Coevolving protein residues: maximum likelihood identification and relationship to structure

The identification of protein sites undergoing correlated evolution (coevolution) is of great interest due to the possibility that these pairs will tend to be adjacent in the three-dimensional structure. Identification of such pairs should provide useful information for understanding the evolutionary process, predicting the effects of site-directed substitution, and potentially for predicting protein structure. Here, we develop and apply a maximum likelihood method with the aim of improving detection of coevolution. Unlike previous methods which have had limited success, this method allows for correlations induced by phylogenetic relationships and for variation in rate of evolution along branches, and does not rely on accurate reconstruction of ancestral nodes. In order to reduce the complexity of coevolutionary relationships and identify the primary component of pairwise coevolution between two sites, we reduce the data to a two-state system at each site, regardless of the actual number of residues observed at that site. Simulations show that this strategy is good at identifying simple correlations and at recognizing cases in which the data are insufficient to distinguish between coevolution and spurious correlations. The new method was tested by using size and charge characteristics to group the residues at each site, and then evaluating coevolution in myoglobin sequences. Grouping based on physicochemical characteristics allows categorization of coevolving sites into positive and negative coevolution, depending on the correlation between equilibrium state frequencies. We detected a striking excess of negative coevolution (corresponding to charge) at sites brought into proximity by the periodicity of the alpha-helix, and there was also a tendency for sites with significant likelihood ratios to be close in the three-dimensional structure. Sites on the surface of the protein appear to coevolve both when they are close in the structure, and when they are distant, implying a role for folding and/or avoidance of quaternary structure in the coevolution process.     

Low-flow vascular remodeling in the metabolic syndrome X

Peripheral microvascular dysfunction is a common affliction in patients with the metabolic syndrome X. Previous studies have described a number of vascular impairments in vasomotor control in both human patients and animal models of syndrome X, but the net effect of these impairments on microvascular structure has not been examined. The goal of the current study was to test the hypothesis that syndrome X reduces muscle perfusion and induces vascular remodeling. The obese Zucker rat was used as a model of syndrome X, and the microcirculation of the hindlimb and brain were examined. Obese Zucker rats were obese, hyperlipidemic, hyperinsulinemic, and hyperglycemic. Blood flow to the hindlimb was reduced by 59% in obese rats relative to lean rats. Skeletal muscle resistance arteries of the hindlimb microcirculation of obese rats had thinner walls, smaller lumens, and reduced distensibility. Hindlimb microvessels from obese rats also demonstrated reduced expression of vascular smooth muscle cell markers. Each of these traits is consistent with low-flow remodeling. In contrast, the cerebral microcirculation, where flow is vigorously autoregulated, showed no vascular remodeling nor were there changes in microvascular smooth muscle marker expression. Neither physical activity nor muscle mass were significantly different between lean and obese rats. Taken together, these findings suggest that syndrome X, by reducing hindlimb blood flow, induces a marked remodeling of microcirculation to favor smaller, less distensible vessels. This remodeling may result in an architectural limitation of maximum perfusion capacity and may be an important maladaption in the progression of peripheral microvascular disease.     

Biosynthesis of unusual monocyclic alkenes by the diatom Rhizosolenia setigera (Brightwell)

Novel, polyunsaturated monocyclic sester- and triterpenes isolated from the diatom Rhizosolenia setigera (Brightwell), are biosynthesised mainly via the mevalonate pathway. The experiments involved incubation of the alga with [1-(13)C]acetate, isolation of the alkenes by extraction and silver ion HPLC, followed by determination of the labelling pattern of one of the monocyclic triterpenes by (13)C-NMR spectroscopy. In addition, the extent of (13)C incorporation was also measured by mass spectrometry which revealed that the involvement of the mevalonate route in the biosynthesis of these cyclic compounds was less than for the co-occurring acyclic highly branched isoprenoid alkenes.     

Analysis of among-site variation in substitution patterns

Substitution patterns among nucleotides are often assumed to be constant in phylogenetic analyses. Although variation in the average rate of substitution among sites is commonly accounted for, variation in the relative rates of specific types of substitution is not. Here, we review details of methodologies used for detecting and analyzing differences in substitution processes among predefined groups of sites. We describe how such analyses can be performed using existing phylogenetic tools, and discuss how new phylogenetic analysis tools we have recently developed can be used to provide more detailed and sensitive analyses, including study of the evolution of mutation and substitution processes. As an example we consider the mitochondrial genome, for which two types of transition deaminations (C⇒T and A⇒G) are strongly affected by single-strandedness during replication, resulting in a strand asymmetric mutation process. Since time spent single-stranded varies along the mitochondrial genome, their differential mutational response results in very different substitution patterns in different regions of the genome. Published: September 2, 2004.     

