A novel conserved protein region – the BON (bacterial OsmY and nodulation) domain – is found in the bacterial osmotic-shock-resistance protein OsmY, a family of haemolysins, a group of nodulation specificity proteins and secretory channels, and several hypothetical proteins. Functional annotation in the literature suggests that it interacts with phospholipid membranes. A lack of catalytic residues in the sequence alignment supports the hypothesis that it is a binding domain.
"ygaU encodes an uncharacterized protein demonstrated to be induced by salt stress in E. coli and to be a novel member of the RpoS regulon in S. Typhimurium . It contains a BON domain, which is characteristic of osmotic shock protection proteins , and a LysM domain, which was first reported in bacterial cell wall degrading enzymes and recently in other proteins with a variety of functions . In the current investigation, ygaU was found to be significantly regulated in eight tested conditions, but due to our difficulties with construction of a defined mutant we could not assess the importance for stress adaptation. "
[Show abstract][Hide abstract] ABSTRACT: Salmonella Typhimurium is an important pathogen of human and animals. It shows a broad growth range and survives in harsh conditions. The aim of this study was to analyze transcriptional responses to a number of growth and stress conditions as well as the relationship of metabolic pathways and/or cell functions at the genome-scale-level by network analysis, and further to explore whether highly connected genes (hubs) in these networks were essential for growth, stress adaptation and virulence.
De novo generated as well as published transcriptional data for 425 selected genes under a number of growth and stress conditions were used to construct a bipartite network connecting culture conditions and significantly regulated genes (transcriptional network). Also, a genome scale network was constructed for strain LT2. The latter connected genes with metabolic pathways and cellular functions. Both networks were shown to belong to the family of scale-free networks characterized by the presence of highly connected nodes or hubs which are genes whose transcription is regulated when responding to many of the assayed culture conditions or genes encoding products involved in a high number of metabolic pathways and cell functions.The five genes with most connections in the transcriptional network (wraB, ygaU, uspA, cbpA and osmC) and in the genome scale network (ychN, siiF (STM4262), yajD, ybeB and dcoC) were selected for mutations, however mutagenesis of ygaU and ybeB proved unsuccessful. No difference between mutants and the wild type strain was observed during growth at unfavorable temperatures, pH values, NaCl concentrations and in the presence of H2O2. Eight mutants were evaluated for virulence in C57/BL6 mice and none differed from the wild type strain. Notably, however, deviations of phenotypes with respect to the wild type were observed when combinations of these genes were deleted.
Network analysis revealed the presence of hubs in both transcriptional and functional networks of S. Typhimurium. Hubs theoretically confer higher resistance to random mutation but a greater susceptibility to directed attacks, however, we found that genes that formed hubs were dispensable for growth, stress adaptation and virulence, suggesting that evolution favors non-essential genes as main connectors in cellular networks.
"PSI-BLAST searches confirm that EscD also contains a cytoplasmic FHA domain (Figure 2). In addition, these searches revealed the presence of at least one putative phospholipid-binding domain (also called a BON domain ) in the periplasmic portion of the protein (Figure 3). Two compelling hypotheses arise from these observations. "
[Show abstract][Hide abstract] ABSTRACT: Like many other pathogens, enterohaemorrhagic and enteropathogenic strains of Escherichia coli employ a type-III secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. This system is encoded by the locus for enterocyte effacement. Many of the genes within this locus have been assigned names and functions through homology with the better characterised Ysc-Yop system from Yersinia spp. However, the functions and homologies of many LEE genes remain obscure.
We have performed a fresh bioinformatics analysis of the LEE. Using PSI-BLAST we have been able to identify several novel homologies between LEE-encoded and Ysc-Yop-associated proteins: Orf2/YscE, Orf5/YscL, rORF8/EscI, SepQ/YscQ, SepL/YopN-TyeA, CesD2/LcrR. In addition, we highlight homology between EspA and flagellin, and report many new homologues of the chaperone CesT.
We conclude that the vast majority of LEE-encoded proteins do indeed possess homologues and that homology data can be used in combination with experimental data to make fresh functional predictions.
[Show abstract][Hide abstract] ABSTRACT: A novel approximately 60-residue domain has been identified in Homo sapiens MGC5297 and various other proteins in eukaryotes. Sequence searches reveal that the domain is particularly abundant in apicomplexans and is predicted to be involved in diverse RNA-binding activities.
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