Occurrence, genes and expression of the W/Se-containing class II benzoyl-coenzyme A reductases in anaerobic bacteria

Benzoyl-coenzyme A (CoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds and catalyse the reductive dearomatization of benzoyl-CoA to cyclohexa-1,5-dienoyl-1-carboxyl-CoA. Class I BCRs are ATP-dependent FeS enzymes, whereas class II BCRs are supposed to be ATP-independent and contain W, FeS clusters, and most probably selenocysteine. The active site components of a putative eight subunit class II BCR, BamBCDEFGHI, were recently characterized in Geobacter metallireducens. In this organism bamB was identified as structural gene for the W-containing active site subunit; bamF was predicted to code for a selenocysteine containing electron transfer subunit. In this work the occurrence and expression of BCRs in a number of anaerobic, aromatic compound degrading model microorganisms was investigated with a focus on the BamB and BamF components. Benzoate-induced class II BCR in vitro activities were determined in the soluble protein fraction in all obligately anaerobic bacteria tested. Where applicable, the results were in agreement with Western blot analysis using BamB targeting antibodies. By establishing a specific bamB targeting PCR assay, bamB homologues were identified in all tested obligately anaerobic bacteria with the capacity to degrade aromatic compounds; a number of bamB sequences from Gram-negative/positive sulfate-reducing bacteria were newly sequenced. In several organisms at least two bamB paralogues per genome were identified; however, in nearly all cases only one of them was transcribed during growth on an aromatic substrate. These benzoate-induced bamB genes are proposed to code for the active site subunit of class II BCRs; the major part of them group into a phylogenetic subcluster within the bamB homologues. Results from in silico analysis suggested that all class II BCRs contain selenocysteine in the BamF, and in many cases also in the BamE subunit. The results obtained indicate that the distribution of the two classes of BCRs in anaerobic bacteria appears to be strictly ruled by the available free energy from the oxidation of the aromatic carbon source rather than by phylogenetic relationships.     

Flashback and foreshadowing—a review of the taxon Opisthobranchia

Opisthobranchia have experienced an unsettled taxonomic history. At the moment their taxonomy is in state of dramatic flux as recent phylogenetic studies have revealed traditional Opisthobranchia to be paraphyletic or even polyphyletic, allocating some traditional opisthobranch taxa to other groups of Heterobranchia, e.g. Pulmonata. Here we review the history of Opisthobranchia and their subgroups, explain their traditionally proposed relationships, and outline the most recent phylogenetic analyses based on various methods (morphology, single gene and multiple gene analyses, as well as genomic data). We also present a phylogenetic hypothesis on Heterobranchia that, according to the latest results, represents a consensus and is the most probable one available to date. The proposed phylogeny supports the Acteonoidea outside of monophyletic Euthyneura, the basal euthyneuran split into Nudipleura (Nudibranchia plus Pleurobranchoidea) and the recently established taxon Tectipleura. The latter divides into the Euopisthobranchia, containing most of the major traditional opisthobranch clades, and the Panpulmonata, with a mix of the former opisthobranch, putative allogastropod and pulmonate taxa. This “new euthyneuran tree” rejects the traditional taxa Opisthobranchia and Pulmonata, and, in particular, has profound implications for preconceived textbook scenarios of opisthobranch and pulmonate evolution, which must now be reconsidered. In the absence of systematic barriers, research communities—which have traditionally investigated marine and non-marine heterobranchs separately—need to interact and finally merge for the sake of science.     

Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii

A new pathway for aerobic benzoate oxidation has been postulated for Azoarcus evansii and for a Bacillus stearothermophilus-like strain. Benzoate is first transformed into benzoyl coenzyme A (benzoyl-CoA), which subsequently is oxidized to 3-hydroxyadipyl-CoA and then to 3-ketoadipyl-CoA; all intermediates are CoA thioesters. The genes coding for this benzoate-induced pathway were investigated in the beta-proteobacterium A. evansii. They were identified on the basis of N-terminal amino acid sequences of purified benzoate metabolic enzymes and of benzoate-induced proteins identified on two-dimensional gels. Fifteen genes probably coding for the benzoate pathway were found to be clustered on the chromosome. These genes code for the following functions: a putative ATP-dependent benzoate transport system, benzoate-CoA ligase, a putative benzoyl-CoA oxygenase, a putative isomerizing enzyme, a putative ring-opening enzyme, enzymes for beta-oxidation of CoA-activated intermediates, thioesterase, and lactone hydrolase, as well as completely unknown enzymes belonging to new protein families. An unusual putative regulator protein consists of a regulator protein and a shikimate kinase I-type domain. A deletion mutant with a deletion in one gene (boxA) was unable to grow with benzoate as the sole organic substrate, but it was able to grow with 3-hydroxybenzoate and adipate. The data support the proposed pathway, which postulates operation of a new type of ring-hydroxylating dioxygenase acting on benzoyl-CoA and nonoxygenolytic ring cleavage. A beta-oxidation-like metabolism of the ring cleavage product is thought to lead to 3-ketoadipyl-CoA, which finally is cleaved into succinyl-CoA and acetyl-CoA.     

