Biochimie
○ Elsevier BV
All preprints, ranked by how well they match Biochimie's content profile, based on 25 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.
Li, H.-Z.; Wang, Y.-F.; Zheng, Y.-S.; Liu, Y.-L.; Xu, Z.-G.; Guo, Z.-Y.
Show abstract
The gastric peptide ghrelin and its receptor GHSR have important functions in energy metabolism. Recently, liver-expressed antimicrobial peptide 2 (LEAP2) was identified as an endogenous antagonist for GHSR. Ghrelin, LEAP2, and GHSR are ubiquitously present from fishes to mammals and are highly conserved in evolution. However, our recent study suggested that GHSRs from the Actinopterygii fish Danio rerio (zebrafish) and Larimichthys crocea (large yellow croaker) have lost their binding to ghrelin, despite binding normally to LEAP2. Do these fish GHSRs use another peptide as their agonist? To answer this question, in the present study, we tested to two fish motilins that are closely related to ghrelin. In ligand binding and activation assays, the fish GHSRs from D. rerio and L. crocea displayed no detectable or very low binding to all tested motilins; however, the GHSR from the Sarcopterygii fish Latimeria chalumnae (coelacanth) bound to its motilin with high affinity and was efficiently activated by it. Therefore, it seemed that motilin is not a ligand for GHSR in D. rerio and L. crocea, but is an efficient agonist for GHSR in L. chalumnae, which is known as a living fossil and is believed to be one of the closest fish ancestors of tetrapods. The results of present study suggested that in ancient fishes, GHSR had two efficient agonists, ghrelin and motilin; however, this feature might be only preserved in some extant fishes with ancient evolutionary origins. Our present work shed new light on the ligand usage of GHSR in different fish species and in evolution.
Klejnot, M.; Skowron, A. N.; Szymanski, J.; Ulatowski, F.; Bista, M.; Cottens, S.; Dabrowiecka, G.; Gajewska, D.; Gorecka-Minakowska, K. M.; Kotlarek, D.; Leszkowicz, K.; Pastok, M. W.; Sypien, M.; Wierzbicki, I. H.; Wisniewski, J.; Walczak, M. J.
Show abstract
This study presents a robust crystallographic platform for assessing compounds binding to {beta}-catenin. We developed a standardized protein production protocol for the armadillo domain of {beta}-catenin (BC-ARM) and performed biophysical screens using Surface Plasmon Resonance (SPR) and Differential Scanning Fluorimetry (DSF). These findings led to the successful determination of the co-crystal structure of BC-ARM with compound 1 binding to previously reported site but distinct from known transcription factor binding sites. To broaden the search for novel BC binding sites, we utilized FragLites library with a cyclic peptide-stabilized BC-ARM construct. This yielded two high-resolution co-crystal structures identifying a previously unreported binding hotspot. Recognizing the limitations of the cyclic peptide-bound construct for general screening, we designed a novel, truncated BC-ARM construct. This new construct eliminates unstructured regions, reliably producing high-quality, diffracting crystals suitable for high-throughput crystallographic studies. In conclusion, the ligand-bound {beta}-catenin structures and this novel, robust BC-ARM construct establish a powerful platform for further {beta}-catenin investigation.
Kuzikov, M.; Morasso, S.; Reinshagen, J.; Wolf, M.; Monaco, V.; Cozzolino, F.; Grdadolnik, S. G.; Sket, P.; Plavec, J.; Iaconis, D.; Summa, V.; Esposito, F.; Tramontano, E.; Monti, M.; Beccari, A. R.; Windshugel, B.; Gribbon, P.; Storici, P.; Zaliani, A.
