The catalytic action of human d-lactate dehydrogenase is severely inhibited by oxalate and is impaired by mutations triggering d-lactate acidosis

d-lactate dehydrogenases are known to be expressed by prokaryotes and by eukaryotic invertebrates, and over the years the functional and structural features of some bacterial representatives of this enzyme ensemble have been investigated quite in detail. Remarkably, a human gene coding for a putative d-lactate dehydrogenase (DLDH) was identified and characterized, disclosing the occurrence of alternative splicing of its primary transcript. This translates into the expression of two human DLDH (hDLDH) isoforms, the molecular mass of which is expected to differ by 2.7 kDa. However, no information on these two hDLDH isoforms is available at the protein level. Here we report on the catalytic action of these enzymes, along with a first analysis of their structural features. In particular, we show that hDLDH is strictly stereospecific, with the larger isoform (hDLDH-1) featuring higher activity at the expense of d-lactate when compared to its smaller counterpart (hDLDH-2). Furthermore, we found that hDLDH is strongly inhibited by oxalate, as indicated by a Ki equal to 1.2 μM for this dicarboxylic acid. Structurally speaking, hDLDH-1 and hDLDH-2 were determined, by means of gel filtration and dynamic light scattering experiments, to be a hexamer and a tetramer, respectively. Moreover, in agreement with previous studies performed with human mitochondria, we identified FAD as the cofactor of hDLDH, and we report here a model of FAD binding by the human d-lactate dehydrogenase. Interestingly, the mutations W323C and T412 M negatively affect the activity of hDLDH, most likely by impairing the enzyme electron-acceptor site.

Reversal of arterial oxygen desaturation with the use of an oxygen concentrator during injectable anaesthesia in feral cats positioned in the Trendelenburg, dorsal or lateral surgical position

INTRODUCTION

This study observed the effects of oxygen supplementation, via an oxygen concentrator, on peripheral arterial blood oxygenation (SpO2) measured by pulse oximetry in anaesthetised cats undergoing spay in three different surgical positions. A total of 192 female feral cats were investigated for a large-scale trap-neuter-release program. Cats were anaesthetised with an intramuscular combination of butorphanol (0,4 mg / kg), ketamine (7-10 mg / kg) and medetomidine (0,03-0,05 mg / kg). Cats were randomly allocated to undergo spay in either Trendelenburg (TR) (70° downward head tilt), lateral (LR) or dorsal (DR) recumbency. Cats were breathing spontaneously either room air or 2 L/minute oxygen via a tight-fitting face mask. Pulse rate (in beats per minute), respiratory rate (in breaths per minute) and SpO2 (in percentage) were measured at baseline in left lateral recumbency and afterwards continuously after being positioned in allocated surgical position. At the end of surgery, cats were placed again in left recumbency, and all parameters were re-evaluated after five minutes. Overall, 33 % of cats showed severe arterial oxygen desaturation (SpO2 < 90 %) at baseline when breathing room air. When oxygen was supplemented during the procedure, arterial oxygen desaturation resolved in all cats. At the end of the procedure, 29 % of cats were hypoxaemic when oxygen was not supplemented, with an overall higher percentage of hypoxaemic cats in TR as compared to DR and LR recumbencies. All cats recovered well from surgery and were released within 24 hours post-anaesthesia. Arterial oxygen desaturation is frequent in cats anaesthetised with injectable anaesthesia for spay under field conditions. Oxygen supplementation administered via a tight-fitting mask resolved arterial oxygen desaturation in this feral cat population regardless of the surgical position and therefore oxygen supplementation is recommended in any case.

The Mycobacterium tuberculosis protein tyrosine phosphatase MptpA features a pH dependent activity overlapping the bacterium sensitivity to acidic conditions

The Mycobacterium tuberculosis low-molecular weight protein tyrosine phosphatase (MptpA) is responsible for the inhibition of phagosome-lysosome fusion and is essential for the bacterium pathogenicity. This inhibition implies that M. tuberculosis is not exposed to a strongly acidic environment in vivo, enabling successful propagation in host cells. Remarkably, MptpA has been previously structurally and functionally investigated, with special emphasis devoted to the enzyme properties at pH 8.0. Considering that the virulence of M. tuberculosis is strictly dependent on the avoidance of acidic conditions in vivo, we analysed the pH-dependence of the structural and catalytic properties of MptpA. Here we show that this enzyme undergoes pronounced conformational rearrangements when exposed to acidic pH conditions, inducing a severe decrease of the enzymatic catalytic efficiency at the expense of phosphotyrosine (pTyr). In particular, a mild decrease of pH from 6.5 to 6.0 triggers a significant increase of K0.5 of MptpA for phosphotyrosine, the phosphate group of which we determined to feature a pKa2 equal to 5.7. Surface plasmon resonance experiments confirmed that MptpA binds poorly to pTyr at pH values < 6.5. Notably, the effectiveness of the MptpA competitive inhibitor L335-M34 at pH 6 does largely outperform the inhibition exerted at neutral or alkaline pH values. Overall, our observations indicate a pronounced sensitivity of MptpA to acidic pH conditions, and suggest the search for competitive inhibitors bearing a negatively charged group featuring pKa values lower than that of the substrate phosphate group.