Cell-associated proteoheparan sulfate from bovine arterial smooth muscle cells

Cell-associated proteoheparan sulfate has been isolated from bovine arterial smooth muscle cells preincubated with [35S]sulfate or a combination of [3H]glucosamine and [35S]methionine. The purified proteoheparan sulfate had an apparent Mr of 200,000 on calibrated Sepharose CL-2B columns. The glycosaminoglycan component (Mr approximately 30,000) was identified as heparan sulfate by its susceptibility to specific enzymatic and chemical degradation. After degradation of the proteoheparan sulfate by microbial heparitinase the resulting protein core had an apparent Mr of 92,000 on SDS-polyacrylamide gels. Its mobility was similar in the absence and presence of reducing agents indicating that the protein core consists of a single polypeptide chain. Pulse-chase experiments revealed that about 40% of the cell layer-associated proteoheparan sulfate was released into the medium, while the remainder was internalized and converted to smaller species through a series of degradation steps. Initially there was a proteolytical cleavage of the protein core generating glycosaminoglycan peptide intermediates with polysaccharides chains similar in size to the original. The half-life of the native proteoheparan sulfate was found to be about 4 h.     

Structural investigation of cellobiose dehydrogenase IIA: Insights from small angle scattering into intra- and intermolecular electron transfer mechanisms

Background

Cellobiose dehydrogenases have gained interest due to their potential applications in sectors from biofuel production to biomedical devices. The CDHIIA variant is comprised of a cytochrome domain (CYT), a dehydrogenase domain (DH), and a carbohydrate-binding module (CBM) that are connected by two flexible linkers. Upon cellobiose oxidation at the DH, intramolecular electron transfer (IaET) occurs from the DH to the CYT. In vivo, CDHIIA CYT subsequently performs intermolecular electron transfer (IeET) to a lytic polysaccharide monooxygenase (LPMO). The relevant solution-state CDH domain conformations for IaET and IeET have not been fully characterized.

Morphological deformities occurring in Belarusian chironomids (Diptera: Chironomidae) subsequent to the Chernobyl nuclear disaster

1. Chironomid larvae and adults were collected from several freshwater habitats around the Chernobyl site from 1990 to 1994 (4–8 years after a nuclear accident) and examined for morphological deformities.
2. Deformities were found in larvae of nine of the 13 species collected, and were most obvious in headcapsule structures, particularly the antennae, mentum, mandibles and epipharyngeal pectens.
3. In species of Chironomus , the most abundant genus, there was a positive linear relationship between the incidence of deformity and radiation level. Indices of severity of deformity showed similar trends. It is suggested that these deformities resulted largely from ingestion of irradiated, plant-derived, fine particulate food.
4. Among adult male Ch. riparius , the deformity index decreased both with increasing time from the accident and with increasing distance from the reactor, although these trends were not statistically significant. There was also a trend of increased severity of deformity closer to the accident, both in time and space.
5. Overall, there was a greater incidence of deformity in the larvae than in the adults (e.g. 60 versus 20%, respectively, at the Krasnoselye site and 33 versus 20%, respectively, at the more distant Dron'ki site).
6. It was not possible to determine whether the deformities were inherited from previous generations or were somatic occurrences in each new generation as a consequence of the radiation that continues to pervade the region.     

Induction of enzymes of phytoalexin synthesis in cultured soybean cells by an elicitor from Phytophthora megasperma f. sp. glycinea

The glucan elicitor from cell walls of the fungal pathogen, Phytophthora megasperma f. sp. glycinea, induced rapid but transient increases in enzyme activities of general phenylpropanoid metabolism (phenylalanine ammonia-lyase and 4-coumarate: CoA ligase) and of the flavonoid pathway (chalcone synthase) in cell suspension cultures of soybean (Glycine max). After transferring cells into fresh medium, two peaks of inducibility for the enzymes by elicitor were observed, one shortly after transfer (stage I), and one at the end of the linear growth phase (stage II). Only one of the two isoenzymes of 4-coumarate: CoA ligase (isoenzyme 2), for which a specific involvement in flavonoid biosynthesis has been postulated, was affected by the elicitor. For two of the induced enzymes, phenylalanine ammonia-lyase and chalcone synthase, the changes in activity at stage I were shown to be preceded by large changes in their rates of synthesis, as determined by in vivo labelling with [³⁵S] methionine and immunoprecipitation.Abbreviations Pmg Phytophthora megasperma f. sp. glycinea - glyceollin is a term used to designate the 3 isomers which accumulate in challenged soybean tissue (Moesta and Grisebach 1981b)     

Novel cell line selectively expressing neuropeptide Y-Y2 receptors

Neuropeptide Y (NPY) recognition by the human neuroblastoma cell lines SiMa, Kelly, SH-SY5Y, CHP-234, and MHH-NB-11 was analyzed in radioactive binding assays using tritiated NPY. For the cell lines CHP-234 and MHH-NB-11 binding of [3H]propionyl-NPY was observed with Kd-values of 0.64 +/- 0.07 nM and 0.53 +/- 0.12 nM, respectively, determined by saturation analysis with non-linear regression. The receptor subtype was determined by competition analysis using the subtype selective NPY analogues [Leu31, Pro34]-NPY (NPY-Y1, NPY-Y5), [Ahx(5-24)]-NPY (NPY-Y2), [Ala31, Aib32]-NPY (NPY-Y5), NPY [3-36] (NPY-Y2, NPY-Y5), and NPY [13-36] (NPY-Y2). Both cell lines, CHP-234 and MHH-NB-11, the latter one being characterized for NPY receptors for the first time, showed exclusive expression of NPY-Y2 receptors. In both cell lines binding of NPY induced signal transduction, which was monitored as reduction of forskolin-induced cAMP production in an ELISA.