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The FEBS Journal Oct 2019The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This...
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest K values (highest affinity) and highest specificity constant (k /K ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
Topics: Amino Acid Sequence; Aminocaproic Acid; Bacterial Proteins; Caprolactam; Crystallography, X-Ray; Models, Molecular; Phylogeny; Pseudomonas; Pyridoxal Phosphate; Sequence Homology; Substrate Specificity; Transaminases
PubMed: 31162815
DOI: 10.1111/febs.14950 -
Computational and Structural... 2019Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5'-phosphate... (Review)
Review
Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5'-phosphate (PLP) as a cofactor. TAs are categorized according to the amino group position of the donor substrate and respective TAs recognize their own specific substrates. Over the past decade, a number of TA structures have been determined by X-ray crystallography. On the basis of the structural information, the detailed mechanism of substrate recognition by TAs has also been elucidated. In this review, fold type I TAs are addressed intensively. Comparative studies on structural differences between the apo and holo forms of fold type I TAs have demonstrated that regions containing the active site exhibit structural plasticity in the apo form, facilitating PLP insertion into the active site. In addition, given that TAs recognize two different kinds of substrates, they possess dual substrate specificity. It is known that spatial rearrangements of active site residues occur upon binding of the substrates. Intriguingly, positively charged residues are predominantly distributed at the active site cavity. The electric field generated by such charge distributions may attract negatively charged molecules, such as PLP and amino group acceptors, into the active site. Indeed, TAs show remarkable dynamics in diverse aspects. In this review, we describe the comprehensive working mechanism of fold type I TAs, with a focus on conformational changes.
PubMed: 31452855
DOI: 10.1016/j.csbj.2019.07.007 -
Fish & Shellfish Immunology May 2023In recent years, the widespread use of antibiotics in intensive grouper mariculture has resulted in the ineffectiveness of antibiotic treatment, leading to an increasing...
Screening of host gut-derived probiotics and effects of feeding probiotics on growth, immunity, and antioxidant enzyme activity of hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂).
In recent years, the widespread use of antibiotics in intensive grouper mariculture has resulted in the ineffectiveness of antibiotic treatment, leading to an increasing incidence of diseases caused by bacteria, viruses, and parasites, causing serious economic losses. Hence, it is crucial to develop alternative strategies to antibiotics for healthy and sustainable development of the mariculture industry. Here, we aimed to screen host gut-derived probiotics and evaluate its effects on growth and immunity of grouper. In this study, 43 bacterial strains were isolated from the intestine of the hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), and a potential probiotic strain G1-26, which can efficiently secrete amylase, protease, and lipase, was obtained using different screening mediums. Based on 16S rDNA sequencing, the potential probiotic strain G1-26 was identified as Vibrio fluvialis. The results of a biological characteristic evaluation showed that V. fluvialis G1-26 could grow at 25-45 °C, pH 5.5-7.5, salinity 10-40, and bile salt concentration 0-0.030%, and produce amylase, lipase, and protease under different culture conditions. Additionally, V. fluvialis G1-26 is sensitive to many antibiotics and does not exhibit aquatic biotoxicity. Subsequently, hybrid groupers were fed diets containing V. fluvialis G1-26 at different concentrations (0, 10, 10, and 10 CFU/g) for 60 d. The results showed that V. fluvialis G1-26 at 10 CFU/g did not significantly affect the growth performance of the hybrid grouper (P > 0.05). V. fluvialis G1-26 supplementation at 10 and 10 CFU/g significantly promoted the relative expression of immune-related genes in hybrid groupers (TLR3, TLR5, IL-1β, IL-8, IL-10, CTL, LysC, TNF-2, and MHC-2) and improved the activities of alkaline phosphatase, acid phosphatase, total superoxide dismutase, and total protein in the liver. In conclusion, V. fluvialis G1-26, a potential probiotic strain isolated from the intestine of the hybrid grouper, can be used as an effective immunopotentiator at an optimal dose of 10 CFU/g diet. Our results provide a scientific basis for the development and utilization of probiotics in the grouper mariculture industry.
Topics: Animals; Antioxidants; Bass; Diet; Probiotics; Peptide Hydrolases; Amylases; Lipase; Animal Feed
PubMed: 36966895
DOI: 10.1016/j.fsi.2023.108700 -
Complete genomic sequence of strain IDH5335 isolated from a patient with diarrhea in Kolkata, India.Microbiology Resource Announcements Dec 2023We isolated a strain (IDH5335) from a stool sample collected from a patient with diarrhea. In this announcement, we report the complete genomic sequence of this...
We isolated a strain (IDH5335) from a stool sample collected from a patient with diarrhea. In this announcement, we report the complete genomic sequence of this organism, which was obtained by combining Illumina and Oxford Nanopore sequencing data.
PubMed: 37943041
DOI: 10.1128/MRA.00707-23 -
Frontiers in Microbiology 2023High hydrostatic pressure (HHP) regulated gene expression is one of the most commonly adopted strategies for microbial adaptation to the deep-sea environments....
High hydrostatic pressure (HHP) regulated gene expression is one of the most commonly adopted strategies for microbial adaptation to the deep-sea environments. Previously we showed that the HHP-inducible trimethylamine N-oxide (TMAO) reductase improves the pressure tolerance of deep-sea strain QY27. Here, we investigated the molecular mechanism of HHP-responsive regulation of TMAO reductase TorA. By constructing and deletion mutants, we demonstrated that the two-component regulator TorR and sensor TorS are responsible for the HHP-responsive regulation of . Unlike known HHP-responsive regulatory system, the abundance of and was not affected by HHP. Complementation of the Δ mutant with TorS altered at conserved phosphorylation sites revealed that the three sites were indispensable for substrate-induced regulation, but only the histidine located in the alternative transmitter domain was involved in pressure-responsive regulation. Taken together, we demonstrated that the induction of TMAO reductase by HHP is mediated through the TorRS system and proposed a bifurcation of signal transduction in pressure-responsive regulation from the substrate-induction. This work provides novel knowledge of the pressure regulated gene expression and will promote the understanding of the microbial adaptation to the deep-sea HHP environment.