Show abstract
The SARS CoV-2 Papain-Like protease has multiple roles in the viral replication cycle, related to both its polypeptide cleavage function and its capacity to antagonize host immune response. Targeting PLpro function is recognized as a promising mechanism to modulate viral replication whilst supporting host immune responses. However, development of PLpro specific inhibitors remains challenging. Upcoming studies revealed the limitation of reported inhibitors by profiling them through a pipeline of enzymatic, binding and cellular activity assays showing unspecific activity. GRL-0617 remained the only validated molecule with demonstrated anti-viral activity in cells. In this study we refer to the pitfalls of redox-sensitivity of PLpro. Using a screening-based approach to identify inhibitors of PLpro proteolytic activity, we made extensive efforts to validate the active compounds over a range of conditions and readouts, emphasising the need for comprehensive orthogonal data when profiling putative PLpro inhibitors. The remaining active compound CPI-169, showed to compete with GRL-0617 in NMR-based experiments, suggesting to share a similar binding mode, opening novel design opportunities for further developments as antiviral agents. Author summaryThe increasing knowledge about SARS-CoV-2 allowed the development of multiple strategies to contain the spread of COVID-19 infection. Nevertheless, effective antiviral pharmacological treatments are still rare and viral evolution allowed a fast adaptation and escape from available containment methods. The papain like protease (PLpro) has now become the next most promising SARS-CoV-2 therapeutic due to its multiple functions in virus replication cycle and antagonization of host immune response. However, due to inherent flexibility and sensitivity of this enzyme specific inhibitors are rare. Here we report on a screening strategy using repurposing of known drugs that takes into account PLpro characteristics to identify new inhibitors, showing the success of the approach by identifying CPI-169 that competitive targets the well described GRL-0617 inhibitor binding pocket of PLpro and helping to design further antiviral agents.
Maklad, H. R.; Ruys, S. P. d.; Bervoets, I.; Vertommen, D.; Gutierrez, G. J.; Vranken, W. F.; Siebers, B.; Peeters, E.
Show abstract
Protein phosphorylation is a key cellular signaling mechanism that exists in all life forms. Unlike Bacteria and Eukarya, in which protein phosphorylation has thoroughly been studied, post-translational modification by means of phosphorylation have only been limitedly explored in Archaea. A previous study of the phosphoproteome of the model Crenarchaeon Sulfolobus acidocaldarius revealed a widespread occurrence of protein phosphorylation, especially on tyrosine residues. Moreover, several (putative) transcription factors, including AbfR1 and FadR, were previously shown to be phosphorylated on tyrosine residues, a phenomenon that is directly linked to a phosphorylation-mediated regulation of these transcription factors. Despite this potentially important role for tyrosine phosphorylation in S. acidocaldarius, to our knowledge, a kinase capable of directly phosphorylating tyrosine residues has not yet been identified in this organism, neither in Archaea as a whole. Here, we identify and characterize a protein kinase in S. acidocaldarius, Sut1, which displays tyrosine phosphorylation activity in vitro and represents a novel protein kinase family that is widespread in different archaeal organisms.
Paloyan, A.; Sargsyan, A.; Karapetyan, M. D.; Hambardzumyan, A.; Kocharov, S.; Panosyan, H.; Dukova, K. D.; Kinosyan, M.; Krueger, A.; Piergentili, C.; Stanley, W. A.; Basle, A.; Antranikian, G.; Marles-Wright, J.
Show abstract
N-Carbamoyl-{beta}-Alanine Amidohydrolase (C{beta}AA) constitute one of the most important groups of industrially relevant enzymes used in production of optically pure amino acids and derivatives. In this study, a N-carbamoyl-{beta}-alanine amidohydrolase encoding gene from Rhizobium radiobacter MDC 8606 was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme (RrC{beta}AA) showed a specific activity of 14 U/mg using N-carbamoyl-{beta}-alanine as a substrate with an optimum activity of 55{degrees}C at pH 8.0. In this work, we report also the first prokaryotic N-carbamoyl-{beta}-alanine amidohydrolases structure at a resolution of 2.0 [A]. A discontinuous catalytic domain and a dimerization domain attached through a flexible hinge region at the domain interface has been revealed. We have found that the ligand is interacting with a conserved glutamic acid (Glu131), histidine (H385) and arginine (Arg291) residues. Studies let us to explain the preference on the enzyme for linear carbamoyl substrates as large carbamoyl substrates cannot fit in the active site of the enzyme. This work envisages the use of RrC{beta}AA from the Rhizobium radiobacter MDC 8606 for the industrial production of L--, L-{beta}-, and L-{gamma} - amino acids. The structural analysis provides new insights on enzyme-substrate interaction, which shed light on engineering of N-carbamoyl-{beta}-alanine amidohydrolases for high catalytic activity and broad substrate specificity.
