Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking

A major problem in genome annotation is whether it is valid to transfer the function from a characterised protein to a homologue of unknown activity. Here, we show that one can employ a strategy that uses a structure-based prediction of protein functional sites to assess the reliability of functional inheritance. We have automated and benchmarked a method based on the evolutionary trace approach. Using a multiple sequence alignment, we identified invariant polar residues, which were then mapped onto the protein structure. Spatial clusters of these invariant residues formed the predicted functional site. For 68 of 86 proteins examined, the method yielded information about the observed functional site. This algorithm for functional site prediction was then used to assess the validity of transferring the function between homologues. This procedure was tested on 18 pairs of homologous proteins with unrelated function and 70 pairs of proteins with related function, and was shown to be 94 % accurate. This automated method could be linked to schemes for genome annotation. Finally, we examined the use of functional site prediction in protein-protein and protein-DNA docking. The use of predicted functional sites was shown to filter putative docked complexes with a discrimination similar to that obtained by manually including biological information about active sites or DNA-binding residues.     

Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach

Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning—the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system.     

Reconstruction of source water using the δ18O of tree ring phenylglucosazone: A potential tool in paleoclimate studies

The oxygen isotope ratios of tree ring cellulose have a great potential as proxy for the oxygen isotope ratios of source water, which is related to climate. However, source water isotopic signatures can be masked by plant physiological and biochemical processes during cellulose synthesis. To minimize biochemical effects in the recording of source water, we modified the cellulose molecule to phenylglucosazone, which only has oxygen attached to carbon 3–6 (O_C3–6) of the cellulose glucose moieties, thus eliminating the oxygen attached to carbon 2 of the cellulose glucose moieties (O_C-2). Here we developed a method to use small amounts of inter and intra-annual tree ring cellulose for phenylglucosazone synthesis. Using this new method we tested if the oxygen isotope ratios of source water reconstructed from tree ring phenylglucosazone (δ¹⁸O_sw^PG) and the observed source water (δ¹⁸O_sw^obs) would have a better agreement than those reconstructed from the tree ring cellulose molecule. Annual tree ring samples were obtained from Pinus sylvestris (1997–2003) (Finland) and Picea abies (1971–1992) (Switzerland) and intra-annual tree ring samples were obtained from Pinus radiata (October 2004–March 2006) (New Zealand), each near a meteorological station where precipitation and relative humidity (RH) were measured periodically. The δ¹⁸O of tree ring cellulose and tree ring phenylglucosazone for each of the three species were then used to back calculate the δ¹⁸O of source water according to a previous published empirical equation. As expected, the δ¹⁸O of tree ring phenylglucosazone was superior than cellulose in the reconstruction of source water available to the plant. Deviation between δ¹⁸O_sw^PG and δ¹⁸O_sw^obs was in part correlated with variation in atmospheric relative humidity (RH) which was not observed for the cellulose molecule. We conclude that this new method can be applicable to inter and intra-annual tree ring studies and that the use of the tree ring phenylglucosazone will significantly improve the quality of paleoclimate studies.     

Applications of high-throughput sequencing to symbiotic nematodes of the genus <Emphasis Type="Italic">Heterorhabditis</Emphasis>

Entomopathogenic nematodes of the genus Heterorhabditis live in symbiosis with pathogenic Photorhabdus bacteria. Heterorhabditis nematodes are entirely dependent on these bacteria for their food source; in return, the nematodes offer the bacteria a way to infect and kill insects. For their part, Photorhabdus bacteria are lethal to a broad range of insect hosts, to other nematodes, and to other microorganisms, but not to their Heterorhabditis hosts. These nematodes offer the potential to provide a robust experimental system for the in•depth study of a mutually beneficial symbiotic relationship, with both members of the partnership accessible to molecular and genetic studies. New genomic technologies offer the possibility for this potential to be realized, and for Heterorhabditis nematodes to become a standard model system for the investigation of host•symbiote relationships. We present a perspective on the application of these technologies to nematode•bacterial symbiosis and an update on our efforts to sequence three Heterorhabditis species reported at the recent NemaSym meeting.     