PubMed: 38029070
DOI: 10.3389/fmicb.2023.1291578 -
Foods (Basel, Switzerland) Mar 2023Previous research has shown that freshwater edible fish imported into Australia are not compliant with Australian importation guidelines and as a result may be high risk...
Previous research has shown that freshwater edible fish imported into Australia are not compliant with Australian importation guidelines and as a result may be high risk for bacterial contamination. In the present study, the outer surface of imported freshwater fish were swabbed, cultured, confirmatory tests performed and antimicrobial patterns investigated. Channidae fish (Sp. A/n = 66) were contaminated with zoonotic sp./ (n = 1/66) and other bacteria implicated in cases of opportunistic human infection, these being sp. (including . and (n = 34/66)); sp. (n = 32/66); (n = 27/66) and (n = 3/66). Pangasiidae fish (Species B/n = 47) were contaminated with zoonotic (n = 10/47); sp. (n = 6/47) and environmental bacteria sp. (n = 3/47). One sample was resistant to all antimicrobials tested and is considered to be Methicillin Resistant . Mud, natural diet, or vegetation identified in Sp. A fish/or packaging were significantly associated with the presence of spp. The study also showed that visibly clean fish (Sp. B) may harbour zoonotic bacteria and that certain types of bacteria are common to fish groups, preparations, and contaminants. Further investigations are required to support the development of appropriate food safety recommendations in Australia.
PubMed: 36981215
DOI: 10.3390/foods12061288 -
Access Microbiology 2022spp. are Gram-negative bacteria found in marine ecosystems. Non-cholera spp. can cause gastrointestinal infections and can also lead to wound infections through...
spp. are Gram-negative bacteria found in marine ecosystems. Non-cholera spp. can cause gastrointestinal infections and can also lead to wound infections through exposure to contaminated seawater. infections are increasingly documented from the Baltic Sea due to extended warm weather periods. We describe the first isolation of from a wound infection acquired by an impalement injury in the shallow waters of the Baltic Sea. The severe infection required amputation of the third toe. Whole genome sequencing of the isolate was performed and revealed a genome consisting of two circular chromosomes with a size of 1.57 and 3.24 Mb.
PubMed: 35252751
DOI: 10.1099/acmi.0.000312 -
Journal of Global Antimicrobial... Dec 2023
Topics: Genomic Islands; Salmonella; beta-Lactamases
PubMed: 37748579
DOI: 10.1016/j.jgar.2023.09.014 -
Journal of Dairy Science Jan 2023Composting is a common practice used for treating animal manures before they are used as organic fertilizers for crop production. Whether composting can effectively...
Composting is a common practice used for treating animal manures before they are used as organic fertilizers for crop production. Whether composting can effectively reduce microbial pathogens and antibiotic resistance genes remain poorly understood. In this study, we compared 3 different dairy manure composting methods-anaerobic fermentation (AF), static compost (SC), and organic fertilizer production (OFP)-for their effects on antibiotic-resistant bacteria, antibiotic resistance genes, and microbial community diversity in the treated manures. The 3 composting methods produced variable and distinct effects on antibiotic-resistant bacteria, zoonotic bacteria, and resistance genes, some of which were decreased and others of which showed no significant changes during composting. Particularly, SC and OFP reduced chloramphenicol resistance gene fexA and opportunistic pathogen Vibrio fluvialis, whereas AF significantly reduced tetracycline resistance gene tetB and opportunistic pathogens Enterococcus faecium and Escherichia fergusonii. The compositions of microbial communities varied significantly during the composting processes, and there were significant differences between the 3 composting methods. In all 3 composts, the dominant phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Interestingly, Firmicutes, Proteobacteria, and Bacteroidetes remained stable in the entire AF process, whereas they were dominated at the beginning, decreased at the early stage of composting, and rebounded at the later stage during SC and OFP. In general, SC and OFP produced a more profound effect than AF on microbial community diversities, pathogens, and dominant species. Additionally, Enterococcus aquimarinus was isolated from AF for the first time. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States function prediction analysis indicated that the genes related to membrane transport and amino acid metabolism were abundant in the 3 composts. The metabolism of amino acids, lipids, and carbohydrates increased as composting progressed. The biosynthesis of antibiotics was enhanced after fermentation in the 3 composting methods, and the increase in the SC was the most obvious. These results reveal dynamic changes in antibiotic-resistant bacteria, antibiotic resistance genes, microbial community composition, and function succession in different dairy manure composts and provide useful information for further optimization of composting practices.
Topics: Cattle; Animals; Composting; Manure; Anti-Bacterial Agents; Phylogeny; Soil Microbiology; Drug Resistance, Microbial; Bacteria; Genes, Bacterial; Soil
PubMed: 36333143
DOI: 10.3168/jds.2022-22193 -
Microbial Ecology Aug 2020It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease"...
It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.
Topics: Actinobacteria; Animals; Aquaculture; Bacteria; China; Gastrointestinal Microbiome; Penaeidae; Vibrio
PubMed: 32307553
DOI: 10.1007/s00248-020-01511-y