Pyrroloquinoline Quinone-dependent Dehydrogenase Research Articles

Chemoenzymatic synthesis, computational investigation, and antitumor activity of monocyclic lankacidin derivatives

We investigated the importance of the δ-lactone ring (C1–C5) in lankacidin C using chemoenzymatic synthesis and computational prediction and assessing biological activity, including antitumor activity. Pyrroloquinoline quinone-dependent dehydrogenase (Orf23) in Streptomyces rochei was used in the chemoenzymatic synthesis of lankacyclinone C, a novel lankacidin C congener lacking the δ-lactone moiety. Orf23 could convert the monocyclic lankacidinol derivatives, lankacyclinol and 2-epi-lankacyclinol, to the C-24 keto compounds, lankacyclinone C and 2-epi-lankacyclinone C, respectively, elucidating the relaxed substrate specificity of Orf23. Computational prediction using molecular dynamics simulations and the molecular mechanics/generalized Born-surface area protocol indicated that binding energy values of all the monocyclic derivatives are very close to those of lankacidin C, which may reflect a comparable affinity to tubulin. Monocyclic lankacidin derivatives showed moderate antitumor activity when compared with bicyclic lankacidins, suggesting that the δ-lactone moiety is less important for antitumor activity in lankacidin-group antibiotics.

Characterization of a cryptic, pyrroloquinoline quinone-dependent dehydrogenase of Gluconobacter sp. strain CHM43.

We characterized the pyrroloquinoline quinone (PQQ)-dependent dehydrogenase 9 (PQQ-DH9) of Gluconobacter sp. strain CHM43, which is a homolog of PQQ-dependent glycerol dehydrogenase (GLDH). We used a plasmid construct to express PQQ-DH9. The expression host was a derivative strain of CHM43, which lacked the genes for GLDH and the membrane-bound alcohol dehydrogenase and consequently had minimal ability to oxidize primary and secondary alcohols. The membranes of the transformant exhibited considerable d-arabitol dehydrogenase activity, whereas the reference strain did not, even if it had PQQ-DH9-encoding genes in the chromosome and harbored the empty vector. This suggests that PQQ-DH9 is not expressed in the genome. The activities of the membranes containing PQQ-DH9 and GLDH suggested that similar to GLDH, PQQ-DH9 oxidized a wide variety of secondary alcohols but had higher Michaelis constants than GLDH with regard to linear substrates such as glycerol. Cyclic substrates such as cis-1,2-cyclohexanediol were readily oxidized by PQQ-DH9.

Bioelectrocatalysis based on direct electron transfer of fungal pyrroloquinoline quinone-dependent dehydrogenase lacking the cytochrome domain

Direct electron transfer (DET) between oxidoreductases and electrodes is crucial for understanding the fundamental features of redox proteins as well as developing mediator-free bioelectronics devices. Bioelectrocatalysis with pyrroloquinoline quinone (PQQ)-dependent dehydrogenases is promising for both biosensors and biofuel cells. However, a limited number of studies have reported DET between PQQ in the enzyme and the electrode. Here, the PQQ domain (containing only the PQQ cofactor) of the fungal PQQ-dependent pyranose dehydrogenase from Coprinopsis cinerea, was studied in DET with various electrodes. A 2-mercaptoethanol self-assembled monolayer (SAM)-coated polycrystalline gold electrode was found to give excellent DET for the PQQ domain, resulting in 10-times the catalytic current density compared to bare glassy carbon. The amount of immobilized PQQ domain was determined to be 8.2 ± 0.4 pmol/cm2 by using a 27 MHz quartz-crystal microbalance (QCM), suggesting an approximate protein monolayer formation on the SAM modified gold surface. To improve current density, gold nanoparticles (AuNPs) were modified on top of polycrystalline gold electrodes. Importantly, high catalytic current densities of 1.6 mA/cm2 for the oxidation of l-fucose were achieved under optimized conditions. Together, these results demonstrate highly efficient DET to PQQ in the active site of the fungal PQQ-dependent dehydrogenase. Thus, our PQQ-domain/SAM/AuNPs coated polycrystalline gold electrode could serve as an exquisitely sensitive biosensor and a highly active sugar oxidizing anode for biofuel cells.