Mucin secretion by the human colon cell line LS174T is regulated by bile salts

We recently reported that bile salts play a role in the regulation of mucin secretion by cultured dog gallbladder epithelial cells. In this study we have examined whether bile salts also influence mucin secretion by the human epithelial colon cell line LS174T. Solutions of bile salts were applied to monolayers of LS174T cells. Mucin secretion was quantified by measuring the secretion of [3H]GlcNAc labeled glycoproteins. Both unconjugated bile salts as well as taurine conjugated bile salts stimulated mucin secretion by the colon cells in a dose-dependent fashion. Hydrophobic bile salts were more potent stimulators than hydrophilic bile salts. Free (unconjugated) bile salts were more stimulatory compared with their taurine conjugated counterparts. Stimulation of mucin secretion by LS174T cells was found to occur at much lower bile salt concentrations than in the experiments with the dog gallbladder epithelial cells. The protein kinase C activators PMA and PDB had no stimulatory effect on mucin secretion. We conclude that mucin secretion by the human colon epithelial cell line LS174T is regulated by bile salts. We suggest that regulation of mucin secretion by bile salts might be a common mechanism, by which different epithelia protect themselves against the detergent action of bile salts, to which they are exposed throughout the gastrointestinal tract.      

Specific Immune Response of Mares and their Newborn Foals to Actinobacillus spp. Present in the Oral Cavity

Oral swab samples, serum and colostrum was taken from 15 mares and 14 of their foals, within 24 h of birth. The presence of antibody against Actinobacillus spp. isolated from the oral cavity was investigated using agar gel immunodiffusion. Antibodies against 48 out of the 77 Actinobacillus isolates from all horses in the study were present in the respective sera of 13 mares and 9 foals. In 11 mother-foal pairs, the antibody content of the foal serum was similar to that of the mare, and in 9 cases this was reflected in the antibody content of colostrum from the mare. The results indicate that an immune response to Actinobacillus spp. colonising the oral cavity is present in many adult horses and that this immune response can be transferred from mother to foal via colostrum.     

Development of marker-free strains of Bacillus subtilis capable of secreting high levels of industrial enzymes

Different strategies have been employed to achieve high-level expression of single-copy genes encoding secreted enzymes in Bacillus subtilis. A model system was developed which utilizes the aprL gene from Bacillus clausii as a reporter gene for monitoring expression levels during stationary phase. An exceptionally strong promoter was constructed by altering the nuceotide sequence in the −10 and −35 regions of the promoter for the amyQ gene of Bacillus amyloliquefaciens. In addition, two or three tandem copies of this promoter were shown to increase expression levels substantially in comparison to the monomer promoter alone. Finally, the promoter and mRNA stabilization sequences derived from the cry3A gene of Bacillus thuringiensis were used in combination with the mutant amyQ promoter to achieve the highest levels of aprL expression. These promoters were shown to be fully functional in a high-expressing Bacillus strain grown under industrial fermentation conditions. The ability to obtain maximum expression levels from a single copy gene now makes it feasible to construct environmentally friendly, marker-free industrial strains of B. subtilis. Journal of Industrial Microbiology & Biotechnology (2000) 25, 204–212. Received 05 January 2000/ Accepted in revised form 26 June 2000     

Deciphering earth mound origins in central Brazil

Mound fields are a common landscape throughout the world and much of the evidence for their origin has been of a circumstantial nature. It has been hypothesized that earth mounds emerge over grasslands by termite activity; alternatively, they might be formed after erosion. We tested whether a mound field in central Brazil was generated by termite activity or erosion. We used soil organic matter isotopic composition, soil chemical, physical and floristic composition to determine the origin of a mound field. If the mounds emerged by termite activity in an established grassland the soil organic matter below the mound should have the isotopic signature of C₄ dominated grassland, which contrasts with savanna C₃ + C₄ signature. Additionally, soil traits should resemble those of the grassland. All markers indicate that the mounds were formed by erosion. The soil isotopic composition, chemical traits and texture below the mound resembled those of the savanna and not those of the grassland. Moreover, most of the species present in the mound were typical of savanna. Concrete evidence is provided that mound fields in the studied area were produced by erosion of a savanna ecosystem and not termite activity. The use of the techniques applied here would improve the assessments of whether analogous landscapes are of a biogenic nature or not.