Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation.

Triosephosphate isomerase (TPI) performs the 5th step in glycolysis, operates near the limit of diffusion, and is involved in "moonlighting" functions. Its dimer was found singly phosphorylated at Ser20 (pSer20) in human cells, with this post-translational modification (PTM) showing context-dependent stoichiometry and loss under oxidative stress. We generated synthetic pSer20 proteoforms using cell-free protein synthesis that showed enhanced TPI activity by 4-fold relative to unmodified TPI. Molecular dynamics simulations show that the phosphorylation enables a channel to form that shuttles substrate into the active site. Refolding, kinetic, and crystallographic analyses of point mutants including S20E/G/Q indicate that hetero-dimerization and subunit asymmetry are key features of TPI. Moreover, characterization of an endogenous human TPI tetramer also implicates tetramerization in enzymatic regulation. S20 is highly conserved across eukaryotic TPI, yet most prokaryotes contain E/D at this site, suggesting that phosphorylation of human TPI evolved a new switch to optionally boost an already fast enzyme. Overall, complete characterization of TPI shows how endogenous proteoform discovery can prioritize functional versus bystander PTMs.

Thromboembolism after cardiac surgery in a patient with cancer-related thrombosis and severe thrombocytopenia: A case report.

RATIONALE: Patients with cancer have elevated risk of both venous thromboembolism and bleeding compared with patients without cancer due to cancer- and patient-specific factors. Balancing the increased and competing risks of clotting and bleeding in these patients can be difficult because management of cancer-associated thrombosis requires anticoagulation despite its known increased risks for bleeding. The adjustment of blood transfusion or cessation of anticoagulants can be a challenge in surgical diagnosis or treatment of cancer patients with such an imbalanced coagulate status. PATIENT CONCERNS: A 45-year-old woman with no underlying disease was suspected of ovarian cancer and was awaiting diagnostic laparoscopic exploration surgery. DIAGNOSES: While waiting for the surgery, the patient developed chest pain and underwent stent insertion under diagnosis of myocardial infarction. Two weeks later, endocarditis developed, and replacement of the aortic valve and mitral valve was planned. In addition, the patient developed multiple thromboembolisms and was administered anticoagulants to eliminate vegetation of valves and multiple thromboses. Her blood test showed anemia (7.4 g/dL) and severe thrombocytopenia (24 × 109/L). INTERVENTIONS: The patient underwent double valve replacement. OUTCOMES: A color change of the left lower extremity was noted 5 hours after double valve replacement, and angiography was performed. Thrombectomy was performed under diagnosis of thrombosis in the left iliac artery. One month later, the patient underwent laparoscopic exploration surgery as scheduled. LESSONS: This case will help establish the criteria of blood coagulation for surgical treatment of cancer patients with imbalanced clotting and bleeding.

The Protective Effects of Dexmedetomidine Preconditioning on Hepatic Ischemia/Reperfusion Injury in Rats.

BACKGROUND: Ischemia/reperfusion (IR) injury is 1 of the major problems in liver surgery. This study aims to evaluate the histologic and biochemical effects of dexmedetomidine on ischemia/reperfusion injury in the liver of rats. METHODS: Twenty-two Sprague-Dawley male rats were separated into 3 groups: group sham, IR (IR injury), and IR-D (IR with dexmedetomidine). Ischemia was induced for 45 minutes with portal clampage and the reperfusion period was 120 minutes. Group IR-D received 3 µg/kg of dexmedetomidine with loading for 10 minutes and then 3 µg/kg/h of dexmedetomidine was continuously injected intravenously 30 minutes before portal clampage. Biochemical factors (alanine aminotransferase and aspartate aminotransferase), variable cytokines (B cell lymphoma-2 (Bcl-2), Bax, caspase 3, caspase 8, nuclear factor-kappa B, interleukin (IL)-1ß, IL-6, IL-10, mixed lineage kinase domain-like protein, and receptor-interacting protein kinase-3), and histologic findings were investigated. RESULTS: Dexmedetomidine preconditioning significantly suppressed the histologic damage. In the IR-D group, the expression of IL-6 was decreased and the Bcl-2 was increased when compared with the IR group. CONCLUSION: Dexmedetomidine suppresses hepatic IR injury and the protective mechanism appears to involve the decrease of IL-6 and upregulation of Bcl-2 expression, which result in the attenuation of inflammatory response and the inhibition of apoptosis.