Oliveira, I. A.; Allonso, D.; Fernandes, T. V. A.; Lucena, D. M. S.; Ventura, G. T.; Dias, W. B.; Mohana-Borges, R.; Pascutti, P. G.; Todeschini, A. R.
Show abstract
Glycoconjugates play a central role in several cellular processes and alteration in their composition is associated to human pathologies. The hexosamine biosynthetic pathway is a route through which cells obtain substrates for cellular glycosylation, and is controlled by the glutamine: fructose-6-phosphate amidotransferase (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer, however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in E. coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the ordered bi-bi mechanism, and performs the glucosamine-6-phosphate synthesis much slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerase fructose-6-phosphate into glucose-6-phosphate even in presence of equimolar amounts of glutamine, in an unproductive glutamine hydrolysis. Structural analysis of the generated three-dimensional model rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations show such loop as the most flexible portion of the protein, which interacts with the protein mainly through the interdomain region, and plays a key role on conformational states of hGFAT2. Altogether, our study provides the first comprehensive set of data on the structure, kinetics and mechanics of hGFAT2, which will certainly contribute for further studies focusing on drug development targeting hGFAT2.
Vinogradova, E.; Mikhaylina, A.; Nikonov, O.; Nikonova, E.
Show abstract
Aminoacyl-tRNA synthetases (aaRS) are the main enzymes of protein biosynthesis. Human glycyl-tRNA synthetase, in addition to the main function of amino acid transfer to the corresponding tRNA molecules, is also involved in the initiation of IRES I translation. All members of the enterovirus genus have this type of IRES. It is also known that the presence of point mutations in aaRS leads to the occurrence of diseases in which peripheral nerves are affected. One such disorder of the nervous system is the incurable neurodegenerative disorder Charcot-Marie-Tooth (CMT). The most studied enzyme whose mutations cause CMT is glycyl-tRNA synthetase (GlyRS). In this work, we tested the ability of various mutant forms of glycyl-tRNA synthetase associated with Charcot-Marie-Tooth syndrome to form a stable complex with IRES I. It turned out that neither catalytic activity nor the ability to form a dimer are necessary for the interaction of GlyRS with IRES.
Adediran, B.; Vela Rodriguez, C.; Murthy, S.; Rahman, M. M.; Wierenga, R. K.; Lehtio, L.; Koski, M. K.
Show abstract
Collagen prolyl 4-hydroxylase (C-P4H) is an essential enzyme in collagen synthesis and known to be a potential target for drugs that prevent excess collagen formation. Currently known C-P4H inhibitors target the catalytic site of C-P4H, being analogues of 2-oxoglutarate (2OG). However, in mammalian cells there are many other 2OG-dependent dioxygenases with a highly similar catalytic domain, which limits the selective specificity of drugs targeting C-P4H activity. The peptide-substrate-binding (PSB) domain is unique for the C-P4H family and known to be important for the catalytic efficiency of C-P4H. Therefore, interfering with peptide binding to the PSB domain might allow more specific inhibition of the hydroxylation activity of C-P4Hs. We developed a robust FRET-based high-throughput screening assay (Z > 0.73) based on PSB-peptide interactions. This assay was used to screen a peptidomimetic library of 15614 compounds with the PSB domains of C-P4H isoforms I and II. A hit compound (OUL-PSBi-001) was identified with IC50s of 40 {micro}M and 62 {micro}M for PSB-I and PSB-II, respectively. We also showed that this compound indeed inhibits the catalytic activity of the full-length CP4H-I and -II. This FRET assay provides a new strategy for finding selective inhibitors for the treatment of fibrotic diseases and cancer.
Winkler, D.; Gfrerer, S.; Gescher, J.
