Enzymatic production of pyruvate from fumarate — an application of microbial cyclic-imide-transforming pathway

For the purpose of producing pyruvate from fumarate through microbial cyclic-imide-transforming pathway, various cyclic-imide-utilizing microorganisms were isolated from soil. Among them, strain g31 was the best producer and was identified as Pseudomonas sp. With the resting cells of the strain, the conditions were optimized for pyruvate production from fumarate. The cells cultivated in the medium containing 2% (w/v) of fumarate showed the highest production with sufficient yield. The optimized wet-cell concentration, pH and temperature of the reaction were 1% (w/v), pH 6 to 7, and 30°C, respectively. Aeration was found to be an effective factor, and vigorous shaking during the reaction mixture resulted in higher production. Under the optimized reaction conditions, 100 mM of fumarate was almost stoichiometrically converted into pyruvate (94 mM) in 24 h.     

Magnetic resonance spectroscopy and ambulatory cardiovascular monitoring noninvasively gauge timing of phosphate metabolism and circulation

Circadian changes in high-energy phosphate metabolism of the human forearm and the relative independence of these metabolic changes from the circulation were noninvasively demonstrated and quantified by combining nuclear magnetic resonance spectroscopy (MRS), ambulatory blood pressure and heart rate monitoring and chronobiologic time series analysis.     

Geothermally warmed soils reveal persistent increases in the respiratory costs of soil microbes contributing to substantial C losses

Increasing temperatures can accelerate soil organic matter decomposition and release large amounts of CO₂ to the atmosphere, potentially inducing positive warming feedbacks. Alterations to the temperature sensitivity and physiological functioning of soil microorganisms may play a key role in these carbon (C) losses. Geothermally active areas in Iceland provide stable and continuous soil temperature gradients to test this hypothesis, encompassing the full range of warming scenarios projected by the Intergovernmental Panel on Climate Change for the northern region. We took soils from these geothermal sites 7 years after the onset of warming and incubated them at varying temperatures and substrate availability conditions to detect persistent alterations of microbial physiology to long-term warming. Seven years of continuous warming ranging from 1.8 to 15.9 °C triggered a 8.6–58.0% decrease on the C concentrations in the topsoil (0–10 cm) of these sub-arctic silt-loam Andosols. The sensitivity of microbial respiration to temperature (Q₁₀) was not altered. However, soil microbes showed a persistent increase in their microbial metabolic quotients (microbial respiration per unit of microbial biomass) and a subsequent diminished C retention in biomass. After an initial depletion of labile soil C upon soil warming, increasing energy costs of metabolic maintenance and resource acquisition led to a weaker capacity of C stabilization in the microbial biomass of warmer soils. This mechanism contributes to our understanding of the acclimated response of soil respiration to in situ soil warming at the ecosystem level, despite a lack of acclimation at the physiological level. Persistent increases in the respiratory costs of soil microbes in response to warming constitute a fundamental process that should be incorporated into climate change-C cycling models.     

Impact of priming on global soil carbon stocks

Fresh carbon input (above and belowground) contributes to soil carbon sequestration, but also accelerates decomposition of soil organic matter through biological priming mechanisms. Currently, poor understanding precludes the incorporation of these priming mechanisms into the global carbon models used for future projections. Here, we show that priming can be incorporated based on a simple equation calibrated from incubation and verified against independent litter manipulation experiments in the global land surface model, ORCHIDEE. When incorporated into ORCHIDEE, priming improved the model's representation of global soil carbon stocks and decreased soil carbon sequestration by 51% (12 ± 3 Pg C) during the period 1901–2010. Future projections with the same model across the range of CO₂ and climate changes defined by the IPCC‐RCP scenarios reveal that priming buffers the projected changes in soil carbon stocks — both the increases due to enhanced productivity and new input to the soil, and the decreases due to warming‐induced accelerated decomposition. Including priming in Earth system models leads to different projections of soil carbon changes, which are challenging to verify at large spatial scales.     

Cyclic-imide-hydrolyzing activity of D-hydantoinase from Blastobacter sp. strain A17p-4.

The cyclic-imide-hydrolyzing activity of a prokaryotic cyclic-ureide-hydrolyzing enzyme, D-hydantoinase, was investigated. The enzyme hydrolyzed cyclic imides with bulky substituents such as 2-methylsuccinimide, 2-phenylsuccinimide, phthalimide, and 3,4-pyridine dicarboximide to the corresponding half-amides. However, simple cyclic imides without substituents, which are substrates of imidase (ie.g., succinimide, glutarimide, and sulfur-containing cyclic imides such as 2,4-thiazolidinedione and rhodanine), were not hydrolyzed. The combined catalytic actions of bacterial D-hydantoinase and imidase can cover the function of a single mammalian enzyme, dihydropyrimidinase. Prokaryotic D-hydantoinase also catalyzed the dehyrative cyclization of the half-amide phthalamidic acid to the corresponding cyclic imide, phthalimide. The reversible hydrolysis of cyclic imides shown by prokaryotic D-hydantoinase suggested that, in addition to pyrimidine metabolism, it may also function in cyclic-imide metabolism.     

Nociceptin/orphanin FQ increases blood pressure and heart rate via sympathetic activation in sheep.