The impact of COVID-19 on right ventricular function in chronic kidney disease patients

Introduction

In chronic kidney disease (CKD) patients, the case fatality rate caused by the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is higher than in the general population [1]. In patients hospitalised with COVID 19, right heart dysfunction is present in 20% of the cases, associated with an increased risk of all-cause death [2].

Purpose

CARDIO-SCARS in CKD is a currently ongoing multi-center observational match controlled trial that aims to assess the cardiovascular (CV) risk in a CKD (stages 3 to 5), dialysis and kidney transplant population, following SARS-CoV-2 infection, by using clinical evaluation, various techniques and novel biomarkers (ClinicalTrials.gov Identifier NCT05125913). We hereby report the main baseline echocardiographic parameters that assess the right ventricular (RV) function.

Methods

We conducted a cross-sectional study that included 263 patients with CKD (dialysis, transplantation or eGFR <60 ml/min/1.73 m²). For assessing RV function, 5 parameters were measured: fractional area change (FAC, %), tricuspid annular plane systolic excursion (TAPSE, mm), tricuspid S' wave (S tric, cm/s), Tei index and right ventricular free wall longitudinal strain (RVFWLS, %). Patients in atrial fibrillation, with a permanent pacemaker or with a poor acoustic window were excluded.

Results

Our study included 263 patients with CKD, divided in two groups: 168 patients post COVID-19 (94 in dialysis, 38 post kidney transplantation and 36 with CKD) and 95 patients in the control group (57 in dialysis, 30 post kidney transplantation and 8 with CKD).The mean age was 57.3±15.4 years (median 60 years old), 55.2% of the patients were males, 24% were diabetic and 9.5% were smokers. The mean duration of dialysis in the COVID-19 group was 63.8 months vs. 62.6 months in the control group. In the COVID group, the echocardiography was performed at a mean distance of 2.2±2.1 months after testing positive for SARS-CoV-2.All the parameters of RV function were better in the control group (FAC (%): 43.6±11 vs. 41.3±11; TAPSE (mm): 23.2±6.9 vs. 21.4±4.9; S tric (cm/s): 13.4±3.4 vs. 13±3.1; Tei index: 0.5±0.2 vs. 0.6±0.2; RVFWLS (%): −20.1±3.8 vs. −18.6±5.1. After performing a two-sample t-Test, statistical significance was reached only for TAPSE, Tei index and RVFWLS (0.008, 0.0001 and 0.006, respectively).

Conclusions

Our study is the first to describe echocardiographic alterations post-COVID in a CKD population. All CKD patients had lower values of RV parameters than those reported in the general population. Still, the CKD COVID group had lower values than CKD control group, with the same magnitude as the changes reported in the general population [3,4]. The evolution of these parameters and their prognostic significance is of interest, regarding long-term CV sequelae of COVID-19.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Ministry of Research and Innovation, CNCS-UEFISCDI

Cats undergoing spay with medetomidine, ketamine and butorphanol develop arterial oxygen desaturation independent of surgical positioning and increased intraocular pressure in Trendelenburg position

INTRODUCTION

This study observed the effects of three different surgical positions on arterial blood oxygenation measured noninvasively by pulse oximetry (SpO2) and on intraocular pressure (IOP) in anaesthetised cats undergoing spay. A total of 222 female feral cats were anaesthetised for a large-scale trap-neuter-return program with an intramuscular combination of medetomidine (0.03 - 0.05 mg/kg), ketamine (7 - 10 mg/kg) and butorphanol (0.4 mg/kg). Cats were randomly allocated to undergo spay in either Trendelenburg (70° downward head tilt), lateral or dorsal recumbency. SpO2 and pulse rate were measured at baseline, prior to surgical positioning, after one minute in surgical position and in one-minute intervals after surgical incision. Intraocular pressure was measured before positioning and at the end of surgery. At the end of surgery, all cats were placed into left lateral recumbency and all parameters were revaluated after five minutes. No significant differences between the three positions were found regarding SpO2, but an increase over time was observed. In total, 52 ± 10% (mean ± SD) of cats were hypoxaemic (SpO2 < 90%) at baseline. SpO2 improved over time, but 27 ± 3% (mean ± SD) of the cats remained hypoxaemic at the end of surgery. Trendelenburg position increased IOP during surgery (mean 31 ± 6 mmHg, individual max. 48 mmHg, versus 17 ± 4 mmHg in dorsal/lateral recumbency) but normalised after 5 mins in lateral recumbence. All cats recovered well from surgery and were released within 24 hours post-anaesthesia. Surgical position was shown to have no notable influence on SpO2 during anaesthesia in cats not receiving oxygen supplementation, whereas Trendelenburg position led to increased IOP. Oxygen supplementation is recommended with this anaesthetic protocol, as hypoxaemia is frequently observed.

