Structural Insights into Polyhydroxyalkanoates Biosynthesis.

Polyhydroxyalkanoates (PHAs) are diverse biopolyesters produced by numerous microorganisms and have attracted much attention as a substitute for petroleum-based polymers. Despite several decades of study, the detailed molecular mechanisms of PHA biosynthesis have remained unknown due to the lack of structural information on the key PHA biosynthetic enzyme PHA synthase. The recently determined crystal structure of PHA synthase, together with the structures of acetyl-coenzyme A (CoA) acetyltransferase and reductase, have changed this situation. Structural and biochemical studies provided important clues for the molecular mechanisms of each enzyme as well as the overall mechanism of PHA biosynthesis from acetyl-CoA. This new information and knowledge is expected to facilitate production of designed novel PHAs and also enhanced production of PHAs.

Impact of pitavastatin on new-onset diabetes mellitus compared to atorvastatin and rosuvastatin: a distributed network analysis of 10 real-world databases.

BACKGROUND: Statin treatment increases the risk of new-onset diabetes mellitus (NODM); however, data directly comparing the risk of NODM among individual statins is limited. We compared the risk of NODM between patients using pitavastatin and atorvastatin or rosuvastatin using reliable, large-scale data. METHODS: Data of electronic health records from ten hospitals converted to the Observational Medical Outcomes Partnership Common Data Model (n = 14,605,368 patients) were used to identify new users of pitavastatin, atorvastatin, or rosuvastatin (atorvastatin + rosuvastatin) for ≥ 180 days without a previous history of diabetes or HbA1c level ≥ 5.7%. We conducted a cohort study using Cox regression analysis to examine the hazard ratio (HR) of NODM after propensity score matching (PSM) and then performed an aggregate meta-analysis of the HR. RESULTS: After 1:2 PSM, 10,238 new pitavastatin users (15,998 person-years of follow-up) and 18,605 atorvastatin + rosuvastatin users (33,477 person-years of follow-up) were pooled from 10 databases. The meta-analysis of the HRs demonstrated that pitavastatin resulted in a significantly reduced risk of NODM than atorvastatin + rosuvastatin (HR 0.72; 95% CI 0.59-0.87). In sub-analysis, pitavastatin was associated with a lower risk of NODM than atorvastatin or rosuvastatin after 1:1 PSM (HR 0.69; CI 0.54-0.88 and HR 0.74; CI 0.55-0.99, respectively). A consistently low risk of NODM in pitavastatin users was observed when compared with low-to-moderate-intensity atorvastatin + rosuvastatin users (HR 0.78; CI 0.62-0.98). CONCLUSIONS: In this retrospective, multicenter active-comparator, new-user, cohort study, pitavastatin reduced the risk of NODM compared with atorvastatin or rosuvastatin.

Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex.

Cupriavidus necator H16 is a gram-negative chemolithoautotrophic bacterium that has been extensively studied for biosynthesis and biodegradation of polyhydroxyalkanoate (PHA) plastics. To improve our understanding of fatty acid metabolism for PHA production, we determined the crystal structure of multi-functional enoyl-CoA hydratase from Cupriavidus necator H16 (CnFadB). The predicted model of CnFadB created by AlphaFold was used to solve the phase problem during determination of the crystal structure of the protein. The CnFadB structure consists of two distinctive domains, an N-terminal enol-CoA hydratase (ECH) domain and a C-terminal 3-hydroxyacyl-CoA dehydrogenase (HAD) domain, and the substrate- and cofactor-binding modes of these two functional domains were identified. Unlike other known FadB enzymes that exist as dimers complexed with FadA, CnFadB functions as a monomer without forming a complex with CnFadA. Small angle X-ray scattering (SAXS) measurement further proved that CnFadB exists as a monomer in solution. The non-sequential action of FadA and FadB in C. necator appears to affect ß-oxidation and PHA synthesis/degradation.

Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579.

