PIML: the Pathogen Information Markup Language.

Motivation: A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data.

Results: The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information.

Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain.

The leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) from Escherichia coli catalyzes a peptidyltransferase reaction that results in the N-terminal aminoacylation of acceptor proteins using Leu-, Phe-, and Met-tRNAs as amino acid donors. We demonstrated that L/F-transferase homologs are widely distributed throughout the eubacteria, supporting our proposal that the enzyme family is ancient and catalyzes early peptide bond synthesis. However, here we present data suggesting that the L/F-transferase is not a homolog of the peptidyltransferase enzymes involved in cell wall peptidoglycan biosynthesis in Gram-positive species, such as Staphylococcus aureus.

Aminoacyl-tRNA recognition by the leucyl/phenylalanyl-tRNA-protein transferase.

We employ mutant and mischarged aminoacyl-tRNAs to characterize aminoacyl-tRNA recognition by the leucyl/phenylalanyl-tRNA-protein transferase (L/Ftransferase). Wild type Met-tRNAMetm (CAU anticodon) and mischarged Met-tRNAVal-1 (CAU anticodon) are substrates for the L/F-transferase during the NH2-terminal aminoacylation of alpha-casein, whereas Val-tRNAVal-1 (UAC), Val-tRNAMetm (UAC), and Arg-tRNAMetm (CCG, A20) are not. Mutations in the anticodon and extra arm of tRNALeu-1 do not measurably effect its ability to serve as a substrate for the L/F-transferase, and the dissociation constants of the complexes between L/F-transferase and either wild type Leu-tRNALeu-4 (UAA) or mutant Leu-tRNALeu-4 (CUA) are each 0.

The yeast plasma membrane proton pumping ATPase is a viable antifungal target. I. Effects of the cysteine-modifying reagent omeprazole.

The yeast plasma membrane proton pumping ATPase (H(+)-ATPase) was investigated as a potential molecular target for antifungal drug therapy by examining the inhibitory effects of the sulfhydryl-reactive reagent omeprazole on cell growth, glucose-induced medium acidification and H(+)-ATPase activity. Omeprazole inhibits the growth of Saccharomyces cerevisiae and the human pathogenic yeast Candida albicans in a pH dependent manner. Omeprazole action is closely correlated with inhibition of the H(+)-ATPase and is fungicidal.

The leucyl/phenylalanyl-tRNA-protein transferase. Overexpression and characterization of substrate recognition, domain structure, and secondary structure.

Previous work has shown that, in the bacterium Escherichia coli, the aat gene is essential for the degradation of proteins bearing amino-terminal Arg and Lys residues via the N-end rule pathway of protein degradation. We now show that the aat gene encodes directly the leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase). This enzyme catalyzes the transfer of Leu, Phe, and, less efficiently, Met and Trp, from aminoacyl-tRNAs, to the amino terminus of acceptor proteins.