ABSTRACT
Reductive dehalogenases are corrinoid and iron-sulfur cluster-containing enzymes that catalyze the reductive removal of a halogen atom. The oxygen-sensitive and membrane-associated nature of the respiratory reductive dehalogenases has hindered their detailed kinetic study. In contrast, the evolutionarily related catabolic reductive dehalogenases are oxygen tolerant, with those that are naturally fused to a reductase domain with similarity to phthalate dioxygenase presenting attractive targets for further study. We present efficient heterologous expression of a self-sufficient catabolic reductive dehalogenase from Jhaorihella thermophila in Escherichia coli. Combining the use of maltose-binding protein as a solubility-enhancing tag with the btuCEDFB cobalamin uptake system affords up to 40% cobalamin occupancy and a full complement of iron-sulfur clusters. The enzyme is able to efficiently perform NADPH-dependent dehalogenation of brominated and iodinated phenolic compounds, including the flame retardant tetrabromobisphenol, under both anaerobic and aerobic conditions. NADPH consumption is tightly coupled to product formation. Surprisingly, corresponding chlorinated compounds only act as competitive inhibitors. Electron paramagnetic resonance spectroscopy reveals loss of the Co(II) signal observed in the resting state of the enzyme under steady-state conditions, suggesting accumulation of Co(I)/(III) species prior to the rate-limiting step. In vivo reductive debromination activity is readily observed, and when the enzyme is expressed in E. coli strain W, supports growth on 3-bromo-4-hydroxyphenylacetic as a sole carbon source. This demonstrates the potential for catabolic reductive dehalogenases for future application in bioremediation.
Subject(s)
Hydrolases , NADP , Rhodobacteraceae , Escherichia coli/genetics , NADP/metabolism , Oxygen/chemistry , Vitamin B 12/metabolism , Phenols/chemistry , Phenols/metabolism , Electron Spin Resonance Spectroscopy , Hydrolases/chemistry , Hydrolases/genetics , Hydrolases/isolation & purification , Hydrolases/metabolism , Rhodobacteraceae/enzymology , Rhodobacteraceae/genetics , Protein Structure, Tertiary , Models, Molecular , Maltose-Binding Proteins/genetics , Maltose-Binding Proteins/metabolism , Recombinant Fusion Proteins/metabolism , Coenzymes/metabolismABSTRACT
The ubiquitous UbiD family of reversible decarboxylases is implicated in a wide range of microbial processes and depends on the prenylated flavin mononucleotide cofactor for catalysis. However, only a handful of UbiD family members have been characterized in detail, and comparison between these has suggested considerable variability in enzyme dynamics and mechanism linked to substrate specificity. In this study, we provide structural and biochemical insights into the indole-3-carboxylic acid decarboxylase, representing an UbiD enzyme activity distinct from those previously studied. Structural insights from crystal structure determination combined with small-angle X-ray scattering measurements reveal that the enzyme likely undergoes an open-closed transition as a consequence of domain motion, an event that is likely coupled to catalysis. We also demonstrate that the indole-3-carboxylic acid decarboxylase can be coupled with carboxylic acid reductase to produce indole-3-carboxyaldehyde from indole + CO2 under ambient conditions. These insights provide further evidence for a common mode of action in the widespread UbiD enzyme family.
Subject(s)
Carboxy-Lyases , Models, Molecular , Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Flavin Mononucleotide/metabolism , Protein Structure, Tertiary , Structure-Activity Relationship , Substrate SpecificityABSTRACT
BACKGROUND: Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC. METHODS: Parsortix microfluidic-enriched CTCs from 14 treatment-naïve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data. RESULTS: CTCs were detected in 13/14 patients with CTC counts of 2-24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype. DISCUSSION: We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.
