls used to differentiate through the complex parasite life cycle, to the basic biochemical pathways employed for intracellular survival, to the distinctive cell biology necessary for host cell attachment and invasion. Different parasites lend themselves to the study of different aspects of parasite biology: Eimeria for biochemical studies, Toxoplasma for molecular genetic and cell biological investigation, etc. The Plasmodium falciparum Genome Project contributes the first large-scale genomic sequence for an apicomplexan parasite. The Plasmodium Genome Database (http://PlasmoDB.org) has been designed to permit individual investigators to ask their own questions, even prior to formal release of the reference P. falciparum genome sequence. As a case in point, PlasmoDB has been exploited to identify metabolic pathways associated with the apicomplexan plastid, or 'apicoplast' - an essential organelle derived by secondary endosymbiosis of an alga, and retention of the algal plastid.     

MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?

A hallmark of many signaling pathways is the spatial separation of activation and deactivation of signaling proteins. Quantitative analysis demonstrates that the spatial separation of a membrane-bound kinase and a cytosolic phosphatase potentially results in precipitous gradients of target phosphoproteins. Hypothetically, such gradients in the mitogen-activated protein kinase (MAPK) cascade would result in a strong attenuation of the phosphorylation signal towards the nucleus. When effective signal transduction is hampered by slow protein diffusion and rapid dephosphorylation, phosphoprotein trafficking within endocytic vesicles might be an efficient way to propagate the signals. Additional mechanisms facilitating information transfer could involve the assembly of MAP kinases on a scaffolding protein and active transport of signaling complexes by molecular motors. The proposed mechanism explains recent observations that MAPK activation can be strongly suppressed by various inhibitors of endocytosis.     

Injury,inflammation, and remodeling in fetal sheep lung after intra-amniotic endotoxin

Chorioamnionitis is frequent in preterm labor and increases the risk of bronchopulmonary dysplasia. We hypothesized that intra-amniotic endotoxin injures the lung in utero, causing a sequence of inflammation and tissue injury similar to that which occurs in the injured adult lung. Preterm lamb lungs at 125 days gestational age were evaluated for indicators of inflammation, injury, and repair 5 h, 24 h, 72 h, and 7 days after 4 mg of intra-amniotic endotoxin injection. At 5 h, the epithelial cells in large airways expressed heat shock protein 70, and alveolar interleukin-8 was increased. Surfactant protein B (SP-B) decreased in alveolar type II cells at 5 h, and SP-B in lung tissue and alveolar lavage fluid increased by 72 h. By 24 h, neutrophils were recruited into the large airways, and cell death was the highest. Alveolar type II cells decreased by 25% at 24 h, and proliferation was highest at 72 h, consistent with tissue remodeling. Intra-amniotic endotoxin caused surfactant secretion, inflammation, cell death, and remodeling as indications of lung injury. The recovery phase was accompanied by maturational changes in the fetal lung.     

Effects of long duration +2G hypergravity on MHC distribution and maximal tension of rat m.soleus fibers

Effects of long duration hypergravity on skeletal muscles are much less studied than effects of microgravity. For instance, it was revealed that hypergravity of 2 week duration induces decrease in cross sectional area (CSA) of slow fibers (SF), while their size remains constant, or increases. Exposure to +2G of 14 day duration results in decreased number of type I fibers, and in changed myosin heavy chain (MHC) profiles of rat hindlimb extensor muscle. It is interesting that gravitational unloading also decreases number of type I fibers. However, while effects of microgravity on relationship between the structural and functional characteristics of skeletal muscles are studied in detail, similar characteristics of skeletal muscles under conditions of gravitational overloading are very much understudied. The aim of our work was to follow dynamics of MHC in rat m.soleus after exposure to 19 and to 33 days of +2G acceleration, and to compare content of contractile proteins in muscle fibers, and their contractile properties.     

