Esterase EstK from Pseudomonas putida mt-2: An enantioselective acetylesterase with activity for deacetylation of xylan and poly(vinylacetate).

An extracellular esterase gene estK was identified in Pseudomonas putida mt-2 and overexpressed at high levels in Escherichia coli. The recombinant EstK enzyme was purified and characterized kinetically against p-nitrophenyl ester and other aryl-alkyl ester substrates and found to be selective for hydrolysis of acetyl ester substrates with high activity for p-nitrophenyl acetate (kcat 5.5 Sec-1 , KM 285 µM). Recombinant EstK was found to catalyze deacetylation of acetylated beech xylan, indicating a possible in vivo function for this enzyme, and partial deacetylation of a synthetic polymer (poly(vinylacetate)). EstK was found to catalyze enantioselective hydrolysis of racemic 1-phenylethyl acetate, generating 1R-phenylethanol with an enantiomeric excess of 80.4%.

L-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti.

UNLABELLED: Sinorhizobium meliloti forms N2-fixing root nodules on alfalfa, and as a free-living bacterium, it can grow on a very broad range of substrates, including l-proline and several related compounds, such as proline betaine, trans-4-hydroxy-l-proline (trans-4-l-Hyp), and cis-4-hydroxy-d-proline (cis-4-d-Hyp). Fourteen hyp genes are induced upon growth of S. meliloti on trans-4-l-Hyp, and of those, hypMNPQ encodes an ABC-type trans-4-l-Hyp transporter and hypRE encodes an epimerase that converts trans-4-l-Hyp to cis-4-d-Hyp in the bacterial cytoplasm. Here, we present evidence that the HypO, HypD, and HypH proteins catalyze the remaining steps in which cis-4-d-Hyp is converted to α-ketoglutarate. The HypO protein functions as a d-amino acid dehydrogenase, converting cis-4-d-Hyp to Δ(1)-pyrroline-4-hydroxy-2-carboxylate, which is deaminated by HypD to α-ketoglutarate semialdehyde and then converted to α-ketoglutarate by HypH. The crystal structure of HypD revealed it to be a member of the N-acetylneuraminate lyase subfamily of the (α/ß)8 protein family and is consistent with the known enzymatic mechanism for other members of the group. It was also shown that S. meliloti can catabolize d-proline as both a carbon and a nitrogen source, that d-proline can complement l-proline auxotrophy, and that the catabolism of d-proline is dependent on the hyp cluster. Transport of d-proline involves the HypMNPQ transporter, following which d-proline is converted to Δ(1)-pyrroline-2-carboxylate (P2C) largely via HypO. The P2C is converted to l-proline through the NADPH-dependent reduction of P2C by the previously uncharacterized HypS protein. Thus, overall, we have now completed detailed genetic and/or biochemical characterization of 9 of the 14 hyp genes. IMPORTANCE: Hydroxyproline is abundant in proteins in animal and plant tissues and serves as a carbon and a nitrogen source for bacteria in diverse environments, including the rhizosphere, compost, and the mammalian gut. While the main biochemical features of bacterial hydroxyproline catabolism were elucidated in the 1960s, the genetic and molecular details have only recently been determined. Elucidating the genetics of hydroxyproline catabolism will aid in the annotation of these genes in other genomes and metagenomic libraries. This will facilitate an improved understanding of the importance of this pathway and may assist in determining the prevalence of hydroxyproline in a particular environment.

Pathogenic copy number variants and SCN1A mutations in patients with intellectual disability and childhood-onset epilepsy.