Subject(s)
Head and Neck Neoplasms , Neoplastic Cells, Circulating , Humans , Neoplastic Cells, Circulating/pathology , Squamous Cell Carcinoma of Head and Neck , Feasibility Studies , Proteomics , Biomarkers, Tumor , Epithelial-Mesenchymal Transition/geneticsABSTRACT
The family of cobalamin class-III dependent enzymes is composed of the reductive dehalogenases (RDases) and related epoxyqueuosine reductases. RDases are crucial for the energy conserving process of organohalide respiration. These enzymes have the ability to reductively cleave carbon-halogen bonds, present in a number of environmentally hazardous pollutants, making them of significant interest for bioremediation applications. Unfortunately, it is difficult to obtain sufficient yields of pure RDase isolated from organohalide respiring bacteria for biochemical studies. Hence, robust heterologous expression systems are required that yield the active holo-enzyme which requires both iron-sulphur cluster and cobalamin incorporation. We present a comparative study of the heterologous expression strains Bacillus megaterium, Escherichia coli HMS174(DE3), Shimwellia blattae and a commercial strain of Vibrio natrigenes, for cobalamin class-III dependent enzymes expression. The Nitratireductor pacificus pht-3B reductive dehalogenase (NpRdhA) and the epoxyqueuosine reductase from Streptococcus thermophilus (StoQ) were used as model enzymes. We also analysed whether co-expression of the cobalamin transporter BtuB, supports increased cobalamin incorporation into these enzymes in E. coli. We conclude that while expression in Bacillus megaterium resulted in the highest levels of cofactor incorporation, co-expression of BtuB in E. coli presents an appropriate balance between cofactor incorporation and protein yield in both cases.
Subject(s)
Bacterial Proteins/genetics , Escherichia coli/genetics , Gene Expression , Iron-Sulfur Proteins/genetics , Oxidoreductases/genetics , Vitamin B 12/chemistry , Bacillus megaterium/enzymology , Bacillus megaterium/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Binding Sites , Biodegradation, Environmental , Cloning, Molecular , Enterobacteriaceae/enzymology , Enterobacteriaceae/genetics , Escherichia coli/enzymology , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Halogens/chemistry , Halogens/metabolism , Iron-Sulfur Proteins/chemistry , Iron-Sulfur Proteins/metabolism , Kinetics , Models, Molecular , Nucleoside Q/analogs & derivatives , Nucleoside Q/chemistry , Nucleoside Q/metabolism , Oxidoreductases/chemistry , Oxidoreductases/metabolism , Phyllobacteriaceae/enzymology , Phyllobacteriaceae/genetics , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Streptococcus thermophilus/enzymology , Streptococcus thermophilus/genetics , Vibrio/enzymology , Vibrio/genetics , Vitamin B 12/metabolismABSTRACT
Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria, with substrates including polychlorinated biphenyls or dioxins. Reductive dehalogenases form a distinct subfamily of cobalamin (B12)-dependent enzymes that are usually membrane associated and oxygen sensitive, hindering detailed studies. Here we report the characterization of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR (electron paramagnetic resonance) spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-cobalt bond chemistry catalysed by the other cobalamin-dependent subfamilies, we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-cobalt bond formation. This presents a new model in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis.
Subject(s)
Halogenation , Oxidoreductases/chemistry , Oxidoreductases/metabolism , Phyllobacteriaceae/enzymology , Vitamin B 12/metabolism , Biocatalysis , Cobalt/chemistry , Cobalt/metabolism , Crystallography, X-Ray , Electron Spin Resonance Spectroscopy , Models, Molecular , Oxidation-Reduction , Oxygen/metabolism , Phenols/chemistry , Phenols/metabolism , Protein Conformation , Solubility , Vitamin B 12/chemistryABSTRACT
Ubiquinone (also known as coenzyme Q) is a ubiquitous lipid-soluble redox cofactor that is an essential component of electron transfer chains. Eleven genes have been implicated in bacterial ubiquinone biosynthesis, including ubiX and ubiD, which are responsible for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor. Despite structural and biochemical characterization of UbiX as a flavin mononucleotide (FMN)-binding protein, no decarboxylase activity has been detected. Here we report that UbiX produces a novel flavin-derived cofactor required for the decarboxylase activity of UbiD. UbiX acts as a flavin prenyltransferase, linking a dimethylallyl moiety to the flavin N5 and C6 atoms. This adds a fourth non-aromatic ring to the flavin isoalloxazine group. In contrast to other prenyltransferases, UbiX is metal-independent and requires dimethylallyl-monophosphate as substrate. Kinetic crystallography reveals that the prenyltransferase mechanism of UbiX resembles that of the terpene synthases. The active site environment is dominated by π systems, which assist phosphate-C1' bond breakage following FMN reduction, leading to formation of the N5-C1' bond. UbiX then acts as a chaperone for adduct reorientation, via transient carbocation species, leading ultimately to formation of the dimethylallyl C3'-C6 bond. Our findings establish the mechanism for formation of a new flavin-derived cofactor, extending both flavin and terpenoid biochemical repertoires.
