GeneTRACE-reconstruction of gene content of ancestral species

While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.     

Comparison of sequence masking algorithms and the detection of biased protein sequence regions

MOTIVATION: Separation of protein sequence regions according to their local information complexity and subsequent masking of low complexity regions has greatly enhanced the reliability of function prediction by sequence similarity. Comparisons with alternative methods that focus on compositional sequence bias rather than information complexity measures have shown that removal of compositional bias yields at least as sensitive and much more specific results. Besides the application of sequence masking algorithms to sequence similarity searches, the study of the masked regions themselves is of great interest. Traditionally, however, these have been neglected despite evidence of their functional relevance. RESULTS: Here we demonstrate that compositional bias seems to be a more effective measure for the detection of biologically meaningful signals. Typical results on proteins are compared to results for sequences that have been randomized in various ways, conserving composition and local correlations for individual proteins or the entire set. It is remarkable that low-complexity regions have the same form of distribution in proteins as in randomized sequences, and that the signal from randomized sequences with conserved local correlations and amino acid composition almost matches the signal from proteins. This is not the case for sequence bias, which hence seems to be a genuinely biological phenomenon in contrast to patches of low complexity.     

Myriads of protein families,and still counting

From the historical record of genome sequencing, we show that the rate of discovery of new families has remained constant over time, indicating that our knowledge of sequence space is far from complete.     

Classification schemes for protein structure and function

We examine the structural and functional classifications of the protein universe, providing an overview of the existing classification schemes, their features and inter-relationships. We argue that a unified scheme should be based on a natural classification approach and that more comparative analyses of the present schemes are required both to understand their limitations and to help delimit the number of known protein folds and their corresponding functional roles in cells.     

GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

Background  

The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies.     

Effect of CDP-choline on hippocampal acetylcholinesterase and Na+,K(+)-ATPase in adult and aged rats

The aim of this study was to investigate the effect of different cytidine-5'-diphosphocholine (CDP-choline) concentrations (0.1-1 mM) on acetylcholinesterase (AChE), (Na+,K+)-ATPase and Mg(2+)-ATPase activities in homogenates of adult and aged rat hippocampi. Tissues were homogenised, centrifuged at 1000 x g for 10 min and in the supernatant, AChE activity and Na+,K(+)-ATPase and Mg(2+)-ATPase activities were determined according to Ellman's method and Bowler's and Tirri's method, respectively. After an 1-3 h preincubation of the homogenised tissue with CDP-choline, a maximal AChE stimulation of about 25% for both adult and aged rats (p < 0.001) and a Na+,K(+)-ATPase activation of about 50% for adult rats (p < 0.001) and about 60% for aged rats (p < 0.001) were observed, while hippocampal Mg(2+)-ATPase activity was not influenced in either adult or aged animals. It is suggested that: CDP-choline can restore hippocampal AChE and Na+,K(+)-ATPase activities in the aged rat and thus it may play a role in improving memory performance which is impaired by aging and some neuronal disturbances.     

The effect of 12-O-tetradecanoylphorbol-13-acetate on Sertoli cell morphology and cytoskeletal organization: an in vitro study by means of cryo-SEM and fluorescent techniques

By means of cryo-scanning electron microscopy (cryo-SEM) and fluorescent techniques, evidence is provided on how 12-O-tetradecanoylphorbol-13-acetate (TPA) affects Sertoli cell morphology and F-actin and vinculin organization in vitro. In order to visualize the morphological changes, the cells were observed with cryo-SEM. F-actin was localized using rhodamine (TRI)-phalloidin and vinculin using a primary monoclonal antibody and a second TRI-conjugated antibody. The results indicate that after the addition of 10(-7) M TPA, Sertoli cells begin to round up and their cytoplasm is retracted towards a central region. Actin bundle organization is disrupted and vinculin assumes a punctuate distribution throughout the cell. Thus, the reorganization of actin and vinculin and subsequent changes in cell morphology seem to be brought about by TPA affecting not only actin but also the protein vinculin which interacts with actin. A discussion is made concerning the effect of TPA on cytoskeletal reorganization, which is closely related to cell transformation.     

The terminase subunits pUL56 and pUL89 of human cytomegalovirus are DNA-metabolizing proteins with toroidal structure

Herpesvirus DNA packaging involves binding and cleavage of DNA containing the specific DNA-packaging motifs. Here we report a first characterization of the terminase subunits pUL56 and pUL89 of human cytomegalovirus (HCMV). Both gene products were shown to have comparable nuclease activities in vitro. Under limiting protein concentrations the nuclease activity is enhanced by interaction of pUL56 and pUL89. High amounts of 2-bromo-5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole partially inhibited the pUL89-associated nuclease activity. It was demonstrated that pUL56 is able to bind to nucleocapsids in vivo. Electron microscopy (EM) and image analysis of purified pUL56 revealed that the molecules occurred as a distinct ring-shaped structure with a pronounced cleft. EM analysis of purified pUL89 demonstrated that this protein is also a toroidal DNA-metabolizing protein. Upon interaction of pUL56 with linearized DNA, the DNA remains uncut while the cutting event itself is mediated by pUL89. Using biochemical assays in conjunction with EM pUL56 was shown to (i) bind to DNA and (ii) associate with the capsid. In contrast to this, EM analysis implied that pUL89 is required to effect DNA cleavage. The data provide the first insights into the terminase-dependent viral DNA-packaging mechanism of HCMV.     

Protein families and TRIBES in genome sequence space

Accurate detection of protein families allows assignment of protein function and the analysis of functional diversity in complete genomes. Recently, we presented a novel algorithm called TribeMCL for the detection of protein families that is both accurate and efficient. This method allows family analysis to be carried out on a very large scale. Using TribeMCL, we have generated a resource called TRIBES that contains protein family information, comprising annotations, protein sequence alignments and phylogenetic distributions describing 311 257 proteins from 83 completely sequenced genomes. The analysis of at least 60 934 detected protein families reveals that, with the essential families excluded, paralogy levels are similar between prokaryotes, irrespective of genome size. The number of essential families is estimated to be between 366 and 426. We also show that the currently known space of protein families is scale free and discuss the implications of this distribution. In addition, we show that smaller families are often formed by shorter proteins and discuss the reasons for this intriguing pattern. Finally, we analyse the functional diversity of protein families in entire genome sequences. The TRIBES protein family resource is accessible at http://www.ebi.ac.uk/research/cgg/tribes/.     

Genome sequences and great expectations

To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that function can be predicted for almost two-thirds of the 73,500 genes that were analyzed. Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function.