The coding gene for peptidoglycan editing factor (pdeF) is located in the division and cell wall (dcw) cluster, and encodes a protein that has an editing function for misplaced amino acids in peptidoglycan in E. coli. In this study, we determined the crystal structure of PdeF from Bacillus cereus (BcPdeF) at a 1.60 Å resolution. BcPdeF exists as a monomer in solution and consists of two domains: a core domain containing a Pfam motif DUF152 and a smaller subdomain. The X-ray fluorescence spectrum of BcPdeF crystal elucidated that the protein has a Zn2+ ion in its active site and the metal ion was coordinated by two histidine and one cysteine residue. We also performed docking calculations of the N-acetylmuramate (MurNAc)-L-Ser-D-iGlu ligand in the BcPdeF structure and revealed the substrate binding mode of the enzyme. Furthermore, structural comparisons between BcPdeF and human fatty acid metabolism-immunity nexus (FAMIN), which also contains the DUF152 motif in its core domain, provided a structural basis how the two structurally similar proteins have completely different physiological functions.

Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies.

Fumarylacetoacetate hydrolase (FAH) superfamily proteins are found ubiquitously in microbial pathways involved in the catabolism of aromatic substances. Although extensive bioinformatic data on these proteins have been acquired, confusion caused by problems with the annotation of these proteins hinders research into determining their physiological functions. Here we classify 606 FAH superfamily proteins using a maximum likelihood (ML) phylogenetic tree, comparative gene-neighbourhood patterns and in vitro enzyme assays. The FAH superfamily proteins used for the analyses are divided into five distinct subfamilies, and two of them, FPH-A and FPH-B, contain the majority of the proteins of undefined function. These subfamilies include clusters designated FPH-I and FPH-II, respectively, which include two distinct types of fumarylpyruvate hydrolase (FPH), an enzyme involved in the final step of the gentisate pathway. We determined the crystal structures of these FPH enzymes at 2.0 Å resolutions and investigate the substrate binding mode by which these types of enzymes can accommodate fumarylpyruvate as a substrate. Consequentially, we identify the molecular signatures of the two types of FPH enzymes among the broadly conserved FAH superfamily proteins. Our studies allowed us to predict the relationship of unknown FAH superfamily proteins using their sequence information.

Structural insight into bi-functional malonyl-CoA reductase.

The bi-functional malonyl-CoA reductase is a key enzyme of the 3-hydroxypropionate bi-cycle for bacterial CO2 fixation, catalysing the reduction of malonyl-CoA to malonate semialdehyde and further reduction to 3-hydroxypropionate. Here, we report the crystal structure and the full-length architecture of malonyl-CoA reductase from Porphyrobacter dokdonensis. The malonyl-CoA reductase monomer of 1230 amino acids consists of four tandemly arranged short-chain dehydrogenases/reductases, with two catalytic and two non-catalytic short-chain dehydrogenases/reductases, and forms a homodimer through paring contact of two malonyl-CoA reductase monomers. The complex structures with its cofactors and substrates revealed that the malonyl-CoA substrate site is formed by the cooperation of two short-chain dehydrogenases/reductases and one novel extra domain, while only one catalytic short-chain dehydrogenase/reductase contributes to the formation of the malonic semialdehyde-binding site. The phylogenetic and structural analyses also suggest that the bacterial bi-functional malonyl-CoA has a structural origin that is completely different from the archaeal mono-functional malonyl-CoA and malonic semialdehyde reductase, and thereby constitute an efficient enzyme.

Crystal structure of an acetyl-CoA acetyltransferase from PHB producing bacterium Bacillus cereus ATCC 14579.

Bacillus cereus ATCC 14579 is a known polyhydroxybutyrate (PHB)-producing microorganism that possesses genes associated with PHB synthesis such as PhaA, PhaB, and PHA synthases. PhaA (i.e., thiolase) is the first enzyme in the PHA biosynthetic pathway, which catalyze the condensation of two acetyl-CoA molecules to acetoacetyl-CoA. Our study elucidated the crystal structure of PhaA in Bacillus cereus ATCC 14579 (BcTHL) in its apo- and CoA-bound forms. BcTHL adopts a type II biosynthetic thiolase structure by forming a tetramer. The crystal structure of CoA-complexed BcTHL revealed that the substrate binding site of BcTHL is constituted by different residues compared with other known thiolases. Our study also revealed that Arg221, a residue involved in ADP binding, undergoes a positional conformational change upon the binding of the CoA molecule.

Structural basis for stereospecificity to d-amino acid of glycine oxidase from Bacillus cereus ATCC 14579.