This study was undertaken to examine the cardiovascular effects of nociceptin/Orphanin FQ (OFQ). Nociceptin/OFQ (10-300 nmol/kg, IV) stimulates an increase in mean blood pressure (MBP) and heart rate (HR) in chronically catheterized sheep. Pretreatment with phenoxybenzamine (5 mg/kg) attenuated the pressor response, consistent with sympathetically mediated vasoconstriction. Furthermore, the lack of a reflex bradycardia suggests either blunting of the baroreflex by nociceptin/OFQ or direct beta-adrenergic activation. The bradycardic response to norepinephrine (0.6 microg/kg, IV) remained intact after nociceptin/OFQ administration, demonstrating that nociceptin/OFQ does not blunt the baroreflex. Additionally, the increase in HR was completely reversed by pretreatment with propranolol. These data suggest that nociceptin/OFQ plays a role in cardiovascular regulation via sympathetic activation.     

Leishmania amastigote target antigens: the challenge of a stealthy intracellular parasite

The development of a defined molecular vaccine against leishmaniasis involves the determination of candidate molecules that elicit protection against infection. As the amastigote stage is the developmental form found in the infected mammalian host, molecules specific to or upregulated in this stage represent potential antigenic vaccine targets. Diane McMahon-Pratt, Peter Kima and Lynn Soong summarize experiments which indicate that immunization with molecules upregulated in the amastigote stage can provide effective protection against infection. In the immunized host, both CD4(+) and CD8(+) T cells appear to be crucial to protection. Studies of antigen presentation of Leishmania-infected macrophages indicate that the amastigote stage can sequester endogenous leishmanial antigen from the major histocompatability complex (MHC) class II presentation pathway. However, evidence indicates that MHC class I presentation may be sustained in the infected macrophage. The effect of these findings on the design of a leishmanial vaccine are considered.     

Tyrosine kinase-independent inhibition by genistein on spermatogenic T-type calcium channels attenuates mouse sperm motility and acrosome reaction

Although the protein tyrosine kinase (PTK) inhibitor, genistein, has been widely used to investigate the possible involvement of PTK during reproductive functions, it is unknown whether it modulates sperm calcium channel activity. In the present study, we recorded T-type calcium currents (I(Ca,T)) in mouse spermatogenic cells using whole-cell patch clamp and found that extracellular application of genistein reversibly decreased I(Ca,T) in a concentration-dependent manner (IC(50) approximately 22.7 microM). To determine whether TK activity is required for I(Ca,T) inhibition, we found that peroxovanadate, a tyrosine phosphatase inhibitor, was ineffective in preventing the inhibitory effect of genistein. Furthermore, intracellular perfusion of the cells with ATP-gamma-S also did not alter the inhibitory effect of genistein. To further reveal the direct inhibitory mechanism of genistein on I(Ca,T), we applied into the bath lavendustin A, a PTK inhibitor structurally unrelated to genistein, and found that the current amplitude remained unchanged. Moreover, daidzein, an inactive structural analog of genistein, robustly inhibited the currents. The inhibitory effect of genistein on T-type calcium channels was associated with a hyperpolarizing shift in the voltage-dependence of inactivation. Genistein was observed to decrease sperm motility and to significantly inhibit sperm acrosome reaction (AR) evoked by zona pellucida. Using transfected HEK293 cells system, only Cav3.1 and Cav3.2, instead of Cav3.3, channels were inhibited by genistein. Since T-type calcium channels are the key components in the male reproduction, such as in AR and sperm motility, our data suggest that this PTK-independent inhibition of genistein on I(Ca,T) might be involved in its anti-reproductive effects.     

Structural genomics is the largest contributor of novel structural leverage

The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large families without structural coverage, as well as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative in the PDB on the date of deposition). The structural coverage of the protein universe represented by today’s UniProt (v12.8) has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849–851, 2007) has resulted from systematic targeting of large families. PSI’s per structure contribution to novel leverage was over 4-fold higher than that for non-PSI structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another ~15 years to cover most sequences in the current UniProt database.     

Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel

The envelope (E) protein from coronaviruses is a small polypeptide that contains at least one α-helical transmembrane domain. Absence, or inactivation, of E protein results in attenuated viruses, due to alterations in either virion morphology or tropism. Apart from its morphogenetic properties, protein E has been reported to have membrane permeabilizing activity. Further, the drug hexamethylene amiloride (HMA), but not amiloride, inhibited in vitro ion channel activity of some synthetic coronavirus E proteins, and also viral replication. We have previously shown for the coronavirus species responsible for severe acute respiratory syndrome (SARS-CoV) that the transmembrane domain of E protein (ETM) forms pentameric α-helical bundles that are likely responsible for the observed channel activity. Herein, using solution NMR in dodecylphosphatidylcholine micelles and energy minimization, we have obtained a model of this channel which features regular α-helices that form a pentameric left-handed parallel bundle. The drug HMA was found to bind inside the lumen of the channel, at both the C-terminal and the N-terminal openings, and, in contrast to amiloride, induced additional chemical shifts in ETM. Full length SARS-CoV E displayed channel activity when transiently expressed in human embryonic kidney 293 (HEK-293) cells in a whole-cell patch clamp set-up. This activity was significantly reduced by hexamethylene amiloride (HMA), but not by amiloride. The channel structure presented herein provides a possible rationale for inhibition, and a platform for future structure-based drug design of this potential pharmacological target.