Subject(s)
Biocatalysis , Carboxy-Lyases/metabolism , Dimethylallyltranstransferase/metabolism , Flavins/metabolism , Pseudomonas aeruginosa/enzymology , Pseudomonas aeruginosa/metabolism , Ubiquinone/biosynthesis , Alkyl and Aryl Transferases/chemistry , Alkyl and Aryl Transferases/metabolism , Aspergillus niger/enzymology , Aspergillus niger/genetics , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Catalytic Domain , Crystallography, X-Ray , Cycloaddition Reaction , Decarboxylation , Dimethylallyltranstransferase/chemistry , Dimethylallyltranstransferase/genetics , Electron Transport , Flavin Mononucleotide/metabolism , Flavins/biosynthesis , Flavins/chemistry , Models, Molecular , Pseudomonas aeruginosa/geneticsABSTRACT
The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthesis or microbial biodegradation of aromatic compounds, respectively. Despite biochemical studies on individual gene products, the composition and cofactor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear. Here we show that Fdc1 is solely responsible for the reversible decarboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesized by the associated UbiX/Pad1. Atomic resolution crystal structures reveal that two distinct isomers of the oxidized cofactor can be observed, an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with markedly altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor-cofactor adduct suggests that 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. Although 1,3-dipolar cycloaddition is commonly used in organic chemistry, we propose that this presents the first example, to our knowledge, of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc1/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.
Subject(s)
Biocatalysis , Carboxy-Lyases/metabolism , Cycloaddition Reaction , Alkenes/chemistry , Alkenes/metabolism , Aspergillus niger/enzymology , Aspergillus niger/genetics , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Crystallography, X-Ray , Decarboxylation , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Flavins/biosynthesis , Flavins/chemistry , Flavins/metabolism , Isomerism , Ligands , Models, Molecular , Ubiquinone/biosynthesisABSTRACT
Rates of loco-regional recurrence and distant metastasis remain high among head and neck squamous cell carcinoma (HNSCC) patients, despite advancing cancer treatment modalities and therapeutic agents. One area that has generated considerable interest is the immune landscape of the tumour, heralding a wave of immune checkpoint inhibitors with notable efficacy in recurrent/metastatic HNSCC patients. However, HNSCC remains poorly served by biomarkers that can direct treatment in a personalised fashion to target the tumour heterogeneity seen between patients. Detection and analysis of circulating tumour cells (CTCs) in HNSCC has provided a previously unseen view of the metastasis forming cells that are potentially contributing to poor clinical outcomes. In particular, identifying CTC expression of phenotypic and druggable protein markers has allowed CTC sub-populations to be defined that hold prognostic value or are potential therapeutic targets themselves. The aim of this systematic review was to examine the role of CTC immune-marker expression as prognostic/therapeutic biomarkers in HNSCC by evaluating progress to date and discussing areas for future research. Our results highlight how few studies have been able to demonstrate prognostic significance of immune-marker expression in CTCs. As expected, the immune checkpoint PD-L1 was the most widely investigated marker. However, no studies evaluated CTC target immune marker expression in immunotherapy cohorts. Despite these findings, the data presented demonstrate promise that CTCs may be a source of future biomarkers for immunotherapy and will provide valuable information regarding the potential immune evasion of these metastasis forming cells.