BACKGROUND: Copy number variants (CNVs) have been linked to neurodevelopmental disorders such as intellectual disability (ID), autism, epilepsy and psychiatric disease. There are few studies of CNVs in patients with both ID and epilepsy. METHODS: We evaluated the range of rare CNVs found in 80 Welsh patients with ID or developmental delay (DD), and childhood-onset epilepsy. We performed molecular cytogenetic testing by single nucleotide polymorphism array or microarray-based comparative genome hybridisation. RESULTS: 8.8 % (7/80) of the patients had at least one rare CNVs that was considered to be pathogenic or likely pathogenic. The CNVs involved known disease genes (EHMT1, MBD5 and SCN1A) and imbalances in genomic regions associated with neurodevelopmental disorders (16p11.2, 16p13.11 and 2q13). Prompted by the observation of two deletions disrupting SCN1A we undertook further testing of this gene in selected patients. This led to the identification of four pathogenic SCN1A mutations in our cohort. CONCLUSIONS: We identified five rare de novo deletions and confirmed the clinical utility of array analysis in patients with ID/DD and childhood-onset epilepsy. This report adds to our clinical understanding of these rare genomic disorders and highlights SCN1A mutations as a cause of ID and epilepsy, which can easily be overlooked in adults.

Annotation of epilepsy clinic letters for natural language processing.

BACKGROUND: Natural language processing (NLP) is increasingly being used to extract structured information from unstructured text to assist clinical decision-making and aid healthcare research. The availability of expert-annotated documents for the development and validation of NLP applications is limited. We created synthetic clinical documents to address this, and to validate the Extraction of Epilepsy Clinical Text version 2 (ExECTv2) NLP pipeline. METHODS: We created 200 synthetic clinic letters based on hospital outpatient consultations with epilepsy specialists. The letters were double annotated by trained clinicians and researchers according to agreed guidelines. We used the annotation tool, Markup, with an epilepsy concept list based on the Unified Medical Language System ontology. All annotations were reviewed, and a gold standard set of annotations was agreed and used to validate the performance of ExECTv2. RESULTS: The overall inter-annotator agreement (IAA) between the two sets of annotations produced a per item F1 score of 0.73. Validating ExECTv2 using the gold standard gave an overall F1 score of 0.87 per item, and 0.90 per letter. CONCLUSION: The synthetic letters, annotations, and annotation guidelines have been made freely available. To our knowledge, this is the first publicly available set of annotated epilepsy clinic letters and guidelines that can be used for NLP researchers with minimum epilepsy knowledge. The IAA results show that clinical text annotation tasks are difficult and require a gold standard to be arranged by researcher consensus. The results for ExECTv2, our automated epilepsy NLP pipeline, extracted detailed epilepsy information from unstructured epilepsy letters with more accuracy than human annotators, further confirming the utility of NLP for clinical and research applications.

Control of hydroxyproline catabolism in Sinorhizobium meliloti.

Hydroxyproline (Hyp) in decaying organic matter is a rich source of carbon and nitrogen for microorganisms. A bacterial pathway for Hyp catabolism is known; however, genes and function relationships are not established. In the pathway, trans-4-hydroxy-L-proline (4-L-Hyp) is epimerized to cis-4-hydroxy-D-proline (4-D-Hyp), and then, in three enzymatic reactions, the D-isomer is converted via Δ-pyrroline-4-hydroxy-2-carboxylate (HPC) and α-ketoglutarate semialdehyde (KGSA) to α-ketoglutarate (KG). Here a transcriptional analysis of cells growing on 4-L-Hyp, and the regulation and functions of genes from a Hyp catabolism locus of the legume endosymbiont Sinorhizobium meliloti are reported. Fourteen hydroxyproline catabolism genes (hyp), in five transcripts hypR, hypD, hypH, hypST and hypMNPQO(RE)XYZ, were negatively regulated by hypR. hypRE was shown to encode 4-hydroxyproline 2-epimerase and a hypRE mutant grew with 4-D-Hyp but not 4-L-Hyp. hypO, hypD and hypH are predicted to encode 4-D-Hyp oxidase, HPC deaminase and α-KGSA dehydrogenase respectively. The functions for hypS, hypT, hypX, hypY and hypZ remain to be determined. The data suggest 4-Hyp is converted to the tricarboxylic acid cycle intermediate α-ketoglutarate via the pathway established biochemically for Pseudomonas. This report describes the first molecular characterization of a Hyp catabolism locus.