Neurolytic abdominal wall blocks with alcohol for intractable gastrostomy site pain in a cancer patient -a case report.

BACKGROUND: There have been reports of neurolytic transversus abdominis plane (TAP) block using different agents such as alcohol or phenol for the treatment of chronic abdominal pain caused by malignant abdominal wall invasion. However, to date, there have been no reports on neurolytic abdominal wall blocks for pain with non-cancer-related origin in cancer patients. CASE: We performed subcostal TAP neurolysis using ethanol in a patient with esophageal cancer with constant pain at the site of gastrostomy. After neurolysis, the patient's overall pain decreased, with the exception of pain in the medial part of the gastrostomy site. We performed additional rectus sheath neurolysis using ethanol for the treatment of continuous pain at the medial site, and the effect of neurolysis has persisted for over 4 months. CONCLUSIONS: Alcohol-based TAP neurolysis and rectus sheath neurolysis provide effective pain control in a cancer patient with chronic treatment-related pain involving the abdominal wall.

Native top-down mass spectrometry provides insights into the copper centers of membrane-bound methane monooxygenase.

Aerobic methane oxidation is catalyzed by particulate methane monooxygenase (pMMO), a copper-dependent, membrane metalloenzyme composed of subunits PmoA, PmoB, and PmoC. Characterization of the copper active site has been limited by challenges in spectroscopic analysis stemming from the presence of multiple copper binding sites, effects of detergent solubilization on activity and crystal structures, and the lack of a heterologous expression system. Here we utilize nanodiscs coupled with native top-down mass spectrometry (nTDMS) to determine the copper stoichiometry in each pMMO subunit and to detect post-translational modifications (PTMs). These results indicate the presence of a mononuclear copper center in both PmoB and PmoC. pMMO-nanodisc complexes with a higher stoichiometry of copper-bound PmoC exhibit increased activity, suggesting that the PmoC copper site plays a role in methane oxidation activity. These results provide key insights into the pMMO copper centers and demonstrate the ability of nTDMS to characterize complex membrane-bound metalloenzymes.

Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria.

Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined CuA site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical to the global carbon and nitrogen cycles.

Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C.

In methylotrophic bacteria, which use one-carbon (C1) compounds as a carbon source, methanol is oxidized by pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) enzymes. Methylotrophic genomes generally encode two distinct MDHs, MxaF and XoxF. MxaF is a well-studied, calcium-dependent heterotetrameric enzyme whereas XoxF is a lanthanide-dependent homodimer. Recent studies suggest that XoxFs are likely the functional MDHs in many environments. In methanotrophs, methylotrophs that utilize methane, interactions between particulate methane monooxygenase (pMMO) and MxaF have been detected. To investigate the possibility of interactions between pMMO and XoxF, XoxF was isolated from the methanotroph Methylomicrobium buryatense 5GB1C (5G-XoxF). Purified 5G-XoxF exhibits a specific activity of 0.16 µmol DCPIP reduced min-1 mg-1. The 1.85 Å resolution crystal structure reveals a La(III) ion in the active site, in contrast to the calcium ion in MxaF. The overall fold is similar to other MDH structures, but 5G-XoxF is a monomer in solution. An interaction between 5G-XoxF and its cognate pMMO was detected by biolayer interferometry, with a KD value of 50 ± 17 µM. These results suggest an alternative model of MDH-pMMO association, in which a XoxF monomer may bind to pMMO, and underscore the potential importance of lanthanide-dependent MDHs in biological methane oxidation.

Recent Advances in the Genetic Manipulation of Methylosinus trichosporium OB3b.

Methanotrophic bacteria utilize methane as their sole carbon and energy source. Studies of the model Type II methanotroph Methylosinus trichosporium OB3b have provided insight into multiple aspects of methanotrophy, including methane assimilation, copper accumulation, and metal-dependent gene expression. Development of genetic tools for chromosomal editing was crucial for advancing these studies. Recent interest in methanotroph metabolic engineering has led to new protocols for genetic manipulation of methanotrophs that are effective and simple to use. We have incorporated these newer molecular tools into existing protocols for Ms. trichosporium OB3b. The modifications include additional shuttle and replicative plasmids as well as improved gene delivery and genotyping. The methods described here render gene editing in Ms. trichosporium OB3b efficient and accessible.