Subject(s)
Biomarkers, Tumor/genetics , Head and Neck Neoplasms/diagnosis , Immunologic Factors/genetics , Neoplastic Cells, Circulating/metabolism , Squamous Cell Carcinoma of Head and Neck/diagnosis , Adult , Aged , Aged, 80 and over , B7-H1 Antigen/genetics , B7-H1 Antigen/metabolism , Biomarkers, Tumor/metabolism , Female , Gene Expression Regulation, Neoplastic/immunology , Head and Neck Neoplasms/epidemiology , Head and Neck Neoplasms/genetics , Head and Neck Neoplasms/pathology , Humans , Immunologic Factors/metabolism , Male , Middle Aged , Prognosis , Squamous Cell Carcinoma of Head and Neck/epidemiology , Squamous Cell Carcinoma of Head and Neck/genetics , Squamous Cell Carcinoma of Head and Neck/pathologyABSTRACT
The UbiD family of reversible decarboxylases act on aromatic, heteroaromatic, and unsaturated aliphatic acids and utilize a prenylated flavin mononucleotide (prFMN) as cofactor, bound adjacent to a conserved Glu-Arg-Glu/Asp ionic network in the enzyme's active site. It is proposed that UbiD activation requires oxidative maturation of the cofactor, for which two distinct isomers, prFMNketimine and prFMNiminium, have been observed. It also has been suggested that only the prFMNiminium form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Aspergillus niger Fdc1 as a model system, we reveal that isomerization of prFMNiminium to prFMNketimine is a light-dependent process that is largely independent of the Glu277-Arg173-Glu282 network and accompanied by irreversible loss of activity. On the other hand, efficient catalysis was highly dependent on an intact Glu-Arg-Glu network, as only Glu â Asp substitutions retain activity. Surprisingly, oxidative maturation to form the prFMNiminium species is severely affected only for the R173A variant. In summary, the unusual irreversible isomerization of prFMN is light-dependent and probably proceeds via high-energy intermediates but is independent of the Glu-Arg-Glu network. Our results from mutagenesis, crystallographic, spectroscopic, and kinetic experiments indicate a clear role for the Glu-Arg-Glu network in both catalysis and oxidative maturation.
Subject(s)
Aspergillus niger/enzymology , Carboxy-Lyases/chemistry , Carboxy-Lyases/metabolism , Flavin Mononucleotide/metabolism , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Aspergillus niger/chemistry , Aspergillus niger/genetics , Binding Sites , Carboxy-Lyases/genetics , Catalysis , Catalytic Domain , Conserved Sequence , Flavin Mononucleotide/chemistry , Fungal Proteins/genetics , Isomerism , Kinetics , Oxidation-ReductionABSTRACT
Reductive dehalogenases are corrinoid and iron-sulfur cluster-dependent enzymes that mostly act as the terminal oxidoreductases in the bacterial organohalide respiration process. This process often leads to detoxification of recalcitrant organohalide pollutants. While low cell yields and oxygen sensitivity hamper the study of many reductive dehalogenases, this is not the case for the nonrespiratory reductive dehalogenase NpRdhA from Nitratireductor pacificus. We here report in vitro and in vivo reconstitution of an NADPH-dependent reducing system for NpRdhA. Surprisingly, NpRdhA mediated organohalide reduction could not be supported using N. pacificus ferredoxin-NAD(P)H oxidoreductase and associated ferredoxins. Instead, we found a nonphysiological system comprised of the Escherichia coli flavodoxin reductase (EcFldr) in combination with spinach ferredoxin (SpFd) was able to support NADPH-dependent organohalide reduction by NpRdhA. Using this system, organohalide reduction can be performed under both anaerobic and aerobic conditions, with 1.1 ± 0.1 and 3.5 ± 0.3 equiv of NADPH consumed per product produced, respectively. No significant enzyme inactivation under aerobic conditions was observed, suggesting a Co(I) species is unlikely to be present under steady state conditions. Furthermore, reduction of the Co(II) resting state was not observed in the absence of substrate. Only the coexpression of EcFldr, SpFd, and NpRdhA in Bacillus megaterium conferred the latter with the ability to reduce brominated NpRdhA substrates in vivo, in agreement with our in vitro observations. Our work provides new insights into biological reductive dehalogenase reduction and establishes a blueprint for the minimal functional organohalide reduction module required for bioremediation in situ.
