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Microbiology (Reading, England) Nov 2020the aetiological agent of cholera, possesses multiple iron acquisition systems, including those for the transport of siderophores. How these systems benefit in...
the aetiological agent of cholera, possesses multiple iron acquisition systems, including those for the transport of siderophores. How these systems benefit in low-iron, polymicrobial communities in environmental settings or during infection remains poorly understood. Here, we demonstrate that in iron-limiting conditions, co-culture of with a number of individual siderophore-producing microbes significantly promoted growth . We further show that in the host environment with low iron, colonizes better in adult mice in the presence of the siderophore-producing commensal . Taken together, our results suggest that in aquatic reservoirs or during infection, may overcome environmental and host iron restriction by hijacking siderophores from other microbes.
Topics: Animals; Bacterial Outer Membrane Proteins; Coculture Techniques; Enterobactin; Escherichia coli; Gastrointestinal Microbiome; Iron Deficiencies; Mice; Microbial Viability; Receptors, Cell Surface; Seawater; Siderophores; Vibrio cholerae
PubMed: 33074088
DOI: 10.1099/mic.0.000975 -
ChemCatChem May 2021Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a versatile class of biocatalysts and feature a variety of industrial applications. However, PLP is light sensitive...
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a versatile class of biocatalysts and feature a variety of industrial applications. However, PLP is light sensitive and can cause inactivation of enzymes in certain light conditions. As most of the PLP-dependent enzymes are usually not handled in dark conditions, we evaluated the effect of visible light on the activity of PLP-dependent enzymes during production as well as transformation. We tested four amine transaminases, from , , and a variant from as well as two lysine decarboxylases, from and the LDCc from . It appeared that five of these six enzymes suffered from a significant decrease in activity by up to 90 % when handled in laboratory light conditions. Surprisingly, only the amine transaminase variant from appeared to be unaffected by light exposure and even showed an activation to 150 % relative activity over the course of 6 h regardless of the light conditions.
PubMed: 34249169
DOI: 10.1002/cctc.202100163 -
Bioresources and Bioprocessing Nov 2023(+)-Neomenthylamine is an important industrial precursor used to synthesize high value-added chemicals. Here, we report a novel biocatalytic route to synthesize...
(+)-Neomenthylamine is an important industrial precursor used to synthesize high value-added chemicals. Here, we report a novel biocatalytic route to synthesize (+)-neomenthylamine by amination of readily available (-)-menthone substrate using ω-transaminase. By screening a panel of ω-transaminases, an ω-transaminase from Vibrio fluvialis JS17 was identified with considerable amination activity to (-)-menthone, and then characterization of enzymatic properties was conducted for the enzyme. Under optimized conditions, 10 mM (-)-menthone was transformed in a mild aqueous phase with 4.7 mM product yielded in 24 h. The biocatalytic route using inexpensive starting materials (ketone substrate and amino donor) and mild reaction conditions represents an easy and green approach for (+)-neomenthylamine synthesis. This method underscores the potential of biocatalysts in the synthesis of unnatural terpenoid amine derivatives.
PubMed: 38647910
DOI: 10.1186/s40643-023-00693-w -
Marine Pollution Bulletin Nov 2022Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined...
Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics.
Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.
Topics: Avicennia; Wetlands; Rhizosphere; Metagenomics; Cadmium; Metals, Heavy; Microbiota
PubMed: 36219973
DOI: 10.1016/j.marpolbul.2022.114204 -
Heliyon Oct 2022This study investigated the bacteriological quality of ready-to-eat (RTE) African salads in Enugu metropolis, Enugu, Nigeria. A total of 10 samples of African salad were...
Culture-dependent examination of the bacteriological quality of ready-to-eat African salads in Enugu metropolis, Nigeria and antibiotic resistance profile of associated bacteria.
This study investigated the bacteriological quality of ready-to-eat (RTE) African salads in Enugu metropolis, Enugu, Nigeria. A total of 10 samples of African salad were purchased from 10 different vendors in Enugu metropolis. The samples were purchased from Agbani Road, Ogbete, Mayor, Uwani, Kenyatta, Achara Layout, Obiagu and Timber. Isolation and enumeration of bacterial isolates were done using Nutrient agar, Eosin Methylene Blue (EMB) agar, Thiosulphate-citrate-bile salts-sucrose (TCBS) agar, Salmonella-Shigella Agar (SSA) and MacConkey agar, following standard methods. Identification of the bacterial isolates were done through biochemical tests and the Analytical Profile Index (API 20E) test kit. The antibiotic sensitivity of the bacterial isolates was also done using the Kirby Bauer disc diffusion method. Total culturable heterotrophic count was above 300 colonies across the samples. The highest bacterial counts recorded on EMB, SSA and TCBS across the samples were 6.3 × 10 CFU/g, 7.4 × 10 CFU/g and 1.21 × 10 CFU/g respectively. The identities of the organisms were; spp., , , , , and . The prevalent organism across the samples was spp. The antibiotic sensitivity test suggested that spp. was resistant to Ampiclox and Amoxycillin but sensitive to Erythromycin, Pefloxacin and Septrin. From this study, it was discovered that consumers of RTE African salad from majority of the vendors across Enugu metropolis are at risk of severe food poisoning.
PubMed: 36212018
DOI: 10.1016/j.heliyon.2022.e10782 -
Frontiers in Microbiology 2021Despite an increasing appreciation in the importance of host-microbe interactions in ecological and evolutionary processes, information on the gut microbial communities...
Despite an increasing appreciation in the importance of host-microbe interactions in ecological and evolutionary processes, information on the gut microbial communities of some marine mammals is still lacking. Moreover, whether diet, environment, or host phylogeny has the greatest impact on microbial community structure is still unknown. To fill part of this knowledge gap, we exploited a natural experiment provided by an aquarium with belugas () affiliated with family Monodontidae, Pacific white-sided dolphins () and common bottlenose dolphin () affiliated with family Delphinidae, and Cape fur seals () affiliated with family Otariidae. Results show significant differences in microbial community composition of whales, dolphins, and fur seals and indicate that host phylogeny (family level) plays the most important role in shaping the microbial communities, rather than food and environment. In general, the gut microbial communities of dolphins had significantly lower diversity compared to that of whales and fur seals. Overall, the gut microbial communities were mainly composed of Firmicutes and Gammaproteobacteria, together with some from Bacteroidetes, Fusobacteria, and Epsilonbacteraeota. However, specific bacterial lineages were differentially distributed among the marine mammal groups. For instance, , , and were the dominant bacterial lineages in the gut of belugas, while for Cape fur seals, and were the main bacterial lineages. Moreover, gut microbial communities in both Pacific white-sided dolphins and common bottlenose dolphins were dominated by a number of pathogenic bacteria, including , , and , reflecting the poor health condition of these animals. Although there is a growing recognition of the role microorganisms play in the gut of marine mammals, current knowledge about these microbial communities is still severely lacking. Large-scale research studies should be undertaken to reveal the roles played by the gut microbiota of different marine mammal species.
PubMed: 34745077
DOI: 10.3389/fmicb.2021.769012 -
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 -
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