The ambush hypothesis: hidden stop codons prevent off-frame gene reading

Coding sequences lack stop codons, but many stops appear off-frame. Off-frame stops (stops in -1 and +1 shifted reading frames, termed hidden stops) terminate frame-shifted translation, potentially decreasing energy, and resource waste on nonfunctional proteins. Benefits may include reduced waste elimination costs and avoidance of potentially cytotoxic frame-shifted products. Our "ambush" hypothesis suggests that hidden stops are sometimes selected for. Codons of many amino acids can contribute to hidden stops, depending on the synonymous position state and adjacent codons. In vertebrate mitochondria, 31.75% of all amino acid combinations can form hidden stops. Codons with more potential to form hidden stops have greater usage frequency and bias in their favor among synonymous codons. Among primates, predicted mitochondrial rRNA secondary structure stability correlates negatively with the number of hidden stops in the mitochondrial genome. The taxonomic distribution of genetic codes suggests that +1 frameshifts might be more frequent than -1 frameshifts. This is confirmed by analyses of primate mitochondrial genomes: species with unstable rRNAs have more +1 stops, but the correlation is weak for -1 stops. High hidden stop density seems to be an adaptation in species with slippage prone ribosomes (unstable rRNAs). Hidden stops may thus compensate for reduced efficiency of some parts of the biosynthetic machinery. Some experimental data confirm our hypothesis: gene expression increases with the experimentally manipulated number of stops in the promoter region of a gene, suggesting biotechnological applications.     

Model selection methodology in supervised learning with evolutionary computation

The expressive power, powerful search capability, and the explicit nature of the resulting models make evolutionary methods very attractive for supervised learning applications in bioinformatics. However, their characteristics also make them highly susceptible to overtraining or to discovering chance relationships in the data. Identification of appropriate criteria for terminating evolution and for selecting an appropriately validated model is vital. Some approaches that are commonly applied to other modelling methods are not necessarily applicable in a straightforward manner to evolutionary methods. An approach to model selection is presented that is not unduly computationally intensive. To illustrate the issues and the technique two bioinformatic datasets are used, one relating to metabolite determination and the other to disease prediction from gene expression data.     

High glucose and endothelial cell growth: novel effects independent of autocrine TGF-beta 1 and hyperosmolarity

Human endothelial cells wereexposed to 5 mM glucose (control), 25 mM (high) glucose, or osmoticcontrol for 72 h. TGF-1 production, cell growth, death, andcell cycle progression, and the effects of TGF-1 and TGF-neutralization on these parameters were studied. High glucose andhyperosmolarity increased endothelial TGF-1 secretion(P < 0.0001) and bioactivity (P < 0.0001). However, high glucose had a greater effect on reducingendothelial cell number (P < 0.001) and increasingcellular protein content (P < 0.001) than the osmoticcontrol. TGF- antibody only reversed the antiproliferative andhypertrophic effects of high glucose. High glucose altered cell cycleprogression and cyclin-dependent kinase inhibitor expressionindependently of hyperosmolarity. High glucose increased endothelialcell apoptosis (P < 0.01), whereashyperosmolarity induced endothelial cell necrosis (P < 0.001). TGF- antibody did not reverse the apoptotic effectsobserved with high glucose. Exogenous TGF-1 mimicked the increased Sphase delay but not endoreduplication observed with high glucose. High glucose altered endothelial cell growth, apoptosis, and cellcycle progression. These growth effects occurred principally via aTGF-1 autocrine pathway. In contrast, apoptosis andendoreduplication occurred independently of this cytokine and hyperosmolarity.

     

Tumor necrosis factor receptor-associated factor 2 (TRAF2)-deficient B lymphocytes reveal novel roles for TRAF2 in CD40 signaling

CD40 function is initiated by tumor necrosis factor (TNF) receptor-associated factor (TRAF) adapter proteins, which play important roles in signaling by numerous receptors. Characterizing roles of individual TRAFs has been hampered by limitations of available experimental models and the poor viability of most TRAF-deficient mice. Here, B cell lines made deficient in TRAF2 using a novel homologous recombination system reveal new roles for TRAF2. We demonstrate that TRAF2 participates in synergy between CD40 and B cell antigen receptor signals, and in CD40-mediated, TNF-dependent IgM production. We also find that TRAF2 participates in the degradation of TRAF3 associated with CD40 signaling, a role that may limit inhibitory actions of TRAF3. Finally, we show that TRAF2 and TRAF6 have overlapping functions in CD40-mediated NF-kappaB activation and CD80 up-regulation. These findings demonstrate previously unappreciated roles for TRAF2 in signaling by TNF receptor family members, using an approach that facilitates the analysis of genes critical to the viability of whole organisms.     

Muc1 mucins on the cell surface are adhesion sites for Pseudomonas aeruginosa

Recently, we cloned and characterized a full-length cDNA of the hamster Muc1 gene, the expression of which appears to be associated with secretory cell differentiation (Park HR, Hyun SW, and Kim KC. Am J Respir Cell Mol Biol 15: 237-244, 1996). The role of Muc1 mucins in the airway, however, is unknown. In this study, we investigated whether cell surface mucins are adhesion sites for Pseudomonas aeruginosa. Chinese hamster ovary (CHO) cells not normally expressing Muc1 mucin were stably transfected with the hamster Muc1 cDNA, and binding to P. aeruginosa was examined. Our results showed that 1) stably transfected CHO cells expressed both Muc1 mRNA and Muc1 mucins based on Northern and Western blot analyses, 2) Muc1 mucins present on the cell surface were degraded by neutrophil elastase, and 3) expression of Muc1 mucins on the cell surface resulted in a significant increase in adhesion of P. aeruginosa that was completely abolished by either proteolytic cleavage with neutrophil elastase or deletion of the extracellular domain by mutation. We conclude that Muc1 mucins expressed on the surface of CHO cells serve as adhesion sites for P. aeruginosa, suggesting a possible role for these glycoproteins in the early stage of airway infection and providing a model system for studying epithelial cell responses to bacterial adhesion that leads to airway inflammation in general and cystic fibrosis in particular.