Purification from Deinococcus radiodurans of a 66 kDa ABC transporter acting on peptides containing at least 3 amino acids

Deinococcus radiodurans is a Gram positive bacterium the capability of which to withstand high doses of ionizing radiations is well known. Physiologically speaking, D. radiodurans is a proteolytic prokaryote able to express and secrete quite a number of proteases, and to use amino acids as an energy source. When considering this, it is surprising that little information is available on the biochemical components responsible for the uptake of peptides in D. radiodurans. Here we report on the purification and characterization of an ABC peptide transporter, isolated from D. radiodurans cells grown in tryptone-glucose-yeast extract (TGY) medium. In particular, we show here that the action of this transporter (denoted DR1571, SwissProt data bank accession number Q9RU24 UF71_DEIRA) is exerted on peptides containing at least 3 amino acids. Further, using tetra-peptides as model systems, we were able to observe that the DR1571 protein does not bind to peptides containing phenylalanine or valine, but associates with high efficiency to tetra-glycine, and with moderate affinity to tetra-peptides containing arginine or aspartate.

Substrate Activation of the Low-Molecular Weight Protein Tyrosine Phosphatase from Mycobacterium tuberculosis

Mycobacterium tuberculosis is known to express a low-molecular weight protein tyrosine phosphatase. This enzyme, denoted as MptpA (Mycobacterium protein tyrosine phosphatase A), is essential for the pathogen to escape the host immune system and therefore represents a target for the search of antituberculosis drugs. MptpA was shown to undergo a conformational transition during catalysis, leading to the closure of the active site, which is by this means poised to the chemical step of dephosphorylation. Here we show that MptpA is subjected to substrate activation, triggered by p-nitrophenyl phosphate or by phosphotyrosine. Moreover, we show that the enzyme is also activated by phosphoserine, with serine being ineffective in enhancing MptpA activity. In addition, we performed assays under pre-steady-state conditions, and we show here that substrate activation is kinetically coupled to the closure of the active site. Surprisingly, when phosphotyrosine was used as a substrate, MptpA did not obey Michealis–Menten kinetics, but we observed a sigmoidal dependence of the reaction velocity on substrate concentration, suggesting the presence of an allosteric activating site in MptpA. This site could represent a promising target for the screening of MptpA inhibitors exerting their action independently of the binding to the enzyme active site.

Structural and catalytic insights into HoLaMa, a derivative of Klenow DNA polymerase lacking the proofreading domain

We report here on the stability and catalytic properties of the HoLaMa DNA polymerase, a Klenow sub-fragment lacking the 3’-5’ exonuclease domain. HoLaMa was overexpressed in Escherichia coli, and the enzyme was purified by means of standard chromatographic techniques. High-resolution NMR experiments revealed that HoLaMa is properly folded at pH 8.0 and 20°C. In addition, urea induced a cooperative folding to unfolding transition of HoLaMa, possessing an overall thermodynamic stability and a transition midpoint featuring ΔG and C_M equal to (15.7 ± 1.9) kJ/mol and (3.5 ± 0.6) M, respectively. When the catalytic performances of HoLaMa were compared to those featured by the Klenow enzyme, we did observe a 10-fold lower catalytic efficiency by the HoLaMa enzyme. Surprisingly, HoLaMa and Klenow DNA polymerases possess markedly different sensitivities in competitive inhibition assays performed to test the effect of single dNTPs.

Manganese is a Deinococcus radiodurans growth limiting factor in rich culture medium

To understand the effects triggered by Mn²⁺ on Deinococcus radiodurans, the proteome patterns associated with different growth phases were investigated. In particular, under physiological conditions we tested the growth rate and the biomass yield of D. radiodurans cultured in rich medium supplemented or not with MnCl2. The addition of 2.5-5.0 µM MnCl2 to the medium neither altered the growth rate nor the lag phase, but significantly increased the biomass yield. When higher MnCl2 concentrations were used (10-250 µM), biomass was again found to be positively affected, although we did observe a concentration-dependent lag phase increase. The in vivo concentration of Mn²⁺ was determined in cells grown in rich medium supplemented or not with 5 µM MnCl2. By atomic absorption spectroscopy, we estimated 0.2 and 0.75 mM Mn²⁺ concentrations in cells grown in control and enriched medium, respectively. We qualitatively confirmed this observation using a fluorescent turn-on sensor designed to selectively detect Mn²⁺in vivo. Finally, we investigated the proteome composition of cells grown for 15 or 19 h in medium to which 5 µM MnCl2 was added, and we compared these proteomes with those of cells grown in the control medium. The presence of 5 µM MnCl2 in the culture medium was found to alter the pI of some proteins, suggesting that manganese affects post-translational modifications. Further, we observed that Mn²⁺ represses enzymes linked to nucleotide recycling, and triggers overexpression of proteases and enzymes linked to the metabolism of amino acids.