Glycine oxidase (GO) is an enzyme that catalyzes the oxidation of the primary and secondary amines of various chemicals, including glycine, and the enzyme has been applied in a variety of fields, such as biosensor and genetically modified glyphosate resistance plants. Here, we report that the gene product of BC0747 from Bacillus cereus (BcGO) shows oxidase activity for glycine and small d-amino acids, such as d-proline and d-alanine. We also determined the crystal structure of BcGO complexed with the FAD cofactor at a 2.36 Å resolution and revealed how the cofactor binds to the deep pocket of the enzyme. We performed the molecular docking calculation of the glycine substrate to the BcGO structure and identified how the carboxyl- and amine-groups of the d-amino acid are stabilized at the substrate binding site. Structural analysis of BcGO also provided information on the structural basis for the stereospecificity of the enzyme to d-amino acids. In addition, we placed the glyphosate molecule, a plant herbicide, at the substrate binding site, and explained how the mutation of Gly51 to arginine enhances enzyme activity.

Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4.

Methylobacterium extorquens is a methylotroph model organism that has the ability to assimilate formate using the tetrahydrofolate (THF) pathway. The formate-tetrahydrofolate ligase from M. extorquens (MeFtfL) is an enzyme involved in the THF pathway that catalyzes the conversion of formate, THF, and ATP into formyltetrahydrofolate and ADP. To investigate the biochemical properties of MeFtfL, we evaluated the metal usage and enzyme kinetics of the enzyme. MeFtfL uses the Mg ion for catalytic activity, but also has activity for Mn and Ca ions. The enzyme kinetics analysis revealed that Km value of farmate was much higher than THF and ATP, which shows that the ligation activity of MeFtfL is highly dependent on formation concentration. We also determined the crystal structure of MeFtfL at 2.8 Å resolution. MeFtfL functions as a tetramer, and each monomer consists of three domains. The structural superposition of MeFtfL with FtfL from Moorella thermoacetica allowed us to predict the substrate binding site of the enzyme.

Biochemical properties and crystal structure of isocitrate lyase from Bacillus cereus ATCC 14579.

The glyoxylate cycle is an important anabolic pathway and acts under a C2 compound (such as acetic acid) rich condition in bacteria. The isocitrate lyase (ICL) enzyme catalyzes the first step in the glyoxylate cycle, which is the cleavage of isocitrate to glyoxylate and succinate. This enzyme is a metalo-enzyme that contains an Mg2+ or a Mn2+ion at the active site for enzyme catalysis. We expressed and purified ICL from Bacillus cereus (BcICL) and investigated its biochemical properties and metal usage through its enzyme activity and stability with various divalent metal ion. Based on the results, BcICL mainly utilized the Mg2+ ion for enzyme catalysis as well as the Mn2+, Ni2+ and Co2+ ions. To elucidate its molecular mechanisms, we determined the crystal structure of BcICL at 1.79 Å. Through this structure, we analyzed a tetrameric interaction of the protein. We also determined the BcICL structure in complex with both the metal and its products, glyoxylate and succinate at 2.50 Å resolution and revealed each ligand binding modes.

Holographic augmented reality based on three-dimensional volumetric imaging for a photorealistic scene.

In this paper, we propose a new system for a real-time holographic augmented reality (AR) video service based on a photorealistic three-dimensional (3D) object point for multiple users to use simultaneously at various locations and viewpoints. To observe the object from all viewpoints, a camera system capable of acquiring the 3D volume of a real object is developed and is used to generate a real object in real-time. Using the normal of the object point, the observable points are mapped to the viewpoint at which the user is located, and a hologram based on the object point is generated. The angle at which the reflected light from each point is incident on the hologram plane is calculated, and the intensity of the interference light is adjusted according to the angle to generate a hologram with a higher 3D effect. The generated hologram is transmitted to each user to provide a holographic AR service. The entire system consists of a camera system comprising eight RGB-D (depth) cameras and two workstations for photorealistic 3D volume and hologram generation. Using this technique, a realistic hologram was generated. Through experiments displaying holograms simultaneously from several different viewpoints, it is confirmed that multiple users can concurrently receive hologram AR.