Show abstract
Despite several discoveries in recent years, the physiology of acidophilic Micrarchaeota remains largely enigmatic. "Candidatus Micrarchaeum harzensis A_DKE", for example, highly expresses numerous genes encoding hypothetical proteins and their function is difficult to elucidate due to a lacking genetic system. Still, not even the intracellular pH value of A_DKE is known, and heterologous production attempts are generally missing so far. Hence, A_DKEs isocitrate dehydrogenase (MhIDH) was recombinantly produced in Escherichia coli and purified for bio-chemical characterisation. MhIDH appeared to be specific for NADP+, yet promiscuous regarding divalent cations as cofactors. Kinetic studies showed KM-values of 53.03{+/-}5.63 {micro}M and 1.94{+/-}0.12 mM and kcat-values of 38.48{+/-}1.62 s-1 and 43.99{+/-}1.46 s-1 for DL-isocitrate and NADP+, respectively. MhIDHs exceptionally low affinity for NADP+, potentially limiting its reaction rate, can be likely attributed to the presence of a proline residue in the NADP+ binding-pocket, which might cause a decrease in hydrogen bonding of the cofactor and a distortion of local secondary structure. Furthermore, a pH optimum of 7.89 implies, that A_DKE applies potent mechanisms of proton homoeostasis, to maintain a slightly alkaline cytosolic milieu in a highly acidic environment.
Samadaei Ghadikolaei, M.; Asad, S.; Hassan-Zadeh, V.
Show abstract
The shortened L-asparaginases half-life in leukemia patients due to elevated serum proteases, poses a challenge. This study aimed to enhance the stability of Halomonas elongata L-asparaginase against trypsin. Employing the trRosetta server, we modeled the enzymes 3D structure with a quality score of 96.5, revealing predominant secondary structure of random coils (42%), alpha helices (33%), and extended strands (20%) organized in two domains. Molecular docking unveiled a triad alignment among residues Thr16, Ser65, and Asp97 with L-asparagine. Site selection for mutation considered secondary structure prediction, dimerization analysis, trypsin cleavage site determination and epitope mapping. A library of enzyme variants was constructed through site saturation mutagenesis which led to the identification of the Arg206 to Thr, resulting in a 1.7-fold increased enzyme-specific activity (2400 U/mg) and heightened trypsin resistance. The mutant displayed a half-life of 3.47 hin human serum, approximately 50% longer than the wild type. In silico analyses confirmed structural stability, reduced flexibility, and enhanced substrate binding, contributing to increased proteolysis resistance and enzymatic activity. The Arg206Thr mutant exhibited anti-proliferative activity (IC50 of 1.45 U/ml) on leukemia cell line K562, suggesting potential therapeutic implications.
Stanurova, J.; Cermakova, K.; Zakova, L.; Sacha, P.; Jiracek, J.; Konvalinka, J.
Show abstract
Insulin is a key hormone in glucose homeostasis. Its lack causes severe health complications and has to be compensated by regular administration of insulin. Despite intense long-lasting research, a more stable and efficient substitute has yet to be discovered to alleviate patients issues. Here we report the development of a new assay for screening potential insulin receptor ligands based on the DNA-linked inhibitor antibody assay (DIANA). Our assay meets the need for a fast, sensitive, non-radioactive method as an alternative to the commonly used radioligand receptor binding assay.
Knight, A.; Houser, J.; Otasevic, T.; Juran, V.; Vybihal, V.; Smrcka, M.; martin, D.
Show abstract
The overexpression of MYC genes is frequently found in many human cancers including adult and pediatric malignant brain tumors. Targeting MYC genes continues to be challenging due to their undruggable nature. The nine-amino-acid activation domain (9aaTAD) has been identified using our prediction algorithm in all four Yamanaka factors including c-Myc and showed to activate transcription as short peptides. We generated a set of c-Myc constructs (1-108, 69-108 and 98-108) in the N-terminal regions and tested their ability to initiate transcription. We discovered strong interactions in nanomolar scale between the 9aaTAD of c-Myc and N-Myc proteins with the KIX domain of CBP coactivator. The c-Myc 9aaTAD (region 98-108) was not overlapping with the MBII (region 128-143) and therefore represents TRRAP independent activation region. Next, we showed the 9aaTADs in human c-Myc and N-Myc conservation within the MYC family. Interestingly, the loss of the 9aaTAD in L-Myc paralogs was identified in higher metazoans suggesting the deletions had occurred in early tetrapod evolution. In summary, as c-Myc is largely intrinsically disordered protein and therefore difficult to target by small molecule inhibitors, our finding of the c-Myc 9aaTAD in complex with the KIX domain represents a promising druggable target for development of new peptide inhibitors in MYC-driven tumors.