Pyrroloquinoline quinone-dependent dehydrogenases of acetic acid bacteria.

Pyrroloquinoline quinone (PQQ)-dependent dehydrogenases (quinoproteins) of acetic acid bacteria (AAB), such as the membrane-bound alcohol dehydrogenase (ADH) and the membrane-bound glucose dehydrogenase, contain PQQ as the prosthetic group. Most of them are located on the periplasmic surface of the cytoplasmic membrane, and function as primary dehydrogenases in cognate substance-oxidizing respiratory chains. Here, we have provided an overview on the function and molecular architecture of AAB quinoproteins, which can be categorized into six groups according to the primary amino acid sequences. Based on the genomic data, we discuss the types of quinoproteins found in AAB genome and how they are distributed. Our analyses indicate that a significant number of uncharacterized orphan quinoproteins are present in AAB. By reviewing recent experimental developments, we discuss how to characterize the as-yet-unknown enzymes. Moreover, our bioinformatics studies also provide insights on how quinoproteins have developed into intricate enzymes. ADH comprises at least two subunits: the quinoprotein dehydrogenase subunit encoded by adhA and the cytochrome subunit encoded by adhB, and the genes are located in a polycistronic transcriptional unit. Findings on stand-alone derivatives of adhA encourage us to speculate on a possible route for ADH development in the evolutional history of AAB. A combination of bioinformatics studies on big genome sequencing data and wet studies assisted with genetic engineering would unravel biochemical functions and physiological role of uncharacterized quinoproteins in AAB, or even in unculturable metagenome.

New insights into the metabolic potential of the phototrophic purple bacterium Rhodopila globiformis DSM 161T from its draft genome sequence and evidence for a vanadium-dependent nitrogenase.

Rhodopila globiformis: is the most acidophilic anaerobic anoxygenic phototrophic purple bacterium and was isolated from a warm acidic sulfur spring in Yellowstone Park. Its genome is larger than genomes of other phototrophic purple bacteria, containing 7248Mb with a G + C content of 67.1% and 6749 protein coding and 53 RNA genes. The genome revealed some previously unknown properties such as the presence of two sets of structural genes pufLMC for the photosynthetic reaction center genes and two types of nitrogenases (Mo-Fe and V-Fe nitrogenase), capabilities of autotrophic carbon dioxide fixation and denitrification using nitrite. Rhodopila globiformis assimilates sulfate and utilizes the C1 carbon substrates CO and methanol and a number of organic compounds, in particular, sugars and aromatic compounds. It is among the few purple bacteria containing a large number of pyrroloquinoline quinone-dependent dehydrogenases. It has extended capacities to resist stress by heavy metals, demonstrates different resistance mechanisms to antibiotics, and employs several toxin/antitoxin systems.

Development of label-free impedimetric platform based on new conductive polyaniline polymer and three-dimensional interdigitated electrode array for biosensor applications

Novel label-free impedimetric platform based on a three-dimensional interdigitated electrode array (3D-IDEA) sensor and new conductive polymer as a transducer for oxidoreductases is introduced. This platform is cost-effective, simple to construct and miniaturize. Monomer of conductive polymer N-(N’,N’-diethyldithiocarbamoylethylamidoethyl) aniline (AnD) was deposited onto 3D-IDEA by chemical polymerisation. It was found that the polymer film resistance depends on the redox-potential of the solution. For the first time polyAnD was used as enzyme immobilisation matrix. Pyrroloquinolinequinone (PQQ) dependent alcohol and glucose dehydrogenases were immobilized on 3D-IDEA covered with polyAnD by two different methods. 3D-IDEA sensors with enzymes, which were immobilised by physisorption on polyAnD layer, showed specific response in the presence of 1μM of the corresponding substrates. Obtained results revealed that PQQ dependent dehydrogenases can re-oxidize on polyAnD via direct electron transfer (DET) from enzyme active site to the polymer surface. This process can be monitored by methods of electrochemical impedance spectroscopy (EIS) and chronoamperometry. Presented study shows that EIS method gives a useful tool for research of re-oxidation process and interaction of electroactive enzymes with conducting materials giving information required to construct and develop analytical devices.