New compression method for full-complex holograms using the modified zerotree algorithm with the adaptive discrete wavelet transform.

In this paper, we propose a new method for coding a full complex hologram with random phase. Since holograms with random phase have very unique spatial and frequency characteristics, a new compression method suitable for such holograms is required. We analyze the frequency characteristics of holograms with random phases and propose a new adaptive discrete wavelet transform (aDWT). Next, we propose a new modified zerotree alogrithm (mZTA) suitable for the subband configuration generated by the modified wavelet transform method. The results of the compression using the proposed method showed higher efficiency than the previous method, and the reconstructed images showed visually superior results.

Crystal structure of γ-aminobutyrate aminotransferase in complex with a PLP-GABA adduct from Corynebacterium glutamicum.

γ-Aminobutyrate (GABA), a four carbon non-protein amino acid, is used by some microorganisms as a source of carbon and/or nitrogen. Corynebacterium glutamicum has an incomplete GABA shunt that lacks a glutamate decarboxylase coding gene for the conversion of glutamate to GABA. Recently, a novel GABA assimilation system was identified in C. glutamicum. In the cell, GABA aminotransferase (GABA-AT) is the first step of GABA assimilation in the process of utilizing GABA as a carbon and/or nitrogen source. In this study, we report the crystal structure of CgGABA-AT in complex with PLP-GABA. We used structural studies and site-directed mutagenesis experiments to identify the key residues that contribute to the formation of the active site. Furthermore, based on structural comparisons and amino acid sequence alignment, we demonstrate the differences between the GABA-ATs of bacteria, fungi, and animals.

Structure and biochemical studies of a pseudomonad maleylpyruvate isomerase from Pseudomonas aeruginosa PAO1.

Pseudomonas aeruginosa PAO1 can utilize various aromatic hydrocarbons as a carbon source. Among the three genes involved in the gentisate pathway of P. aeruginosa, the gene product of PA2473 belongs to the ζ-class glutathione S-transferase and is predicted to be a maleylpyruvate isomerase. In this study, we determined the crystal structure of maleylpyruvate isomerase from Pseudomonas aeruginosa PAO1 (PaMPI) at a resolution of 1.8 Å. PaMPI functions as a dimer and shows the glutathione S-transferase fold. The structure comparison with other glutathione S-transferase structures enabled us to predict the glutathione cofactor binding site and suggests that PaMPI has differences in residues that make up the putative substrate binding site. Biochemical study of PaMPI showed that the protein has an MPI activity. Interestingly, unlike the reported glutathione S-transferases so far, the purified PaMPI showed isomerase activity without the addition of the reduced glutathione, although the protein showed much higher activity when the glutathione cofactor was added to the reaction mixture. Taken together, our studies reveal that the gene product of PA2473 functions as a maleylpyruvate isomerase and might be involved in the gentisate pathway.

Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula.

Metallosphaera sedula is a thermoacidophilic autotrophic archaeon and known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as a carbon fixation pathway. The 3-HP/4-HB cycle in M. sedula is associated with central metabolism, and malate dehydrogenase (MDH) is an enzyme involved in the central metabolism that converts malate to oxaloacetate. To elucidate the enzymatic properties of MDH from M. sedula (MsMDH), we determined the crystal structure of MsMDH as a complex with NAD+ and a ternary complex with malate and NAD+. Based on its complex structures and biochemical experiments, we observed that MsMDH can utilize both NAD+ and NADP+ as a cofactor. In addition, we revealed that MsMDH shows a conformational change at the active site upon substrate binding. Based on the comparison with other MDHs, we revealed that MsMDH was distinguished from general MDHs due to a Lys80 residue, and this difference is likely to influence the unique cofactor specificity of MsMDH.

Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula.

