Functional Annotation Analytics of Rhodopseudomonas palustris Genomes

Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R. palustris genomes

Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni

The draft nuclear genome sequence of the snail-transmitted, dimorphic, parasitic, platyhelminth Schistosoma mansoni revealed eight genes encoding proteins that contain the Universal Stress Protein (USP) domain. Schistosoma mansoni is a causative agent of human schistosomiasis, a severe and debilitating Neglected Tropical Disease (NTD) of poverty, which is endemic in at least 76 countries. The availability of the genome sequences of Schistosoma species presents opportunities for bioinformatics and genomics analyses of associated gene families that could be targets for understanding schistosomiasis ecology, intervention, prevention and control. Proteins with the USP domain are known to provide bacteria, archaea, fungi, protists and plants with the ability to respond to diverse environmental stresses. In this research investigation, the functional annotations of the USP genes and predicted nucleotide and protein sequences were initially verified. Subsequently, sequence clusters and distinctive features of the sequences were determined. A total of twelve ligand binding sites were predicted based on alignment to the ATP-binding universal stress protein from Methanocaldococcus jannaschii. In addition, six USP sequences showed the presence of ATP-binding motif residues indicating that they may be regulated by ATP. Public domain gene expression data and RT-PCR assays confirmed that all the S. mansoni USP genes were transcribed in at least one of the developmental life cycle stages of the helminth. Six of these genes were up-regulated in the miracidium, a free-swimming stage that is critical for transmission to the snail intermediate host. It is possible that during the intra-snail stages, S. mansoni gene transcripts for universal stress proteins are low abundant and are induced to perform specialized functions triggered by environmental stressors such as oxidative stress due to hydrogen peroxide that is present in the snail hemocytes. This report serves to catalyze the formation of a network of researchers to understand the function and regulation of the universal stress proteins encoded in genomes of schistosomes and their snail intermediate hosts

Evaluation of the Effects of Butyltin Exposures on Expression of Interleukin 1 Beta and Interleukin 6 in Human Immune Cells

Tributyltin (TBT) and dibutyltin (DBT) are organotin compounds that have been used in a variety of applications; as a result, they have been found in human blood. Butyltins (BTs) can decrease the ability of human natural killer (NK) cells to destroy tumor cells and alter the secretion of pro-inflammatory cytokines tumor necrosis factor alpha (TNFα), interferon gamma (IFNγ), and interleukin 1 beta (IL-1β) from human lymphocytes ex vivo. Alterations of IL-1β and IL-6 levels in human immune cells by BTs are examined. Increasingly reconstituted human immune cell preparations were exposed to concentrations of BTs at various lengths of exposure. In addition, the role of ILβ processing enzyme (Caspase-1), mitogen-activated protein kinases (MAPKs) (p38, p44/42, JNK), and nuclear factor kappa B (NFκB) activation in TBT-induced alterations of IL-1β and IL-6 levels were investigated. Results showed that both TBT and DBT altered IL-1? and IL-6 levels. Higher concentrations of DBT (5 and 2.5 μM) decreased the secretion of IL-1β, while lower concentrations of DBT (0.1 and 0.05 μM) increased the secretion of IL-1β. Significant decreases of IL-6 secretion were seen at the highest concentration of TBT (200 nM) and DBT (5-2.5 μM) while the lower concentrations of DBT (0.05 and 0.1 μM) caused elevation of IL-6 secretion. Caspase 1 and MAPK pathways appear to be utilized by DBT in increasing IL-1β secretion. Studies examining the time course of TBT-induced stimulation of IL-1β and IL-6 production showed that substantial changes in the levels of these cytokines require an incubation of 24 h. TBT relies on the activation of the p44/42 and p38 MAPK signaling pathways to cause increases in IL-1β and IL-6 production. TBT-induced increases in IL-1β and IL-6 at the highest concentration were due to increases in their mRNA. p38 is needed for these TBT-induced increases in IL-1β and IL-6 mRNA. Additional studies were performed to address changes seen in TBT-induced production and the ability of TNFα and IL-1β to stimulate IL-6. These data suggest that BT exposures can disrupt cytokine function which has the potential to affect the inflammatory response and immune competence thus leading to predisposition to chronic illness

Tributyltin alters secretion of interleukin 1 beta from human immune cells

Tributyltin (TBT) is an organotin compound that has been used as a biocide in a variety of industrial applications such as wood preservation, antifouling paint, and antifungal agents. Known for contaminating the marine environment, it has been found in human blood samples, and mammals with TBT exposure have shown increased incidences of tumors. Interleukin 1 beta (IL-1β) is a pro-inflammatory cytokine that promotes cell growth, tissue repair, and immune response regulation. Produced predominately by both monocytes and macrophages, IL-1β appears to increase the invasiveness of certain tumors. This study shows that TBT modifies the secretion of IL-1β from increasingly reconstituted preparations of human immune cells. IL-1β secretion was examined after 24h, 48h, or 6 day exposures to TBT concentrations of 25 to 200 nM in a preparation of highly enriched human NK cells, a monocyte-depleted (MD) preparation of human peripheral blood mononuclear cells (MD-PBMCs), PBMCs, granulocytes, and a preparation combining both PBMCs and granulocytes. TBT altered IL-1β secretion from all of the cells preparations. The 200 nM concentration of TBT normally blocked the secretion of IL-1β, while some of the lower concentrations of TBT elevated secretion of IL-1β. The concentrations and lengths of exposure to TBT that caused statistically significant increases in IL-1β secretion from human immune cells varied from one donor to the next. MD-PBMCs were further studied to determine if TBT-induced increases in IL-1β secretion were due to TBT-induced alterations of the ILβ processing enzyme (Caspase-1), mitogen-activated protein kinases (MAPKs), or nuclear factor kappa B (NFκB)