Characterization of a periplasmic quinoprotein from Sphingomonas wittichii that functions as aldehyde dehydrogenase

The α-proteobacterium Sphingomonas wittichii RW1 is known for its ability to degrade dioxins and related toxic substances. Bioinformatic analysis of the genome indicated that this organism may contain the largest number of pyrroloquinoline quinone-dependent dehydrogenases of any bacteria sequenced so far. Sequence analysis also showed that one of these genes (swit_4395) encodes an enzyme that belongs to the class of periplasmic glucose dehydrogenases. This gene was fused to a pelB signal sequence and a strep-tag coding region at the 5' and 3' ends, respectively. The fusion product was cloned into the broad-host range expression vector pBBR1p264-Streplong and the corresponding protein was heterologously produced in Escherichia coli, purified via Strep-Tactin affinity chromatography, and characterized. The protein Swit_4395 had a subunit mass of 39.3kDa and formed active homooctamers and homododecamers. The enzyme showed the highest activities with short- and medium-chain aldehydes (chain length C1-C6) and ketoaldehydes, such as methylglyoxal and phenylglyoxal. Butyraldehyde was the best substrate, with V max and apparent K M values of 3,970U/mg protein and 12.3mM, respectively. Pyrroloquinoline quinone was detected using UV-Vis spectroscopy and was found to be a prosthetic group of the purified enzyme. Therefore, Swit_4395 was identified as a pyrroloquinoline quinone-dependent aldehyde dehydrogenase. The enzyme could be purified from the native host when the expression vector was introduced into S. wittichii RW1, indicating homologous protein production. Overproduction of Swit_4395 in S. wittichii RW1 dramatically increased the tolerance of the bacterium toward butyraldehyde and thus might contribute to the detoxification of toxic aldehydes.

Simultaneous detection of ethanol, glucose and glycerol in wines using pyrroloquinoline quinone-dependent dehydrogenases based biosensors

Amperometric biosensors based on corresponding dehydrogenases have been developed for the determination of ethanol, glucose and glycerol. The enzymes have been integrated in redox hydrogels using an Os complex-modified non-conducting polymer employed as the electrochemical mediator and poly(ethyleneglycol)-diglycidyl ether (PEGDGE) as the cross-linking agent. The developed biosensors showed a sensitive response to ethanol, glucose and glycerol within the concentration range 2.5–250, 20–800, and 1–200 μM, detection limits of 1.2, 9 and 1 μM, and sensitivities of 220, 87 and 32 mA M −1 cm −2, respectively. The ethanol, glucose and glycerol content of several types of wine was determined with these biosensors, and the results were compared with those obtained by spectrophotometric methods. The developed biosensors have been successfully employed for simultaneous determination of all these substrates at the required sensitivity.

Cloning, mapping, and sequencing of the gene encoding Escherichia coli quinoprotein glucose dehydrogenase

Escherichia coli contains pyrroloquinoline quinone-dependent glucose dehydrogenase. We cloned and sequenced the gene (gcd) encoding this enzyme and showed that the derived amino acid sequence is highly homologous to that of the gdhA gene product of Acinetobacter calcoaceticus. Stretches of homology also exist between the amino acid sequence of E. coli glucose dehydrogenase and other pyrroloquinoline quinone-dependent dehydrogenases from several bacterial species. The position of gcd on the chromosomal map of E. coli was determined to be at 3.1 min.