Subject(s)
Bacterial Proteins/metabolism , NADH, NADPH Oxidoreductases/metabolism , NADP/metabolism , Phyllobacteriaceae/enzymology , Bacterial Proteins/chemistry , Halogenation , Hydrogen-Ion Concentration , Models, Molecular , NADH, NADPH Oxidoreductases/chemistry , Osmolar Concentration , Oxidation-Reduction , Phyllobacteriaceae/chemistry , Phyllobacteriaceae/metabolismABSTRACT
The activity of the reversible decarboxylase enzyme Fdc1 is dependent on prenylated FMN (prFMN), a recently discovered cofactor. The oxidized prFMN supports a 1,3-dipolar cycloaddition mechanism that underpins reversible decarboxylation. Fdc1 is a distinct member of the UbiD family of enzymes, with the canonical UbiD catalyzing the (de)carboxylation of para-hydroxybenzoic acid-type substrates. Here we show that the Escherichia coli UbiD enzyme, which is implicated in ubiquinone biosynthesis, cannot be isolated in an active holoenzyme form despite the fact active holoFdc1 is readily obtained. Formation of holoUbiD requires reconstitution in vitro of the apoUbiD with reduced prFMN. Furthermore, although the Fdc1 apoenzyme can be readily reconstituted and activated, in vitro oxidation to the mature prFMN cofactor stalls at formation of a radical prFMN species in holoUbiD. Further oxidative maturation in vitro occurs only at alkaline pH, suggesting a proton-coupled electron transfer precedes formation of the fully oxidized prFMN. Crystal structures of holoUbiD reveal a relatively open active site potentially occluded from solvent through domain motion. The presence of a prFMN sulfite-adduct in one of the UbiD crystal structures confirms oxidative maturation does occur at ambient pH on a slow time scale. Activity could not be detected for a range of putative para-hydroxybenzoic acid substrates tested. However, the lack of an obvious hydrophobic binding pocket for the octaprenyl tail of the proposed ubiquinone precursor substrate does suggest UbiD might act on a non-prenylated precursor. Our data reveals an unexpected variation occurs in domain mobility, prFMN binding, and maturation by the UbiD enzyme family.
Subject(s)
Carboxy-Lyases/metabolism , Escherichia coli/metabolism , Flavin Mononucleotide/metabolism , Ubiquinone/metabolism , Binding Sites , Carboxy-Lyases/chemistry , Crystallography, X-Ray , Electron Spin Resonance Spectroscopy , Electron Transport , Escherichia coli/chemistry , Models, Molecular , Oxidation-Reduction , Prenylation , Protein Domains , Ubiquinone/chemistryABSTRACT
Nitrification of high total ammonia nitrogen-strength wastewaters is challenging due to free ammonia (FA) inhibition of nitrification. FA inhibition can potentially be alleviated by temporarily adsorbing ammonium (NH4+) to natural zeolite, such as chabazite, followed by direct zeolite bioregeneration via nitrification. In this research, the effectiveness of chabazite addition for reducing nitrification inhibition during treatment of centrate from anaerobic digestion of swine waste was quantified. A mathematical model was developed that accounts for ion exchange of NH4+ and sodium at the chabazite surface, surface diffusion of adsorbed NH4+ within the chabazite grains, sequential nitrification of aqueous NH4+ to nitrite and nitrate, and inhibition of nitritation and nitratation rates by NH4+. The model was calibrated using results of abiotic ion exchange and nitrification studies. Subsequently, nitrification tests were carried out with synthetic wastewater with a NH4+-N concentration of 1000 mg L-1, with and without chabazite. A chabazite dose of 150 g L-1 decreased the FA concentration to below the inhibitory level and increased the nitrification rate from 0.16 to 0.36 mg-N (g-VSS)-1 h-1. Following calibration, the model could predict the experimental data with no additional fitting parameters or parameter adjustment, in both the presence and absence of chabazite. The results suggest that the mathematical model provides a theoretically sound conceptual understanding of ion exchange assisted nitrification.