Ramos Ricciuti, F. E.; Herrera Seitz, M. K.; Gasperotti, A. F.; Boyko, A.; Jung, K.; Bellinzoni, M.; Studdert, C. A.; Lisa, M.-N.
Show abstract
The chemosensory pathway HtChe2 from the marine bacterium Halomonas titanicae KHS3 controls the activity of a diguanylate cyclase. Constitutive activation of the pathway results in colony morphology alterations and increased ability to form biofilm. Such characteristics resemble the behaviour of the Wsp pathway of Pseudomonas. In this work we investigate the specificity of Htc10, the only chemoreceptor coded within the HtChe2 gene cluster. Thermal shift analyses performed with the Htc10 ligand-binding domain led to the identification of purine derivatives as ligands. This ligand-binding domain was crystallized in the presence of guanine or hypoxanthine and its structure was solved by X-ray protein crystallography. The sensor domain adopts a double-cache folding, with ligands bound to the membrane-distal pocket. A high-resolution structure of the occupied guanine-binding pocket allowed the identification of the involved residues. These residues were validated by site directed mutagenesis and thermal shift or isothermal calorimetry analyses of the protein variants. The dissociation constants for guanine or hypoxanthine of the intact domain were in the low micromolar range. To our knowledge, this is the first description of binding specificity for a chemoreceptor that controls the activity of an associated diguanylate cyclase, and opens the way for dynamic studies of the signalling behaviour of this kind of sensory complex. A comparison between Htc10 and the functionally equivalent WspA receptor from Pseudomonas revealed no significant sequence similarities. In contrast, highly conserved Htc10-like receptors were found in distant bacteria carrying HtChe2-like clusters.
Villard, C.; Bayer, C.; Medici, N. P.; van de Peppel, A. C.; Cankar, K.; Verstappen, F.; Kappers, I. F.; Schranz, M. E.; Daniel, B.; van Velzen, R.
Show abstract
Cannabinoids are well-known specialised metabolites from the plant Cannabis sativa L. (cannabis). They exhibit various therapeutical to intoxicating psychoactive effects and have potential for medicinal applications. Among the enzymes involved in cannabinoid biosynthesis, cannabinoid oxidocyclases such as the tetrahydrocannabinolic acid (THCA) synthase play a key role in determining cannabis chemotype. To improve our understanding of cannabinoid oxidocyclase structure-function relationship, we proposed a new approach to targeted mutagenesis. By reviewing cannabis natural variation, three cannabinoid oxidocyclase mutations (S355N, CONF, G376R) associated to atypical plant chemotypes were selected. In-vitro characterization of THCA synthase mutants demonstrated these mutations significantly impact enzyme activity, correlating with the associated chemotype: S355N nearly inactivated the THCA synthase, CONF impaired CBGA metabolization and altered product specificity, while G376R drastically reduced enzyme activity and altered product specificity. In-silico docking experiments permitted to model the successive steps of THCA synthase substrate metabolization, revealing that the three mutations hamper substrate binding. Collectively, our results demonstrated how plant diversity can be leveraged to guide enzyme targeted mutagenesis, highlighted a key region of cannabinoid oxidocyclases, and permitted the establishment of a new model of the THCA synthase catalytic mechanism. This provides new insights into enzyme function, which can ultimately help developing medicinal cannabis cultivars and cannabinoid biotechnological production.
Kamale, C.; Rauniyar, A.; Bhaumik, P.