CYCLOPS, a mediator of symbiotic intracellular accommodation.

The initiation of intracellular infection of legume roots by symbiotic rhizobia bacteria and arbuscular mycorrhiza (AM) fungi is preceded by the induction of calcium signatures in and around the nucleus of root epidermal cells. Although a calcium and calmodulin-dependent kinase (CCaMK) is a key mediator of symbiotic root responses, the decoding of the calcium signal and the molecular events downstream are only poorly understood. Here, we characterize Lotus japonicus cyclops mutants on which microbial infection was severely inhibited. In contrast, nodule organogenesis was initiated in response to rhizobia, but arrested prematurely. This arrest was overcome when a deregulated CCaMK mutant version was introduced into cyclops mutants, conferring the development of full-sized, spontaneous nodules. Because cyclops mutants block symbiotic infection but are competent for nodule development, they reveal a bifurcation of signal transduction downstream of CCaMK. We identified CYCLOPS by positional cloning. CYCLOPS carries a functional nuclear localization signal and a predicted coiled-coil domain. We observed colocalization and physical interaction between CCaMK and CYCLOPS in plant and yeast cell nuclei in the absence of symbiotic stimulation. Importantly, CYCLOPS is a phosphorylation substrate of CCaMK in vitro. Cyclops mutants of rice were impaired in AM, and rice CYCLOPS could restore symbiosis in Lotus cyclops mutants, indicating a functional conservation across angiosperms. Our results suggest that CYCLOPS forms an ancient, preassembled signal transduction complex with CCaMK that is specifically required for infection, whereas organogenesis likely requires additional yet-to-be identified CCaMK interactors or substrates.

Determination of 4-hydroxyproline-2-epimerase activity by capillary electrophoresis: A stereoselective platform for inhibitor screening of amino acid isomerases.

Isomerases involved in the metabolism of D/L-amino acids represent promising therapeutic targets for treatment of disease. Herein, we report a tunable platform for the assessment of enzymatic kinetics involving amino acid isomerization by CE that offers improved selectivity and sensitivity over traditional methods. Enzyme activity and competition assays were evaluated for various hydroxyproline diastereoisomers, proline enantiomers and their structural analogs using 4-hydroxyproline-2-epimerase as a model system. In this work, pyrrole 2-carboxylic acid was found to be a selective inhibitor of 4-hydroxyproline-2-epimerase with a half-maximal inhibition concentration of (2.3 + or - 0.1) mM. Reliable methods for unambiguous characterization of amino acid isomerases are required for the screening of novel inhibitors with epimerase and/or racemase activity.

Identification of a hydroxyproline transport system in the legume endosymbiont Sinorhizobium meliloti.

Hydroxyproline-rich proteins in plants offer a source of carbon and nitrogen to soil-dwelling microorganisms in the form of root exudates and decaying organic matter. This report describes an ABC-type transport system dedicated to the uptake of hydroxyproline in the legume endosymbiont Sinorhizobium meliloti. We have designated genes involved in hydroxyproline metabolism as hyp genes and show that an S. meliloti strain lacking putative transport genes (DeltahypMNPQ) is unable to grow with or transport trans-4-hydroxy-l-proline when this compound is available as a sole source of carbon. Expression of hypM is upregulated in the presence of trans-4-hydroxy-l-proline and cis-4-hydroxy-d-proline, as modulated by a repressor (HypR) of the GntR/FadR subfamily. Although alfalfa root nodules contain hydroxyproline-rich proteins, we demonstrate that the transport system is not highly expressed in nodules, suggesting that bacteroids are not exposed to high levels of free hydroxyproline in planta. In addition to hypMNPQ, we report that S. meliloti encodes a second independent mechanism that enables transport of trans-4-hydroxy-l-proline. This secondary transport mechanism is induced in proline-grown cells and likely entails a system involved in l-proline uptake. This study represents the first genetic description of a prokaryotic hydroxyproline transport system, and the ability to metabolize hydroxyproline may contribute significantly toward the ecological success of plant-associated bacteria such as the rhizobia.

