Functional genomics of ageing

Ageing is the most complex phenotype currently known, since it becomes manifest in all organs and tissues, affects an organism's entire physiology, impacts function at all levels and increases susceptibility to all major chronic diseases. Insight into the molecular and cellular targets of the ageing process would offer the unprecedented opportunity to postpone and prevent some, if not all, of its deteriorative aspects by preventive and therapeutic means. Thus far, our understanding of the causes of ageing is limited. To an important extent this is due to our inability, in the past, to study ageing systems. Instead, ample information has been gathered about individual cellular components at various ages, but this has not allowed a clear understanding of the integrated genomic circuits that control mechanisms of ageing, survival and stress responses. With the emergence of functional genomics, we finally have the opportunity to study ageing in a comprehensive manner, as a function of the dynamic network of genes that determines the physiology of an individual organism over time.     

Functional heterogeneity of type 1 fimbriae of Escherichia coli.

Escherichia coli and other members of the family Enterobacteriaceae express surface fibrillar structures, fimbriae, that promote bacterial adhesion to host receptors. Type 1 fimbriae possess a lectinlike component, FimH, that is commonly thought to cause binding to mannose-containing oligosaccharides of host receptors. Since adhesion of type 1 fimbriated organisms are inhibited by mannose, the reactions are described as mannose sensitive (MS). We have studied the adhesion of the type 1 fimbriated CSH-50 strain of E. coli (which expresses only type 1 fimbriae) to fibronectin (FN). E. coli CSH-50 does not bind detectable amounts of soluble FN but adheres well to immobilized plasma or cellular FN. This adhesion was inhibited by mannose-containing saccharides. By using purified domains of FN, it was found that E. coli CSH-50 adheres primarily to the amino-terminal and gelatin-binding domains, only one of which is glycosylated, in an MS fashion. Binding of the mannose-specific lectin concanavalin A to FN and ovalbumin was eliminated or reduced, respectively, by incubation with periodate or endoglycosidase. Adhesion of E. coli CSH-50 to ovalbumin was reduced by these treatments, but adhesion to FN was unaffected. E. coli CSH-50 also adheres to a synthetic peptide copying a portion of the amino-terminal FN domain (FNsp1) in an MS fashion. Purified CSH-50 fimbriae bound to immobilized FN and FNsp1 in an MS fashion and inhibited adhesion of intact organisms. However, fimbriae purified from HB101 (pPKL4), a recombinant strain harboring the entire type 1 fim gene locus and expressing functional type 1 fimbriae, neither bound to FN or FNsp1 nor inhibited E. coli adhesion to immobilized FN or FNsp1. These novel findings suggest that there are two forms of type 1 MS fimbriae. One form exhibits only the well-known MS lectinlike activity that requires a substratum of mannose-containing glycoproteins. The other form exhibits not only the MS lectinlike activity but also binds to nonglycosylated regions of proteins in an MS manner.     

Functional genomics in rodent models of hypertension

Inbred strains of rodents have been used to study mammalian physiology and pathophysiology in an attempt to understand the contribution of genes in the pathogenesis of the disease process. In this review we focus on experimental animal models to identify quantitative trait loci (QTL) and possible strategies for identifying underlying genetic determinants responsible for hypertension. Confirmation of the existence of the QTL and dissection of the implicated region can be undertaken by production of either recombinant inbred, consomic or congenic strains. Despite complex interactions and the relatively few confirmed causative genes underlying QTL, recent developments in rat genome resources and advancement in statistical and bioinformatic methods will facilitate the identification of major gene(s) responsible for complex, polygenic traits.     

Functional similarity between the haemolysins of Escherichia coli and Morganella morganii

Haemolysin produced by a clinical isolate of Morganella morganii was examined for antigenic relatedness to the haemolysin of Escherichia coli and for similarities in mode of action. The M. morganii haemolysin migrated in SDS-PAGE as a single protein band with a slightly higher molecular weight than that of E. coli haemolysin. Several murine monoclonal antibodies against E. coli haemolysin cross-reacted with the M. morganii haemolysin in Western blots. Diminished haemolysis in the presence of osmotically-stabilising solutes indicated the formation of a pore by M. morganii haemolysin with an effective diameter of 1.5-3 nm. Results from dose-response experiments indicated that a single "hit" was sufficient for lysis of an erythrocyte. Detergent solubilisation of toxin-treated membranes led to recovery of bound toxin exclusively in monomeric form. M. morganii haemolysin was a potent leucocidin, that caused rapid leakage of ATP and death of human polymorphonuclear leucocytes. Under in-vitro conditions M. morganii haemolysin displayed similar leucocidal and haemolytic efficiency. The data demonstrate that M. morganii haemolysin shows functional properties virtually identical with those of E. coli haemolysin.     

