Testing statistical significance scores of sequence comparison methods with structure similarity

Background  

In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences.     

Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3

The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.     

The hyp operon gene products are required for the maturation of catalytically active hydrogenase isoenzymes in Escherichia coli

The hyp operon of Escherichia coli comprises several genes which are required for the synthesis of all three hydrogenase isoenzymes. Deletions were introduced into each of the hypA-E genes, transferred to the chromosome and the resulting mutants were analysed for hydrogenase 1, 2 and 3 activity. The products of three of the genes, hypB, hypD and hypE were found to be essential for the synthesis of all three hydrogenase isoenzymes. A defect in hypB, as previously observed, could be complemented by high nickel concentrations in the medium, whereas the effects of mutants in the other genes could not. Lesions in hypA prevented development of hydrogenase 3 activity, did not influence the level of hydrogenase 1 but led to a considerable increase in hydrogenase 2 activity although the amount of hydrogenase 2 protein was not drastically altered. Lesions in hypC, on the other hand, led to a reduction of hydrogenase 1 activity and abolished hydrogenase 3 activity. HYPA and HYPC, besides being required for hydrogenase 3 formation, therefore may have a function in modulating the activities of the three isoenzymes with respect to each other and adjusting their levels to the requirement imposed by the physiological situation. Mutations in all five hyp genes prevented the apparent processing of the large subunits of all three hydrogenase isoenzymes. It is concluded that the products of the hypA-E genes play a role in nickel incorporation into hydrogenase apoprotein and/or processing of the constituent subunits of this enzyme. The importance of their roles is also reflected in their phylogenetic conservation in distantly related organisms.     

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network

Background  

It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems.     

The cytotoxin YopT of Yersinia enterocolitica induces modification and cellular redistribution of the small GTP-binding protein RhoA.

Pathogenic Yersinia enterocolitica produces two virulence plasmid-encoded cytotoxins, YopE and YopT, that are translocated into target cells where they disrupt the actin cytoskeleton. Here we show that infection of cells with wild type Y. enterocolitica and a yopE mutant, but not with a yopT mutant, induces an increase in the electrophoretic mobility of the small GTPase RhoA. As tested by isoelectric focusing, YopT-dependent modification resulted in an acidic shift of RhoA. Furthermore, RhoA modification induced by YopT was accompanied by redistribution of membrane-bound RhoA toward the cytosol. Finally, a yopE mutant of Y. enterocolitica expressing the cytotoxic activity of YopT specifically disrupted RhoA-controlled actin stress fibers. These findings provide evidence for inactivation of RhoA by the translocated Y. enterocolitica cytotoxin YopT and suggest a novel inhibitory modification of RhoA by a bacterial virulence factor.     

Dissection of the Yersinia enterocolitica virulence plasmid pYVO8 into an operating unit and virulence gene modules

Abstract Mesophilic Aeromonas hydrophila from serotypes O:11 and O:34 grown in a glucose-rich medium produce a capsule that can be seen under light and electron microscopy. The purified capsular polysaccharide has a composition qualitatively similar for strains O:11 and O:34, but quantitatively different. The capsular polysaccharides were immunogenic in rabbits, and did not cross-react with specific antibodies against either purified lipopolysaccharide from strains O:34 or O:11 or against the S-layer characteristic of strains from serotype O:11.     

Foraging behavior of Xylocopa (Neoxylocopa) cearensis Ducke (Hymenoptera: Apidae, Xylocopini) in a population of Cuphea brachiata Koehne (Lythraceae)

An analysis of the foraging behavior of the bee Xylocopa (Neoxylocopa) cearensis Ducke among shrubs of Cuphea brachiata Koehne (Lythraceae), a key component in the Abaeté coastal sand dunes, Salvador, BA, Brazil, suggests that this bee is very important for the maintenance of the plant population, performing the pollination. This dispersal, however, is spatially restricted, so the populations in the area are likely to be highly structured genetically.     

Identification of subpopulations from connectivity matrices

Dispersal on the landscape/seascape scale may lead to complex spatial population structure with non‐synchronous demography and genetic divergence. In this study we present a novel approach to identify subpopulations and dispersal barriers based on estimates of dispersal probabilities on the landscape scale. A theoretical framework is presented where the landscape connectivity matrix is analyzed for clusters as a signature of partially isolated subpopulations. Identification of subpopulations is formulated as a minimization problem with a tuneable penalty term that makes it possible to generate population subdivisions with varying degree of dispersal restrictions. We show that this approach produces superior results compared to alternative standard methods. We apply this theory to a dataset of modeled dispersal probabilities for a sessile marine invertebrate with free‐swimming larvae in the Baltic Sea. For a range of critical connectivities we produce a hierarchical partitioning into subpopulations spanning dispersal probabilities that are typical for both genetic divergence and demographic independence. The mapping of subpopulations suggests that the Baltic Sea includes a fine‐scale (100–600 km) mosaic of invisible dispersal barriers. An analysis of the present network of marine protected areas reveal that protection is very unevenly distributed among the suggested subpopulations. Our approach can be used to assess the location and strength of dispersal barriers in the landscape, and identify conservation units when extensive genotyping is prohibitively costly to cover necessary spatial and temporal scales, e.g. in spatial management of marine populations.     

The genetic diversity of two brazilian vellozia (velloziaceae) with different patterns of spatial distribution and pollination biology

BACKGROUND AND AIMS: The genetic structure and variability of two species of Vellozia (Velloziaceae) with restricted distribution in high-altitude quartzitic fields in south-eastern Brazil were studied. Vellozia epidendroides is short, grows on pebbly or sandy soil, and is pollinated by bees. Vellozia leptopetala is arborescent, grows on rock outcrops, and is pollinated by bees and hummingbirds. Both are self-incompatible and have a short, massive flowering strategy. The study aimed to associate differences in their genetic diversity and structure with their microhabitat distribution and pollination ecology. METHODS: Leaves from 106 and 139 plants of V. epidendroides and V. leptopetala, respectively, were collected from five patches of each species and prepared for electrophoretic analyses. KEY RESULTS: Five enzyme systems could be reliably scored for both species. Vellozia epidendroides showed 100 % of the loci polymorphic for almost all patches. The average number of alleles per locus ranged between 2.2 and 2.4 among patches. The Wright's fixation index (F) for this species was 0.226. A significant (p) value indicates that there is a reasonable genetic divergence among patches. Vellozia leptopetala presented 47.5 % of polymorphic loci. All levels of P, A, A(p) and of heterozygosities were lower than those of V. epidendroides. Vellozia leptopetala showed high inbreeding within patches. CONCLUSIONS: The relatively high values of genetic diversity indices found for V. epidendroides may be associated with its large and widespread populations. On the other hand, the low values of genetic diversity found for V. leptopetala may be related to physical isolation on outcrops and intensive foraging by territorial hummingbirds, which may hinder gene flow among patches, aggravated by the very restricted seed dispersal characteristic of the genus, that facilitates sibling mating. It is important to stress the need to preserve the specific habitats of these species of Vellozia, in particular those of V. leptopetala that has lower genetic diversity and is restricted to rock outcrop environments.