Pseudotumor cerebri syndrome in childhood: incidence, clinical profile and risk factors in a national prospective population-based cohort study.

AIM: To investigate the epidemiology, clinical profile and risk factors of pseudotumor cerebri syndrome (PTCS) in children aged 1-16 years. METHODS: A national prospective population-based cohort study over 25 months. Newly diagnosed PTCS cases notified via British Paediatric Surveillance Unit were ascertained using classical diagnostic criteria and categorised according to 2013 revised diagnostic criteria. We derived national age, sex and weight-specific annual incidence rates and assessed effects of sex and weight categories. RESULTS: We identified 185 PTCS cases of which 166 also fulfilled revised diagnostic criteria. The national annual incidence (95% CI) of PTCS in children aged 1-16 years was 0.71 (0.57 to 0.87) per 100 000 population increasing with age and weight to 4.18 and 10.7 per 100 000 in obese boys and girls aged 12-15 years, respectively. Incidence rates under 7 years were similar in both sexes. From 7 years onwards, the incidence in girls was double that in boys, but only in overweight (including obese) children. In children aged 12-15 years, an estimated 82% of the incidence of PTCS was attributable to obesity. Two subgroups of PTCS were apparent: 168 (91%) cases aged from 7 years frequently presented on medication and with headache and were predominantly female and obese. The remaining 17 (9%) cases under 7 years often lacked these risk factors and commonly presented with paralytic squint. CONCLUSIONS: This uniquely large population-based study of childhood PTCS will inform the design of future intervention studies. It suggests that weight reduction is central to the prevention of PTCS.

Validating epilepsy diagnoses in routinely collected data.

PURPOSE: Anonymised, routinely-collected healthcare data is increasingly being used for epilepsy research. We validated algorithms using general practitioner (GP) primary healthcare records to identify people with epilepsy from anonymised healthcare data within the Secure Anonymised Information Linkage (SAIL) databank in Wales, UK. METHOD: A reference population of 150 people with definite epilepsy and 150 people without epilepsy was ascertained from hospital records and linked to records contained within SAIL (containing GP records for 2.4 million people). We used three different algorithms, using combinations of GP epilepsy diagnosis and anti-epileptic drug (AED) prescription codes, to identify the reference population. RESULTS: Combining diagnosis and AED prescription codes had a sensitivity of 84% (95% ci 77-90) and specificity of 98% (95-100) in identifying people with epilepsy; diagnosis codes alone had a sensitivity of 86% (80-91) and a specificity of 97% (92-99); and AED prescription codes alone achieved a sensitivity of 92% (70-83) and a specificity of 73% (65-80). Using AED codes only was more accurate in children achieving a sensitivity of 88% (75-95) and specificity of 98% (88-100). CONCLUSION: GP epilepsy diagnosis and AED prescription codes can be confidently used to identify people with epilepsy using anonymised healthcare records in Wales, UK.

Cell-cell communication in the plant pathogen Agrobacterium tumefaciens.

The plant pathogen Agrobacterium tumefaciens induces the formation of crown gall tumours at wound sites on host plants by directly transforming plant cells. This disease strategy benefits the bacteria as the infected plant tissue produces novel nutrients, called opines, that the colonizing bacteria can use as nutrients. Almost all of the genes that are required for virulence, and all of the opine uptake and utilization genes, are carried on large tumour-inducing (Ti) plasmids. The observation more than 25 years ago that specific opines are required for Ti plasmid conjugal transfer led to the discovery of a cell-cell signalling system on these plasmids that is similar to the LuxR-LuxI system first described in Vibrio fischeri. All Ti plasmids that have been described to date carry a functional LuxI-type N-acylhomoserine lactone synthase (TraI), and a LuxR-type signal receptor and transcriptional regulator called TraR. The traR genes are expressed only in the presence of specific opines called conjugal opines. The TraR-TraI system provides an important model for LuxR-LuxI-type systems, especially those found in the agriculturally important Rhizobiaceae family. In this review, we discuss current advances in the biochemistry and structural biology of the TraR-TraI system.