Metallosphaera sedula is a thermoacidophilic archaeon that has carbon fixation ability using the 3-hydroxypropionate/4-hydroxybutyrate(3-HP/4-HB) cycle, and has an incomplete TCA cycle to produce necessary biosynthetic precursors. The citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA cycle, catalyzing the conversion of oxaloacetate and acetyl-CoA into citrate and coenzyme A. To investigate the molecular mechanism of MsCS, we determined its crystal structure at 1.8 Šresolution. As other known CSs, MsCS functions as a dimer, and each monomer consists of two domains, a large domain and a small domain. We also determined the structure of the complex with acetyl-CoA and revealed the acetyl-CoA binding mode of MsCS. Structural comparison of MsCS with another CS in complex with oxaloacetate enabled us to predict the oxaloacetate binding site. Moreover, we performed inhibitory kinetic analyses of MsCS, and showed that the protein is inhibited by citrate and ATP by competitive and non-competitive inhibition modes, respectively, but not by NADH. Based on these results, we suggest that MsCS belongs to the type-I CS with structural and biochemical properties similar to those of CSs involved in the conventional TCA cycle.

Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls.

Sphingobium sp. strain SYK-6, an aerobic gram-negative bacillus found in soil, is known for utilizing lignin-derived monoaryls and biaryls as carbon sources and degrading aromatic compounds. The Sphingobium sp. strain SYK-6 genome contains three genes involved in salicylate catabolism: SLG_11260, SLG_11270, and SLG_11280. Here, we report that the gene product of SLG_11280 functions as a maleylpyruvate hydrolase (SsMPH) with Km and Kcat values of 166.2 µM and 3.76 min-1, respectively. This study also reveals the crystal structures of both the apo and pyruvate-manganese ion-bound SsMPH, which revealed that like other fumarylacetoacetate hydrolases, SsMPH dimerizes and has nine unique 310-helices. Molecular docking studies of maleylpyruvate also revealed the likely binding mode of SsMPH and its substrate.

Crystal structure and biochemical characterization of O-acetylhomoserine acetyltransferase from Mycobacterium smegmatis ATCC 19420.

Mycobacterium smegmatis is a good model for studying the physiology and pathogenesis of Mycobacterium tuberculosis due to its genetic similarity. As methionine biosynthesis exists only in microorganisms, the enzymes involved in methionine biosynthesis can be a potential target for novel antibiotics. Homoserine O-acetyltransferase from M. smegmatis (MsHAT) catalyzes the transfer of acetyl-group from acetyl-CoA to homoserine. To investigate the molecular mechanism of MsHAT, we determined its crystal structure in apo-form and in complex with either CoA or homoserine and revealed the substrate binding mode of MsHAT. A structural comparison of MsHAT with other HATs suggests that the conformation of the α5 to α6 region might influence the shape of the dimer. In addition, the active site entrance shows an open or closed conformation and might determine the substrate binding affinity of HATs.

Production of extracellular PETase from Ideonella sakaiensis using sec-dependent signal peptides in E. coli.

Poly(ethylene terephthalate) (PET) is the most commonly used polyester polymer resin in fabrics and storage materials, and its accumulation in the environment is a global problem. The ability of PET hydrolase from Ideonella sakaiensis 201-F6 (IsPETase) to degrade PET at moderate temperatures has been studied extensively. However, due to its low structural stability and solubility, it is difficult to apply standard laboratory-level IsPETase expression and purification procedures in industry. To overcome this difficulty, the expression of IsPETase can be improved by using a secretion system. This is the first report on the production of an extracellular IsPETase, active against PET film, using Sec-dependent translocation signal peptides from E. coli. In this work, we tested the effects of fusions of the Sec-dependent and SRP-dependent signal peptides from E. coli secretory proteins into IsPETase, and successfully produced the extracellular enzyme using pET22b-SPMalE:IsPETase and pET22b-SPLamB:IsPETase expression systems. We also confirmed that the secreted IsPETase has PET-degradation activity. The work will be used for development of a new E. coli strain capable of degrading and assimilating PET in its culture medium.

Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.

Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain lengths. We hereby present the crystal structure of geranylgeranyl pyrophosphate synthase from the marine flavobacterium Nonlabens dokdonensis DSW-6 (NdGGPPS). NdGGPPS forms a hexamer composed of homodimeric trimer, and the monomeric structure is composed of 15 α-helices (α1-α15). In this structure, we observed the binding of one pyrophosphate molecule and two glycerol molecules that mimicked substrate binding to the enzyme. The substrate binding site of NdGGPPS contains large hydrophobic residues such as Phe, His and Tyr, and structural and amino acids sequence analyses thereof suggest that the protein belongs to the short-chain prenyltransferase family.