Functional genomics of the Down syndrome

Down syndrome, as a phenotypic result of trisomy 21, is a complex condition with a set of over 30 phenotypic features, which manifest themselves with varying frequencies among affected individuals. The importance for molecular medicine of understanding the molecular mechanisms underlying Down syndrome becomes fully appreciated when a striking feature of Down syndrome is taken into account: that the overdose of otherwise perfectly normal genes causes disorders of human health, indistinguishable from major public health problems of the general population, such as mandatory early onset Alzheimer s degeneration, increased risk of leukemia, and protection from cancer of solid tissues. The DNA sequence of human chromosome 21 is, at the moment, the most complete piece of DNA sequence known in the whole of human genome. The challenge for the future is an integrated, multidisciplinary approach to the molecular biology of chromosome 21 genes, in conjunction with the research into the variation in their genotype, expression, and function in the normal population, in Down syndrome individuals with well-characterized phenotypic traits, and in euploid patients suffering from diseases associated with phenotypic components of Down syndrome: mental retardation, developmental defects, hematological and solid tissue malignancies, and Alzheimer s disease.     

Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coli

We have analyzed the known metabolic enzymes of Escherichia coli in relation to their biochemical reaction properties and their involvement in biochemical pathways. All enzymes involved in small-molecule metabolism and their corresponding protein sequences have been extracted from the EcoCyc database. These 548 metabolic enzymes are clustered into 405 protein families according to sequence similarity. In this study, we examine the functional versatility within enzyme families in terms of their reaction capabilities and pathway participation. In addition, we examine the molecular diversity of reactions and pathways according to their presence across enzyme families. These complex, many-to-many relationships between protein sequence and biochemical function reveal a significant degree of correlation between enzyme families and reactions. Pathways, however, appear to require more than one enzyme type to perform their complex biochemical transformations. Finally, the distribution of enzyme family members across different pathways provides support for the "recruitment" hypothesis of biochemical pathway evolution.     

Functional genomics in the study of autoimmune diseases

Functional genomics can be defined as a series of new biotechnological tools based on whole-genome information that can be used to understand basic mechanisms of gene regulation, structure and function. Most of these tools have been used and modeled in research of lower organisms such as the yeast C. Elegans. The time has come for their use in human genome research and there is hope that the new technologies and possibilities will provide with new knowledge on disease pathogenesis and the development of new drugs.     

Functional genomics of membrane transporters in human populations

Although considerable progress has been made toward characterizing human DNA sequence variation, there remains a deficiency in information on human phenotypic variation at the single-gene level. We systematically analyzed the function of all protein-altering variants of eleven membrane transporters in heterologous expression systems. Coding-region variants were identified by screening DNA from a large sample (n = 247-276) of ethnically diverse subjects. In total, we functionally analyzed 88 protein-altering variants. Fourteen percent of the polymorphic variants (defined as variants with allele frequencies > or =1% in at least one major ethnic group) had no activity or significantly reduced function. Decreased function variants had significantly lower allele frequencies and were more likely to alter evolutionarily conserved amino acid residues. However, variants at evolutionarily conserved positions with approximately normal activity in cellular assays were also at significantly lower allele frequencies, suggesting that some variants with apparently normal activity in biochemical assays may influence occult functions or quantitative degrees of function that are important in human fitness but not measured in these assays. For example, eight (14%) of the 58 variants for which we had measured the transport of at least two substrates showed substrate-specific defects in transport. These variants and the reduced function variants provide plausible candidates for disease susceptibility or variation in clinical drug response.     

Functional genomics and proteomics in control of breathing

New genomic and proteomic techniques offer remarkable promise as tools to address longstanding questions regarding molecular mechanisms involved in the control of breathing. Here, these techniques are described. Additionally, recent examples of the application of these and related molecular techniques are provided-particularly including observations regarding the role of S-nitrosylation signaling reactions in regulating ventilatory responses.     