From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity.

Particulate methane monooxygenase (pMMO) is a copper-dependent integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. Studies of isolated pMMO have been hindered by loss of enzymatic activity upon its removal from the native membrane. To characterize pMMO in a membrane-like environment, we reconstituted pMMOs from Methylococcus (Mcc.) capsulatus (Bath) and Methylomicrobium (Mm.) alcaliphilum 20Z into bicelles. Reconstitution into bicelles recovers methane oxidation activity lost upon detergent solubilization and purification without substantial alterations to copper content or copper electronic structure, as observed by electron paramagnetic resonance (EPR) spectroscopy. These findings suggest that loss of pMMO activity upon isolation is due to removal from the membranes rather than caused by loss of the catalytic copper ions. A 2.7 Å resolution crystal structure of pMMO from Mm. alcaliphilum 20Z reveals a mononuclear copper center in the PmoB subunit and indicates that the transmembrane PmoC subunit may be conformationally flexible. Finally, results from extended X-ray absorption fine structure (EXAFS) analysis of pMMO from Mm. alcaliphilum 20Z were consistent with the observed monocopper center in the PmoB subunit. These results underscore the importance of studying membrane proteins in a membrane-like environment and provide valuable insight into pMMO function.

The biosynthesis of methanobactin.

Metal homeostasis poses a major challenge to microbes, which must acquire scarce elements for core metabolic processes. Methanobactin, an extensively modified copper-chelating peptide, was one of the earliest natural products shown to enable microbial acquisition of a metal other than iron. We describe the core biosynthetic machinery responsible for the characteristic posttranslational modifications that grant methanobactin its specificity and affinity for copper. A heterodimer comprising MbnB, a DUF692 family iron enzyme, and MbnC, a protein from a previously unknown family, performs a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA) to install an oxazolone and an adjacent thioamide, the characteristic methanobactin bidentate copper ligands. MbnB and MbnC homologs are encoded together and separately in many bacterial genomes, suggesting functions beyond their roles in methanobactin biosynthesis.

Methanobactin transport machinery.

Methanotrophic bacteria use methane, a potent greenhouse gas, as their primary source of carbon and energy. The first step in methane metabolism is its oxidation to methanol. In almost all methanotrophs, this chemically challenging reaction is catalyzed by particulate methane monooxygenase (pMMO), a copper-dependent integral membrane enzyme. Methanotrophs acquire copper (Cu) for pMMO by secreting a small ribosomally produced, posttranslationally modified natural product called methanobactin (Mbn). Mbn chelates Cu with high affinity, and the Cu-loaded form (CuMbn) is reinternalized into the cell via an active transport process. Bioinformatic and gene regulation studies suggest that two proteins might play a role in CuMbn handling: the TonB-dependent transporter MbnT and the periplasmic binding protein MbnE. Disruption of the gene that encodes MbnT abolishes CuMbn uptake, as reported previously, and expression of MbnT in Escherichia coli confers the ability to take up CuMbn. Biophysical studies of MbnT and MbnE reveal specific interactions with CuMbn, and a crystal structure of apo MbnE is consistent with MbnE's proposed role as a periplasmic CuMbn transporter. Notably, MbnT and MbnE exhibit different levels of discrimination between cognate and noncognate CuMbns. These findings provide evidence for CuMbn-protein interactions and begin to elucidate the molecular mechanisms of its recognition and transport.

Exploring De Novo metabolic pathways from pyruvate to propionic acid.