Subject(s)
Nitrification , Zeolites , Animals , Bioreactors , Livestock , Nitrogen , Swine , Waste Disposal, Fluid , WastewaterABSTRACT
The UbiX-UbiD system consists of the flavin prenyltransferase UbiX that produces prenylated FMN that serves as the cofactor for the (de)carboxylase UbiD. Recent developments have provided structural insights into the mechanism of both enzymes, detailing unusual chemistry in each case. The proposed reversible 1,3-dipolar cycloaddition between the cofactor and substrate serves as a model to explain many of the key UbiD family features. However, considerable variation exists in the many branches of the UbiD family tree.
Subject(s)
Carboxy-Lyases , Dimethylallyltranstransferase , Escherichia coli Proteins , Escherichia coli , Flavins , Flavoproteins , Prenylation/physiology , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Dimethylallyltranstransferase/chemistry , Dimethylallyltranstransferase/genetics , Dimethylallyltranstransferase/metabolism , Escherichia coli/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Flavins/biosynthesis , Flavins/chemistry , Flavins/genetics , Flavoproteins/chemistry , Flavoproteins/genetics , Flavoproteins/metabolismABSTRACT
Queuosine (Q) is a hypermodified RNA base that replaces guanine in the wobble positions of 5'-GUN-3' tRNA molecules. Q is exclusively made by bacteria, and the corresponding queuine base is a micronutrient salvaged by eukaryotic species. The final step in Q biosynthesis is the reduction of the epoxide precursor, epoxyqueuosine, to yield the Q cyclopentene ring. The epoxyqueuosine reductase responsible, QueG, shares distant homology with the cobalamin-dependent reductive dehalogenase (RdhA), however the role played by cobalamin in QueG catalysis has remained elusive. We report the solution and structural characterization of Streptococcus thermophilus QueG, revealing the enzyme harbors a redox chain consisting of two [4Fe-4S] clusters and a cob(II)alamin in the base-off form, similar to RdhAs. In contrast to the shared redox chain architecture, the QueG active site shares little homology with RdhA, with the notable exception of a conserved Tyr that is proposed to function as a proton donor during reductive dehalogenation. Docking of an epoxyqueuosine substrate suggests the QueG active site places the substrate cyclopentane moiety in close proximity of the cobalt. Both the Tyr and a conserved Asp are implicated as proton donors to the epoxide leaving group. This suggests that, in contrast to the unusual carbon-halogen bond chemistry catalyzed by RdhAs, QueG acts via Co-C bond formation. Our study establishes the common features of Class III cobalamin-dependent enzymes, and reveals an unexpected diversity in the reductive chemistry catalyzed by these enzymes.
