An extended panel of single nucleotide polymorphisms in Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis> L.) mitochondrial DNA

A total of 6,324 base pairs, distributed on eight different regions of the mitochondrial DNA (mtDNA) were re-sequenced for 32 specimens of Norwegian farmed and wild Atlantic salmon. A total of 16 new and three previously reported single nucleotide polymorphisms (SNPs) were detected. These SNPs were validated using 240 farm and 119 wild Norwegian salmon. Alignments of sequences obtained in this study and previously published sequences revealed another 15 previously unreported SNPs. The panel of mitochondrial SNPs detected in the present study will, in combination with previously identified SNPs, prove useful in designing efficient assays for analyzes of mtDNA variation.     

A survey of motif discovery methods in an integrated framework

Background  

There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed. Computational motif discovery has been used with some success in simple organisms like yeast. However, as we move to higher organisms with more complex genomes, more sensitive methods are needed. Several recent methods try to integrate additional sources of information, including microarray experiments (gene expression and ChlP-chip). There is also a growing awareness that regulatory elements work in combination, and that this combinatorial behavior must be modeled for successful motif discovery. However, the multitude of methods and approaches makes it difficult to get a good understanding of the current status of the field.     

Molecular basis of AKAP specificity for PKA regulatory subunits

Localization of cyclic AMP (cAMP)-dependent protein kinase (PKA) by A kinase-anchoring proteins (AKAPs) restricts the action of this broad specificity kinase. The high-resolution crystal structures of the docking and dimerization (D/D) domain of the RIIalpha regulatory subunit of PKA both in the apo state and in complex with the high-affinity anchoring peptide AKAP-IS explain the molecular basis for AKAP-regulatory subunit recognition. AKAP-IS folds into an amphipathic alpha helix that engages an essentially preformed shallow groove on the surface of the RII dimer D/D domains. Conserved AKAP aliphatic residues dominate interactions to RII at the predominantly hydrophobic interface, whereas polar residues are important in conferring R subunit isoform specificity. Using a peptide screening approach, we have developed SuperAKAP-IS, a peptide that is 10,000-fold more selective for the RII isoform relative to RI and can be used to assess the impact of PKA isoform-selective anchoring on cAMP-responsive events inside cells.     

Human Regulatory Subunit RIβ of cAMP-Dependent Protein Kinases: Expression, Holoenzyme Formation and Microinjection into Living Cells

The human regulatory subunit RIβ of cAMP-dependent protein kinases was expressed in Escherichia coli as a fusion protein with glutathione S -transferase. Purification was performed by affinity chromatography on glutathione-agarose beads after cleavage with thrombin. The human recombinant Riff protein migrated at 55 kDa on SDS-PAGE and displayed immunoreactivity with an anti-human RIβ antiserum. Furthermore, the purified recombinant RIβ protein was shown to exist as a dimer that was able to form holoenzyme with the catalytic subunit Cα. The rate of RIβ₂Cα₂ holoenzyme formation was faster in the presence than in the absence of MgATP. The kinase activity measured before and after adding cAMP to the holoenzyme showed that the presence of cAMP resulted in holoenzyme dissociation and release of active Cα-subunit, due to cAMP binding to RIβ. Compared to a RIα₂Cα₂ holoenzyme, the RIβ₂Cα₂ holoenzyme exhibited a more than twofold higher sensitivity to cAMP. The subcellular localization of Riff was analyzed in quiescent REF-52 fibroblasts and Wistar rat thyroid (WRT) cells after microinjection of fluorescently labeled proteins into the cytoplasm. A cytoplasmic distribution was observed when free RIβ was injected, whereas free Cα injected into the cytoplasm appeared in the nucleus. When holoenzymes with labeled Riff and unlabeled Cα, or unlabeled RIβ and labeled Cα, were injected, unstimulated cells showed fluorescence in the cytoplasm of both cell types. REF-52 cells stimulated with 8-bromo-cAMP (8-Br-cAMP) and WRT cells treated with thyrotropin (TSH) showed fluorescence mainly in the cytoplasm when RIβ was the labeled subunit of the in vivo dissociated bioenzyme. In contrast, nuclear fluorescence was evident from the release and translocation of labeled Cα from the holoenzyme complex after stimulation with 8-Br-cAMP or TSH.     

Impact of mitochondrial beta-oxidation in fatty acid-mediated inhibition of glioma cell proliferation

Tetradecylthioacetic acid (TTA), which cannot be beta-oxidized, exerts growth-limiting properties in glioma cells. In order to investigate the importance of modulated lipid metabolism and alterations in mitochondrial properties in this cell death process, we incubated glioma cells both with TTA and the oxidizable fatty acid palmitic acid (PA), in the presence of L-carnitine and the carnitine palmitoyltransferase inhibitors etomoxir and aminocarnitine. L-carnitine partly abolished the PA-mediated growth reduction of glioma cells, whereas etomoxir and aminocarnitine enhanced the antiproliferative effect of PA. The production of acid-soluble products increased and the incorporation of PA into glycerolipids decreased after L-carnitine supplementation. L-carnitine was found to enhance the antiproliferative effect of TTA, but did not affect the incorporation of TTA into glycerolipids, or ceramide. PDMP, sphingosine 1-phosphate, desipramine, fumonisin B(1), and L-cycloserine were able not to rescue the glioma cells from PA and TTA-induced growth inhibition, suggesting that increased ceramide production is not important in the growth reduction. TTA-mediated growth inhibition was accompanied with an increased uptake of PA and increased incorporation of PA into triacylglycerol (TG). Our data suggest that mitochondrial functions are involved in fatty acid-mediated growth inhibition. Whether there is a causal relationship between TG accumulation and the apoptotic process remains to be determined.     

