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Protein-Based Bioscavengers of Organophosphorus Nerve Agents
Published in Brian J. Lukey, James A. Romano, Salem Harry, Chemical Warfare Agents, 2019
Moshe Goldsmith, Yacov Ashani, Tamara. C. Otto, C. Linn Cadieux, David. S. Riddle
Phosphotriesterase (PTE), also termed organophosphate hydrolase (OPH) (EC 3.1.8.1), is a 336-amino acid (36 kDa), zinc-dependent hydrolase, structured as an (αβ)8 TIM-barrel (Benning et al., 1994). It is a bacterial enzyme that belongs to the amidohydrolase superfamily and was first identified in soil bacteria that hydrolyzed the pesticide parathion (Serdar et al., 1982). Since man-made OP pesticides were introduced into the environment only in the 1950s, and since its catalytic efficiency of hydrolysis approaches the diffusion limit (e.g., kcat/KM ~ 109 M−1 min−1 with paraoxon), it was suggested that PTE is the product of the recent and rapid natural evolution of a lactonase (Afriat-Jurnou et al., 2012; Afriat et al., 2006). PTE is encoded on a natural plasmid (pCMS1) in a bacterial strain that was originally classified as Pseudomonas diminuta strain MG (Serdar and Gibson, 1985; Serdar et al., 1982) and later reclassified as Brevundimonas diminuta (Segers et al., 1994). The fact that the gene encoding PTE (opd) was found on a plasmid meant that it could be transferred to other bacterial strains. Indeed, PTE was also found independently in unrelated soil bacteria isolated from different parts of the world, such as Sphingobium fuliginis (former Flavobacterium sp. ATCC 27551) identified in the Philippines (Kawahara et al., 2010; Mulbry and Karns, 1989; Sethunathan and Yoshida, 1973) and Brevundimonas diminuta and Pseudomonas putida, identified in the United States (Iyer et al., 2013b; Serdar et al., 1982). Plasmid pCMS1 from B. diminuta was found to be self-transmissible and responsible for the horizontal transfer of its opd gene between soil bacteria (Pandeeti et al., 2011). OP pesticides can become a valuable source of phosphorus for soil bacteria. However, they need to be imported into the cell and degraded to simpler molecules, such as phosphoric acid, to be used for growth and energy. Accordingly, the expression of PTE from B. diminuta was found to be targeted to the inner membrane of the bacteria, where it becomes membrane bound and associated with phosphatases and with a phosphate transporter (Parthasarathy et al., 2016).
The role of gastric microbiota in gastric cancer
Published in Gut Microbes, 2020
Oliver A. Stewart, Fen Wu, Yu Chen
One study demonstrated decreased abundance of Sphingobium yanoikuyae in patients with gastric cancer compared to patients with superficial gastritis.25 This species is capable of degrading aromatic hydrocarbons, which are a group of molecules that has potential carcinogenic effects.25 This study was the first study to suggest a negative association between Sphingobium yanoikuvae and gastric cancer. Park et al.’s 2019 study found an increased level of abundance of Rhiozobiales in patients with intestinal metaplasia compared to patients with chronic superficial gastritis.26 In addition, they found an increased abundance of genes encoding type IV secretion system (T4SS) proteins in the metagenome of patients with intestinal metaplasia. T4SS is one type of secretion system used by microorganisms to transport macromolecules across the cell envelope.35 Many pathogenic bacteria use the T4SS in order to transfer proteins known as virulence factors that confer a bacterium with its pathogenicity.36 T4SS proteins consist of a smaller subset of proteins that allow injection of H. pylori’s proposed main virulence factor, CagA, from the bacterial cytoplasm to the cytoplasm of gastric epithelial cells.37 Although the researchers did not find direct evidence of horizontal genetic transfer between Rhizobiales and H. pylori, they hypothesized that it is possible that T4SS genetic transfer occurs between H. pylori and members of the microbiota, thus contributing to H. pylori’s carcinogenicity.
Biofilm diversity, structure and matrix seasonality in a full-scale cooling tower
Published in Biofouling, 2018
L. Di Gregorio, R. Congestri, V. Tandoi, T. R. Neu, S. Rossetti, F. Di Pippo
Detailed analysis of the NGS data (Figure 8) showed that in winter, source community 16S rRNA gene sequences affiliated to Betaproteobacteria accounted for 67.7%, comprising mainly the genus Herminiimonas (52.6%) in the family Oxalobacteraceae, which includes arsenite oxidising species, whereas members of the family Comamonadaceae (12.7% of the total) consisted mainly of the genera Hydrogenophaga (4.9%) and Limnohabitans (4.9%). Among the Alphaproteobacteria (24.4%), the Sphingomonadaceae predominated (17.5%), with sequences affiliated to Sphingobium sp. (11.9%).
Application of next-generation sequencing in the diagnosis of gastric cancer
Published in Scandinavian Journal of Gastroenterology, 2022
Narges Moradi, Solmaz Ohadian Moghadam, Siamak Heidarzadeh
In 2018, Hu et al., conducted a study on the role of gastric microbiota in superficial gastritis and GC in 11 patients using shotgun metagenomics sequencing. Their results presented novel changes in the gastric microbiome in patients with GC including depletion of 31 taxa, enrichment of 13 bacterial taxa and reduced species richness. They also reported on the depletion of Sphingobium yanoikuyae, a degrader of carcinogenic compounds. Studying on microbiome composition will lead to better prognosis and diagnosis of GC [84].