Show abstract
Cellulases are an ensemble of enzymes that hydrolyse cellulose chains to fermentable glucose, hence, are widely used in bioethanol production. The last enzyme of the cellulose degradation pathway - {beta}-glucosidase, is inhibited by its product - glucose. The product inhibition by glucose hinders cellulose hydrolysis limiting the saccharification during bioethanol production. Therefore, engineered {beta}-glucosidases with improved glucose tolerance along with the catalytic efficiency are the need of the hour. This study focuses on the rational engineering of {beta}-glucosidase from Acetivibrio thermocellus (WT-AtGH1). Recombinant WT-AtGH1 exhibited activity on cellobiose and p-nitrophenyl-{beta}-D-glucosidase as substrates and retained around 80% of its activity over 48 hours at 55{degrees}C, pH 5.5. However, WT-AtGH1 showed low glucose tolerance of 380 mM as compared to the required IC50 value of > 800 mM for industrial use. Therefore, the rational design approach was applied for improving the glucose tolerance of this enzyme. We determined 3 [A] resolution crystal structure of WT-AtGH1. The structure-based engineered G168W-AtGH1 and S242W-AtGH1 mutants exhibited improved glucose tolerance of 840 mM and 612 mM, respectively. Surprisingly, S242L-AtGH1 mutant showed [~] 2.5-fold increase in the catalytic efficiency as compared to WT-AtGH1. A combinatorial effect of improved glucose tolerance, as well as enhanced catalytic efficiency, was observed for the G168W-S242L-AtGH1 mutant. All the mutants with enhanced properties showed considerable stability at industrial operating conditions of 55{degrees}C and pH 5.5. Thus, we present the next-generation mutants of WT-AtGH1 with improved glucose tolerance and kinetic properties that have the potential to increase the efficiency of the saccharification process for second generation bioethanol production.
Azzi, A.; El Sayed, A.; Serwa, R.; Zakrzewski, M.
Show abstract
Transcriptional and translation control of thymidylate synthase (TYMS) is poorly understood, particularly in response to chemotherapeutic drugs such as 5-Fluorouracil (5-FU) and its derivatives. The current study addressed this gap by demonstrating a biphasic response in TYMS protein levels upon 5-FU treatment. Indeed, we observe an initial reduction within the first few hours, followed by a marked increase at 24 hours. These changes occurred independently of transcriptional regulation, as TYMS mRNA levels remained stable during the early phase and showed only a moderate increase later. We further showed that neither autophagy nor proteasomal degradation contributed to this dynamic, but instead it is driven by change in its translation. Using thermal proteome profiling, we identified SIN1, a key component of the mTORC2 complex, as a key regulator of TYMS protein levels. Functional studies revealed that SIN1 depletion negatively alters TYMS levels and dynamics and sensitizes cancer cells to 5-FU-mediated cell death. These findings uncover a novel mechanism controlling TYMS protein levels and suggest that targeting SIN1 may represent a promising strategy to enhance the therapeutic efficacy of 5-FU-based treatments.
Ou, L.; Zhao, X.; Wu, I.; Xiong, Z.; Ruan, Z.; Zhou, G.; Chen, W.
Show abstract
DBC1 (deleted in breast cancer 1) is a human nuclear protein that modulates the activities of various proteins. NAD+ (oxidized form of nicotinamide adenine dinucleotide) is thought to potentially bind to the Nudix homology domains (NHDs) of DBC1, thereby regulating DBC1-PARP1 [poly (adenosine diphosphate-ribose) polymerase] interactions, the modulation of which may restore DNA repair to protect against cancer, radiation, and aging. Therefore, our study comprehensively employed methods including NMR (Nuclear Magnetic Resonance), ITC (isothermal titration calorimetry), genetic mutation, and computer biology to thoroughly investigate the molecular mechanism of the binding interaction between NAD+ and its precursor NMN with the NHD domain of DBC1 (DBC1354-396). The results from NMR and ITC indicate that NAD+ likely interacts with DBC1354-396 through hydrogen bonding, with a binding affinity nearly twice that of NMN. The key binding sites are primarily E363 and D372. Molecular Docking further revealed the importance of conventional hydrogen bonds and carbon-hydrogen bonds in the binding process. These findings may lead to a better understanding of how NAD+ regulates the physiological functions of DBC1, thereby offering guiding principles for the development of targeted therapies and drug research focused on tumor diseases associated with DBC1.
Dirks, T.; Klopsch, S.; Stoesser, D.; Trenkle, S. D.; Yayci, A.; Schüttler, S.; Golda, J.; Bandow, J. E.