Subject(s)
Nucleoside Q/analogs & derivatives , Nucleoside Q/biosynthesis , Oxidoreductases/chemistry , RNA, Transfer/chemistry , Streptococcus thermophilus/enzymology , Vitamin B 12/chemistry , Amino Acid Sequence , Catalysis , Cobalt/chemistry , Crystallography, X-Ray , Halogenation , Molecular Sequence Data , Nucleoside Q/chemistry , Oxidation-Reduction , Oxidoreductases/genetics , Protein Structure, Secondary , SolutionsABSTRACT
Oral epithelial dysplasia (OED) is a premalignant condition that carries an appreciable risk of malignant progression. The current grading system for severity, as defined by the World Health Organization, is a valuable clinical tool, but further work is required to improve the accuracy of predicting OED malignant progression. This systematic review aimed to assess progress in prognostic biomarker discovery in OED over the past 16 years. The primary objective was to update the latest evidence on prognostic biomarkers that may predict malignant progression of OED, with strict inclusion criteria of studies with a longitudinal design and long-term follow-up data to enhance the robustness and translational clinical potential of the findings. Of 2829 studies identified through the searching of five databases, 20 met our inclusion criteria. These studies investigated a total of 32 biomarkers, 20 of which demonstrated significant potential to predict malignant progression of OED. Meta-analysis demonstrated the significant prognostic value of four biomarkers: podoplanin, EGFR expression, p16 methylation, and DNA aneuploidy. Our review has identified 20 reported biomarkers with prognostic potential to predict malignant progression in OED, but their translation into clinical practice remains elusive. Further research is required, and this should focus on validating the promising biomarkers identified in large cohort studies, with adherence to standardised reporting guidelines.
Subject(s)
Biomarkers, Tumor , Disease Progression , Mouth Neoplasms , Precancerous Conditions , Humans , Prognosis , Mouth Neoplasms/pathology , Biomarkers, Tumor/analysis , Precancerous Conditions/pathology , Mouth Mucosa/pathology , ErbB Receptors/analysis , DNA Methylation , AneuploidyABSTRACT
Background/Objectives: The need for surgical reconstruction of scalp defects following the excision of cutaneous skin cancers is an increasingly common procedure. Particular challenges arise when considering options for reconstruction of large defects not amenable to local skin flap coverage. The use of skin grafts poses the risk of donor site morbidity. This paper investigates the emerging use of Integra®, a synthetic acellular dermal regeneration template, as an alternative or adjunct to skin grafting in scalp reconstruction. Methods: The study presents a retrospective analysis of 101 patients who underwent Integra®-based reconstruction of scalp defects. Demographics, procedure details, complications, need for further surgery, and time to healing were evaluated. Results: The overall success rate of the one-stage Integra®-only procedure was 95%, with a minor complication rate of 30.7%. Anticoagulation medication was identified as an independent risk factor for post-operative infection, while previous head and neck radiotherapy and increased defect depth were associated with the requirement for a second-stage skin graft. Conclusions: These findings support the consideration of Integra® as a safe and viable alternative for both partial and full thickness scalp defects in a select cohort of complex highly co-morbid patients, reducing complications and the need for additional procedures.
ABSTRACT
Background: As circulating tumour DNA (ctDNA) liquid biopsy analysis is increasingly incorporated into modern oncological practice, establishing the impact of genomic intra-tumoural heterogeneity (ITH) upon data output is paramount. Despite advances in other cancer types the evidence base in head and neck squamous cell carcinoma (HNSCC) remains poor. We sought to investigate the utility of ctDNA to detect ITH in HNSCC. Methods: In a pilot cohort of 9 treatment-naïve HNSCC patients, DNA from two intra-tumoural sites (core and margin) was whole-exome sequenced. A 9-gene panel was designed to perform targeted sequencing on pre-treatment plasma cell-free DNA and selected post-treatment samples. Results: Rates of genomic ITH among the 9 patients was high. COSMIC variants from 19 TCGA HNSCC genes demonstrated an 86.9% heterogeneity rate (present in one tumour sub-site only). Across all patients, cell-free DNA (ctDNA) identified 12.9% (range 7.5-19.8%) of tumour-specific variants, of which 55.6% were specific to a single tumour sub-site only. CtDNA identified 79.0% (range: 55.6-90.9%) of high-frequency variants (tumour VAF>5%). Analysis of ctDNA in serial post-treatment blood samples in patients who suffered recurrence demonstrated dynamic changes in both tumour-specific and acquired variants that predicted recurrence ahead of clinical detection. Conclusion: We demonstrate that a ctDNA liquid biopsy identified spatial genomic ITH in HNSCC and reliably detected high-frequency driver mutations. Serial sampling allowed post-treatment surveillance and early identification of treatment failure.