Merlin links to the cAMP neuronal signaling pathway by anchoring the RIbeta subunit of protein kinase A

The cAMP-protein kinase A (PKA) pathway, important in neuronal signaling, is regulated by molecules that bind and target PKA regulatory subunits. Of four regulatory subunits, RIbeta is most abundantly expressed in brain. The RIbeta knockout mouse has defects in hippocampal synaptic plasticity, suggesting a role for RIbeta in learning and memory-related functions. Molecules that interact with or regulate RIbeta are still unknown. We identified the neurofibromatosis 2 tumor suppressor protein merlin (schwannomin), a molecule related to the ezrin-radixin-moesin family of membrane-cytoskeleton linker proteins, as a binding partner for RIbeta. Merlin and RIbeta demonstrated a similar expression pattern in central nervous system neurons and an overlapping subcellular localization in cultured hippocampal neurons and transfected cells. The proteins were coprecipitated from brain lysates by cAMP-agarose and coimmunoprecipited from cellular lysates with specific antibodies. In vitro binding studies verified that the interaction is direct. The interaction appeared to be under conformational regulation and was mediated via the alpha-helical region of merlin. Sequence comparison between merlin and known PKA anchoring proteins identified a conserved alpha-helical PKA anchoring protein motif in merlin. These results identify merlin as the first neuronal binding partner for PKA-RIbeta and suggest a novel function for merlin in connecting neuronal cytoskeleton to PKA signaling.     

Dissociating the centrosomal matrix protein AKAP450 from centrioles impairs centriole duplication and cell cycle progression

Centrosomes provide docking sites for regulatory molecules involved in the control of the cell division cycle. The centrosomal matrix contains several proteins, which anchor kinases and phosphatases. The large A-Kinase Anchoring Protein AKAP450 is acting as a scaffolding protein for other components of the cell signaling machinery. We selectively perturbed the centrosome by modifying the cellular localization of AKAP450. We report that the expression in HeLa cells of the C terminus of AKAP450, which contains the centrosome-targeting domain of AKAP450 but not its coiled-coil domains or binding sites for signaling molecules, leads to the displacement of the endogenous centrosomal AKAP450 without removing centriolar or pericentrosomal components such as centrin, gamma-tubulin, or pericentrin. The centrosomal protein kinase A type II alpha was delocalized. We further show that this expression impairs cytokinesis and increases ploidy in HeLa cells, whereas it arrests diploid RPE1 fibroblasts in G1, thus further establishing a role of the centrosome in the regulation of the cell division cycle. Moreover, centriole duplication is interrupted. Our data show that the association between centrioles and the centrosomal matrix protein AKAP450 is critical for the integrity of the centrosome and for its reproduction.     

Changes in use of lake habitat by experimentally segregated populations of cutthroat trout and Dolly Varden char

The role of competition in a lacustrine community of two salmonid species, cutthroat trout Oncorhynchus clarki and Dolly Varden char Salvelinus malma , was studied in three coastal British Columbia lakes Habitat use by the species alone (allopatric) and in coexistence with each other (sympatric) was investigated by gill netting at 0-40 m depth contours (surface to bottom) so that several habitats (littoral, epipelagic. pelagic, epibenthic) were sampled From June to October, trout used mainly littoral and epipelagic habitats in sympatry and allopatry Char used all habitats in allopatry. and deep habitats (pelagic, epibenthic) not frequented by trout in sympatry The two species were thus spatially segregated with depth in sympatry Diel (day, night) and seasonal changes (spring, summer, autumn) in habitat use were not pronounced The shift in habitat use by experimentally allopatric char but not trout suggests that the effects of competition between sympatric trout and char for habitat resources are greater on the char     

Lifetime success and interactions of farm salmon invading a native population

Farm Atlantic salmon escape and invade rivers throughout the North Atlantic annually, which has generated growing concern about their impacts on native salmon populations. A large-scale experiment was therefore undertaken in order to quantify the lifetime success and interactions of farm salmon invading a Norwegian river. Sexually mature farm and native salmon were genetically screened, radio tagged and released into the River Imsa where no other salmon had been allowed to ascend. The farm fishes were competitively and reproductively inferior, achieving less than one-third the breeding success of the native fishes. Moreover, this inferiority was sex biased, being more pronounced in farm males than females, resulting in the principal route of gene flow involving native males mating with farm females. There were also indications of selection against farm genotypes during early survival but not thereafter. However, evidence of resource competition and competitive displacement existed as the productivity of the native population was depressed by more than 30%. Ultimately, the lifetime reproductive success (adult to adult) of the farm fishes was 16% that of the native salmon. Our results indicate that such annual invasions have the potential for impacting on population productivity, disrupting local adaptations and reducing the genetic diversity of wild salmon populations.