Emergence of a Multidrug-Resistant Shiga Toxin-Producing Enterotoxigenic Escherichia coli Lineage in Diseased Swine in Japan

Enterotoxigenic Escherichia coli (ETEC) and Shiga toxin-producing E. coli (STEC) are important causes of diarrhea and edema disease in swine. The majority of swine-pathogenic E. coli strains belong to a limited range of O serogroups, including O8, O138, O139, O141, O147, O149, and O157, which are the most frequently reported strains worldwide. However, the circumstances of ETEC and STEC infections in Japan remain unknown; there have been few reports on the prevalence or characterization of swine-pathogenic E. coli. In the present study, we determined the O serogroups of 967 E. coli isolates collected between 1991 and 2014 from diseased swine in Japan, and we found that O139, O149, O116, and OSB9 (O serogroup of Shigella boydii type 9) were the predominant serogroups. We further analyzed these four O serogroups using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing, and virulence factor profiling. Most of the O139 and O149 strains formed serogroup-specific PFGE clusters (clusters I and II, respectively), whereas the O116 and OSB9 strains were grouped together in the same cluster (cluster III). All of the cluster III strains belonged to a single sequence type (ST88) and carried genes encoding both enterotoxin and Shiga toxin. This PFGE cluster III/ST88 lineage exhibited a high level of multidrug resistance (to a median of 10 antimicrobials). Notably, these bacteria were resistant to fluoroquinolones. Thus, this lineage should be considered a significant risk to animal production due to the toxigenicity and antimicrobial resistance of these bacteria.     

Functional genomics in single embryo and human oocytes

During three decades human embryo and oocyte analyses have been performed based on morphological or cytogenetical evaluations; molecular techniques, like FISH and PCR, have been gradually incorporated. However, the development of new techniques of individual cell RNA amplification has allowed the analysis of gene expression in oocytes, cumulus-oocyte complex and preimplantation embryos. These techniques will change radically the study of human reproductive biology and assisted reproduction, allowing a powerful and objective analysis of the complex processes and the interactions that may explain the causes of infertility and generate new therapeutics.     

Molecular Epidemiological Characterization of Uropathogenic Escherichia coli from an Outpatient Urology Clinic in Rural Japan

In the remote Japanese community of Saku, a rural town in the Nagano Prefecture, a large proportion of outpatient urinary tract infections was caused by well-recognized globally dispersed clonal lineages of uropathogenic Escherichia coli (UPEC). However, most of these strains were drug susceptible, suggesting that factors other than selection pressure account for the clonal spread of drug-susceptible UPEC.     

Functional transfer of Salmonella pathogenicity island 2 to Salmonella bongori and Escherichia coli

The type III secretion system (T3SS) encoded by the Salmonella pathogenicity island 2 (SPI2) has a central role in systemic infections by Salmonella enterica and for the intracellular phenotype. Intracellular S. enterica uses the SPI2-encoded T3SS to translocate a set of effector proteins into the host cell, which modify host cell functions, enabling intracellular survival and replication of the bacteria. We sought to determine whether specific functions of the SPI2-encoded T3SS can be transferred to heterologous hosts Salmonella bongori and Escherichia coli Mutaflor, species that lack the SPI2 locus and loci encoding effector proteins. The SPI2 virulence locus was cloned and functionally expressed in S. bongori and E. coli. Here, we demonstrate that S. bongori harboring the SPI2 locus is capable of secretion of SPI2 substrate proteins under culture conditions, as well as of translocation of effector proteins under intracellular conditions. An SPI2-mediated cellular phenotype was induced by S. bongori harboring the SPI2 if the sifA locus was cotransferred. An interference with the host cell microtubule cytoskeleton, a novel SPI2-dependent phenotype, was observed in epithelial cells infected with S. bongori harboring SPI2 without additional effector genes. S. bongori harboring SPI2 showed increased intracellular persistence in a cell culture model, but SPI2 transfer was not sufficient to confer to S. bongori systemic pathogenicity in a murine model. Transfer of SPI2 to heterologous hosts offers a new tool for the study of SPI2 functions and the phenotypes of individual effectors.     

Functional analysis of the Tsh autotransporter from an avian pathogenic Escherichia coli strain

The temperature-sensitive hemagglutinin (Tsh) is an autotransporter protein secreted by avian-pathogenic Escherichia coli strains that colonize the respiratory tract and lead to airsacculitis, pericarditis, and colisepticemia. It is synthesized as a 140-kDa precursor protein, whose processing results in a 106-kDa passenger domain (Tshs) and a 33-kDa beta-domain (Tsh(beta)). The presence of a conserved 7-amino-acid serine protease motif within Tshs classifies the protein in a subfamily of autotransporters, known as serine protease autotransporters of the Enterobacteriaceae. In this study, we report that purified Tshs is capable of adhering to red blood cells, hemoglobin, and the extracellular matrix proteins fibronectin and collagen IV. We also demonstrate that Tshs exerts proteolytic activity against casein, and we provide experimental evidence demonstrating that serine 259 is essential for the protease function. However, this residue is not required for adherence to substrates, and its replacement by an alanine does not abolish binding activity. In summary, our results demonstrate that Tsh is a bifunctional protein with both adhesive and proteolytic properties.