Industrial biotechnology provides an efficient, sustainable solution for chemical production. However, designing biochemical pathways based solely on known reactions does not exploit its full potential. Enzymes are known to accept non-native substrates, which may allow novel, advantageous reactions. We have previously developed a computational program named Biological Network Integrated Computational Explorer (BNICE) to predict promiscuous enzyme activities and design synthetic pathways, using generalized reaction rules curated from biochemical reaction databases. Here, we use BNICE to design pathways synthesizing propionic acid from pyruvate. The currently known natural pathways produce undesirable by-products lactic acid and succinic acid, reducing their economic viability. BNICE predicted seven pathways containing four reaction steps or less, five of which avoid these by-products. Among the 16 biochemical reactions comprising these pathways, 44% were validated by literature references. More than 28% of these known reactions were not in the BNICE training dataset, showing that BNICE was able to predict novel enzyme substrates. Most of the pathways included the intermediate acrylic acid. As acrylic acid bioproduction has been well advanced, we focused on the critical step of reducing acrylic acid to propionic acid. We experimentally validated that Oye2p from Saccharomyces cerevisiae can catalyze this reaction at a slow turnover rate (10(-3) s(-1) ), which was unknown to occur with this enzyme, and is an important finding for further propionic acid metabolic engineering. These results validate BNICE as a pathway-searching tool that can predict previously unknown promiscuous enzyme activities and show that computational methods can elucidate novel biochemical pathways for industrial applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:303-311, 2016.

Effect of Red Blood Cell Transfusion on Unfavorable Neurologic Outcome and Symptomatic Vasospasm in Patients with Cerebral Aneurysmal Rupture: Old versus Fresh Blood.

BACKGROUND: Red blood cell (RBC) transfusion, especially with "old" blood, is associated with adverse clinical outcomes. We compared the effects of fresh blood versus old blood transfusion on poor neurologic outcomes and symptomatic vasospasm in patients with ruptured cerebral aneurysms. METHODS: In this retrospective study, 211 patients with aneurysmal rupture were divided into 3 groups: nontransfusion (n = 136), fresh blood (RBC storage ≤ 14 days) transfusion (n = 39), and old blood (RBC storage >14 days) transfusion (n = 36). Unfavorable neurologic outcomes (modified Rankin Scale score ≥ 3) and symptomatic cerebral vasospasm were assessed. RESULTS: The incidence of unfavorable neurologic outcomes was significantly higher in the fresh blood and old blood transfusion groups compared with the nontransfused group (71.8% and 58.3% vs. 21.3%; P < 0.01); the incidence of symptomatic vasospasm was significantly higher in the old blood group compared with the fresh blood and nontransfusion groups (57.1% vs. 26.7% and 22.2%; P < 0.05). On binary logistic regression, old age, Hunt and Hess grade 3-4, high postoperative C-reactive protein level, RBC transfusion, delayed infarction, and hydrocephalus were independent predictors of unfavorable neurologic outcomes. Young age, Fisher grade 3-4, old RBC transfusion, and surgical clipping were independent predictors of postoperative symptomatic vasospasm. CONCLUSIONS: RBC transfusion itself, regardless of the duration of RBC storage, was associated with unfavorable neurologic outcomes in patients with ruptured cerebral aneurysms. Also, old blood transfusion, but not fresh blood transfusion, was associated with increased symptomatic cerebral vasospasm.

Metabolic engineering of cyanobacteria for photosynthetic 3-hydroxypropionic acid production from CO2 using Synechococcus elongatus PCC 7942.

Photosynthetic conversion of CO2 to chemicals using cyanobacteria is an attractive approach for direct recycling of CO2 to useful products. 3-Hydroxypropionic acid (3 HP) is a valuable chemical for the synthesis of polymers and serves as a precursor to many other chemicals such as acrylic acid. 3 HP is naturally produced through glycerol metabolism. However, cyanobacteria do not possess pathways for synthesizing glycerol and converting glycerol to 3 HP. Furthermore, the latter pathway requires coenzyme B12, or an oxygen sensitive, coenzyme B12-independent enzyme. These characteristics present major challenges for production of 3 HP using cyanobacteria. To overcome such difficulties, we constructed two alternative pathways in Synechococcus elongatus PCC 7942: a malonyl-CoA dependent pathway and a ß-alanine dependent pathway. Expression of the malonyl-CoA dependent pathway genes (malonyl-CoA reductase and malonate semialdehyde reductase) enabled S. elongatus to synthesize 3 HP to a final titer of 665 mg/L. ß-Alanine dependent pathway expressing S. elongatus produced 3H P to final titer of 186 mg/L. These results demonstrated the feasibility of converting CO2 into 3 HP using cyanobacteria.