The quorum-sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility.

TraR of Agrobacterium tumefaciens is a member of the LuxR family of transcriptional regulators, and binds to specific DNA sequences (tra boxes) at target promoters of the tumour-inducing (Ti) plasmid. Each tra box has a pronounced dyad symmetry, and each subunit of a TraR dimer binds to one half of a tra box via a helix-turn-helix (HTH) DNA binding motif. Structural analysis has suggested that TraR makes extensive sequence-specific contacts with tra box DNA. In this study, we tested these predictions using synthetic self-complementary oligonucleotides containing variant tra box sequences. Some predictions made from structural analysis were confirmed, while others were shown to be incorrect. Unexpectedly, these experiments also showed that six nucleotides at the centre of the tra box that make no direct contact with TraR are nevertheless critical for high-affinity binding and probably act by facilitating a previously described DNA bend. Variant tra boxes were also tested for transcription activity in vivo. Most transcription assays reflected in vitro binding assays. However, alterations of the outermost nucleotides had little effect on TraR binding but blocked transcription, probably by altering an overlapping -35 promoter motif.

Identification of amino acid residues of the Agrobacterium tumefaciens quorum-sensing regulator TraR that are critical for positive control of transcription.

The LuxR-type quorum-sensing transcription factor TraR regulates replication and conjugal transfer of the tumour-inducing (Ti) plasmid in the plant pathogen Agrobacterium tumefaciens. TraR is a two-domain protein with an N-terminal domain that binds to the quorum-sensing signal N-3-oxooctanoyl- l-homoserine lactone (OOHL) and a C-terminal domain that binds to specific DNA sequences called tra boxes. TraR-OOHL complexes form homodimers that activate transcription of at least seven promoters on the Ti plasmid. At five promoters, a tra box overlaps the binding site of core RNA polymerase (class II promoters), while in the other two promoters, this site is located farther upstream (class I promoters). In this study, we performed saturating point mutagenesis of the surface residues of the TraR C-terminal domain. Each mutant was tested for proteolytic stability and transcription activity in vivo, and for DNA binding activity in vitro. Mutants of TraR with single substitutions at positions W184, V187, K189, E193Q, V197 and D217 have wild-type levels of accumulation and DNA binding, but are defective in transcription of both types of promoters. These residues constitute a patch on the surface of the DNA-binding domain. We propose that this patch is an activating region that recruits RNA polymerase to TraR-dependent promoters through direct contact. As residues of this patch are critical for activation at both a class I and a class II promoter, we predict that these residues may contact the C-terminal domain of the RNA polymerase alpha-subunit.

Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro.

Burkholderia cenocepacia is an opportunistic human pathogen that can aggressively colonize the cystic fibrosis lung. This organism has a LuxR/LuxI-type quorum sensing system that enables cell-cell communication via exchange of acyl homoserine lactones (AHLs). The CepR and CepI proteins constitute a global regulatory system, controlling expression of at least 40 genes, including those controlling swarming motility and biofilm formation. In this study, we isolated seven lacZ fusions in a clinical isolate of B. cenocepacia that are inducible by octanoyl-HSL. Induction of all of these genes requires CepR. The cepI promoter was tested for induction by a set of 33 synthetic autoinducers and analogues, and was most strongly induced by long-chain AHLs lacking 3-oxo substitutions. Expression of this promoter was inhibited by high concentrations of three different autoinducers, each having six-carbon acyl chains. When CepR protein was overproduced in Escherichia coli, it accumulated in a soluble form in the presence of octanoyl-HSL, but accumulated only as insoluble inclusion bodies in its absence. Purified CepR-OHL complexes bound to specific DNA sequences at the cepI and aidA promoters with high specificity. These binding sites included a 16-nucleotide imperfect dyad symmetry. Both CepR binding sites are centred approximately 44 nucleotides upstream of the respective transcription start sites.