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress

The cellular response to environmental changes includes widespread modifications in gene expression. Here we report the identification and characterization of Rsc9, a member of the RSC chromatin-remodeling complex in yeast. The genome-wide localization of Rsc9 indicated a relationship between genes targeted by Rsc9 and genes regulated by stress; treatment with hydrogen peroxide or rapamycin, which inhibits TOR signaling, resulted in genome-wide changes in Rsc9 occupancy. We further show that Rsc9 is involved in both repression and activation of mRNAs regulated by TOR as well as the synthesis of rRNA. Our results illustrate the response of a chromatin-remodeling factor to signaling cascades and suggest that changes in the activity of chromatin-remodeling factors are reflected in changes in their localization in the genome.     

Response of liver and heart trace elements in rats to the interaction between dietary zinc and iron

An analysis of the interaction between dietary iron (Fe) and zinc (Zn) was performed by using data from Sprague-Dawley rats in a 5 x 4 fully crossed factorially arranged experiment. The concentrations of 9 trace elements from the liver and 10 from the heart were determined and subjected to diverse statistical analyses and were classified by their response to the interaction between dietary Fe and Zn. The interaction was studied by using analysis of variance (ANOVA), discriminant analysis, and logistic regression to determine the direction of interaction; that is, did dietary Fe affect dietary Zn or did dietary Zn affect dietary Fe? The use of discriminant analysis allowed for using multiple parameters (rather than a single parameter) to determine possible interactions between Fe and Zn. Thus, two main levels of interaction were studied: the separate response of each tissue mineral and the response of some grouped minerals. The responses studied were the effect of dietary Zn on tissue trace element parameters, the effect of dietary Fe on the parameters, the effect of dietary Zn on combined (grouped) parameters, and the effect of dietary Fe on combined parameters. As determined by ANOVA, only three individual trace elements--liver Fe, Cu, and Mo--were significantly affected by the interaction between Fe and Zn. However, a broader interaction between Fe and Zn is revealed when groups of, rather than single, trace elements arestudied. For example, an interaction between dietary Fe and Zn affects the weighted linear combination of heart Ca, Cu, K, Mg, Mn, P, and Zn. This article presents the hypothesis that grouped parameters may be useful as status indicators. The complete dataset can be found at http://www.gfhnrc.ars. usda.gov/fezn.     

Bcl-2 rescues the germinal center response but does not alter the V gene somatic hypermutation spectrum in MSH2-deficient mice

Ab V genes in mice deficient for the postreplication mismatch repair factor MutS homolog (MSH2) have been reported to display an abnormal bias for hypermutations at G and C nucleotides and hotspots. We previously showed that the germinal center (GC) response is severely attenuated in MSH2-deficient mice. This suggested that premature death of GC B cells might preclude multiple rounds of hypermutation necessary to generate a normal spectrum of base changes. To test this hypothesis, we created MSH2-deficient mice in which Bcl-2 expression was driven in B cells from a transgene. In such mice, the elevated levels of intra-GC apoptosis and untimely GC dissolution characteristic of MSH2-deficient mice are suppressed. However, the spectrum of hypermutation is unchanged. These data indicate that the effects of MSH2 deficiency on GC B cell viability and the hypermutation process are distinct.     

The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues

The methylation patterns of cytosine and adenine residues in the Arabidopsis thaliana gene for domains rearranged methyltransferase (DRM2) were studied in wild-type and several transgene plant lines containing antisense fragments of the cytosine DNA-methyltransferase gene METI under the control of copper-inducible promoters. It was shown that the promoter region of the DRM2 gene is mostly unmethylated at the internal cytosine residue in CCGG sites whereas the 3'-end proximal part of the gene coding region is highly methylated. The DRM2 gene was found to be also methylated at adenine residues in some GATC sequences. Cytosine methylation in CCGG sites and adenine methylation in GATC sites in the DRM2 gene are variable between wild-type and different transgenic plants. The induction of antisense METI constructs with copper ions in transgene plants in most cases leads to further alterations in the DRM2 gene methylation patterns.