ABSTRACT
BACKGROUND AND PURPOSE OF THE STUDY: Although traditionally a "dentistry first, medicine second" training route, UK Oral and Maxillofacial surgery is increasingly populated with medicine-first trainees at ST3 level. Despite this, there is little evidence suggesting any increase in exposure at medical undergraduate level. We sought to evaluate the current level of awareness of OMFS as a medical specialty and potential career pathway amongst 'first-degree' medical undergraduates. METHOD: We distributed an on-line survey amongst 253 medical undergraduates divided between two UK universities. FINDINGS: A total of 72.3% of undergraduates received no exposure to OMFS in any form. Those with exposure had an improved understanding of the scope of the specialty. Regardless of previous exposure to the specialty, only 27.7% correctly identified the essential requirements for entry in OMFS specialty training. Nevertheless, a vast majority (76.7%) wanted more guidance on the possibility of pursuing a career in OMFS. CONCLUSIONS: Undergraduate exposure to OMFS in UK medical schools is limited. Even a small degree of exposure to OMFS improves understanding of the scope of the specialty. Although medical students do not fully understand the career pathway, they wish to explore OMFS as a career option. It is therefore important that UK undergraduate surgical curricula offer greater exposure to the specialty, the career pathway and the clinical opportunities it can provide.
Subject(s)
Career Choice , Education, Medical, Undergraduate , Students, Medical/statistics & numerical data , Surgery, Oral , Female , Humans , Male , Surveys and Questionnaires , United KingdomABSTRACT
Entering into surgical academia can seem a daunting prospect for an oral and maxillofacial surgery (OMFS) trainee. However, the streamlining of academic training by the NIHR to create the integrated academic training (IAT) pathway has simplified academic training and more clearly defined academic positions and entry points for trainees. In this article we review the current NIHR IAT pathway and the various grades and entry points available to OMF surgeons, both pre- and post-doctoral. We highlight the unique challenges facing OMF trainees and provide advice and insight from both junior and senior OMFS academics. Finally, we focus on the planning and application for a doctoral research fellowship - discussing funding streams available to OMF surgeons.
Subject(s)
Surgeons , Surgery, Oral , Humans , Surgery, Oral/education , Fellowships and Scholarships , Surveys and QuestionnairesABSTRACT
BACKGROUND: Smartphone usage has spread to many settings including that of healthcare with numerous potential and realised benefits. The ability to download custom-built software applications (apps) has created a new wealth of clinical resources available to healthcare staff, providing evidence-based decisional tools to reduce medical errors.Previous literature has examined how smartphones can be utilised by both medical student and doctor populations, to enhance educational and workplace activities, with the potential to improve overall patient care. However, this literature has not examined smartphone acceptance and patterns of medical app usage within the student and junior doctor populations. METHODS: An online survey of medical student and foundation level junior doctor cohorts was undertaken within one United Kingdom healthcare region. Participants were asked whether they owned a Smartphone and if they used apps on their Smartphones to support their education and practice activities. Frequency of use and type of app used was also investigated. Open response questions explored participants' views on apps that were desired or recommended and the characteristics of apps that were useful. RESULTS: 257 medical students and 131 junior doctors responded, equating to a response rate of 15.0% and 21.8% respectively. 79.0% (n=203/257) of medical students and 74.8% (n=98/131) of junior doctors owned a smartphone, with 56.6% (n=115/203) of students and 68.4% (n=67/98) of doctors owning an iPhone.The majority of students and doctors owned 1-5 medical related applications, with very few owning more than 10, and iPhone owners significantly more likely to own apps (Chi sq, p<0.001). Both populations showed similar trends of app usage of several times a day. Over 24 hours apps were used for between 1-30 minutes for students and 1-20 minutes for doctors, students used disease diagnosis/management and drug reference apps, with doctors favouring clinical score/calculator apps. CONCLUSIONS: This study found a high level of smartphone ownership and usage among medical students and junior doctors. Both groups endorse the development of more apps to support their education and clinical practice.