Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.     

Interaction between protein kinase C and regulatory ligand is enhanced by a chelatable pool of cellular zinc

At micromolar concentrations, zinc (Zn) and cadmium, but not other metals, greatly augmented binding of [3H]phorbol dibutyrate ([3H]PDBu) to protein kinase C (PKC) in cell homogenates and intact cells (in the presence of ionophore). Increased binding persisted for several hours. The heavy-metal chelating agent 1,10-phenanthroline completely reversed the increased [3H]PDBu binding in cells pretreated with 65Zn and ionophore and this was associated with a decline of about 20% in cell-associated 65Zn, suggesting that a relatively small pool of intracellular Zn acts on PKC. This may be a membrane-associated pool, since 65Zn readily bound to isolated erythrocyte inside-out membranes. Phenanthroline also partially inhibited binding of [3H]PDBu to PKC in untreated cells and extracts in a Zn-reversible manner. Therefore, cellular Zn appears to regulate the interaction of ligand with PKC. PKC bound to a Zn affinity column and was eluted by metal-chelator, confirming that Zn interacts directly with PKC.     

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3′ acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.