Show abstract
Plasma-driven biocatalysis utilizes in situ H2O2 production by atmospheric pressure plasmas to drive H2O2-dependent enzymatic reactions. Having previously established plasma-driven biocatalysis using recombinant unspecific peroxygenase from Agrocybe aegerita (rAaeUPO) to produce (R)-1-phenylethanol from ethylbenzene (ETBE), we here employed CYP152 from Bacillus subtilis (CYP152BS{beta}). CYP152BS{beta} naturally hydroxylates medium and long-chain carboxylic acids, and, with short-chain carboxylic acids as decoy molecules, also converts non-natural substrates such as ETBE. To produce active CYP152BS{beta} overexpression and heme loading were optimized. The conversion of the non-natural substrates guaiacol and ABTS with heptanoic acid as decoy molecule and H2O2 from stock solution yielded 18.28 and 21.13 nmol product min-1 [Formula], respectively. These reactions also served to assess compatibility of CYP152BS{beta} with plasma-driven biocatalysis regarding temperature and H2O2 operating windows. To establish CYP152BS{beta}-based plasma-driven biocatalysis, immobilized enzyme in a rotating bed reactor (5 ml reaction volume) was then supplied with H2O2 from a capillary plasma jet operated with 1280 ppm H2O in helium. After a 120 min run time a turnover number (TON) of 18.82 mol(R)-1-PhOl [Formula] was reached. We conclude that plasma-driven biocatalysis can be extended to other H2O2-dependent enzymes. Future efforts will be directed at increasing the TON and product range.
Voronin, A.; Oscorbin, I. P.; Novikova, L.; Filipenko, M.; Voskoboev, M.
Show abstract
RNases H (EC 3.1.26.4) are a family of enzymes participating in removal of ribonucleotides from double-stranded DNA by hydrolyzing their phosphodiester bonds. Despite a long history of research, several important aspects of RNase HII functioning are poorly known including optimal pH, salts and thermal stability. This lack of empirical data hampers the selection of an optimal RNase HII for a specific practical application. In the present study, we compared biochemical properties of previously cloned RNases HII from E. coli, Geobacillus stearothermophilus and Thermus thermophilus: optimal temperature, pH, salts, divalent cofactors, thermal stability and specific activity. As expected, the most thermostable enzyme was Tth RNase HII, and Mg2+ was the most preferential cofactor for all RNases. Gst RNase HII was partially inhibited by K+ ions, while other enzymes did not demonstrate preferences for any salt. The enzymes from E. coli and G. stearothermophilus were typical RNases HII, while Tth RNase HII was a JRNase (junction ribonuclease). All three RNases did not cleave a DNA-RNA3-DNA2-RNA1-DNA/DNA substrate. The presented results will facilitate usage of RNases HII in practical applications and provide a basis for further comparative studies of RNases HII from various organisms.
Schmidt, T. J.; Hassan, A. H.; Pucker, B.; Kruse, T.
Show abstract
Molybdenum cofactor (Moco) biosynthesis is vitally important for all organisms, yet the domain organization of the eukaryotic molybdenum insertase (Mo-insertase) remains enigmatic. We combine extensive phylogenetic reconstructions, sequence analysis and structural modeling in order to uncover evolutionary and functional principles of eukaryotic Mo-insertases. We note, that the vast majority of plant, fungi and animal species evolved fused E- and G-domains, yet the orientation of both domains in the fusion proteins differs among different eukaryotic lineages. Despite the divergent domain arrangements amongst eukaryotic Mo-insertases the E-domain active site is well conserved, with very few tolerated substitutions in >1,000 sequences. Among the Mo-insertases from different eukaryotic species, vertebrate gephyrin is the only Mo-insertase with a dual function as - next to its metabolic function - it scaffolds inhibitory neurotransmitter receptors in the post synapsis. Gephyrin is surprisingly high conserved, including surface patches not directly involved in catalysis and receptor clustering. This profile suggests additional, as yet uncharacterized, functional constraints on gephyrins evolution. Together, our results reveal how eukaryotic Mo-insertases combine evolutionary domain organization plasticity with stringent active site conservation and recognize the evolutionary constraint on gephyri[n]s surface conservation to be extreme, likely due to its mutual metabolic and neuronal function.