Luminescent protein staining with Re(i) tetrazolato complexes

Re(i) tricarbonyl diiimine complexes for the first time exploited as luminescent staining agents for SDS-PAGE.

Methylation of Ir(iii)-tetrazolato complexes: an effective route to modulate the emission outputs and to switch to antimicrobial properties

Two neutral cyclometalated Ir(iii)-tetrazolato complexes that differ by variations of the substituents on either the phenylpyridine or the tetrazolate ligand have been converted into the corresponding methylated and cationic analogues. NMR (¹H and ¹³C) characterization of the Ir(iii) complexes provided the results in agreement with the chemo- and regioselective character of methylation at the N-3 position of the Ir(iii)-coordinated tetrazolato ring. This evidence was further corroborated by the analysis of the molecular structures of the cationic complexes obtained by X-ray diffraction. In view of the photophysical properties, the addition of a methyl moiety to neutral Ir(iii) tetrazolates, which behave as sky-blue or orange phosphors, caused a systematic red shift of their phosphorescence output. The transformation of neutral Ir(iii) tetrazolates into cationic Ir(iii)-tetrazole complexes was screened for any eventual antimicrobial activity in vitro against Gram negative (E. coli) and Gram positive (D. radiodurans) microorganisms. While both kinds of complexes were not active against E. coli, the conversion of the neutral Ir(iii) tetrazolates into the corresponding methylated and cationic Ir(iii)tetrazole derivatives determined the turn-on of a good to excellent antimicrobial activity toward Gram positive Deinococcus radiodurans, a non-pathogenic bacterium that is listed as one of the toughest microorganisms in light of its outstanding resistance to radiation and oxidative stress.

The expression of the Cuphea palustris thioesterase CpFatB2 in Yarrowia lipolytica triggers oleic acid accumulation

The conversion of industrial by-products into high-value added compounds is a challenging issue. Crude glycerol, a by-product of the biodiesel production chain, could represent an alternative carbon source for the cultivation of oleaginous yeasts. Here, we developed five minimal synthetic glycerol-based media, with different C/N ratios, and we analyzed the production of biomass and fatty acids by Yarrowia lipolytica Po1g strain. We identified two media at the expense of which Y. lipolytica was able to accumulate ∼5 g L(-1) of biomass and 0.8 g L(-1) of fatty acids (0.16 g of fatty acids per g of dry weight). These optimized media contained 0.5 g L(-1) of urea or ammonium sulfate and 20 g L(-1) of glycerol, and were devoid of yeast extract. Moreover, Y. lipolytica was engineered by inserting the FatB2 gene, coding for the CpFatB2 thioesterase from Cuphea palustris, in order to modify the fatty acid composition towards the accumulation of medium-chain fatty acids. Contrary to the expected, the expression of the heterologous gene increased the production of oleic acid, and concomitantly decreased the level of saturated fatty acids.

Simultaneous ternary extension of DNA catalyzed by a trimeric replicase assembled in vivo

According to current models, dimeric DNA Polymerases coordinate the replication of DNA leading and lagging strands. However, it was recently shown that trimeric DNA Polymerases, assembled in vitro, replicate the lagging strand more efficiently than dimeric replicases. Here we show that the τ, α, ε, and θ subunits of Escherichia coli DNA Polymerase III can be assembled in vivo, yielding the trimeric τ3α3ε3θ3 complex. Further, we propose a molecular model of this complex, whose catalytic action was investigated using model DNA substrates. Our observations indicate that trimeric DNA replicases reduce the gap between leading and lagging strand synthesis.

The multifaceted benefits of protein co-expression in Escherichia coli

We report here that the expression of protein complexes in vivo in Escherichia coli can be more convenient than traditional reconstitution experiments in vitro. In particular, we show that the poor solubility of Escherichia coli DNA polymerase III ε subunit (featuring 3'-5' exonuclease activity) is highly improved when the same protein is co-expressed with the α and θ subunits (featuring DNA polymerase activity and stabilizing ε, respectively). We also show that protein co-expression in E. coli can be used to efficiently test the competence of subunits from different bacterial species to associate in a functional protein complex. We indeed show that the α subunit of Deinococcus radiodurans DNA polymerase III can be co-expressed in vivo with the ε subunit of E. coli. In addition, we report on the use of protein co-expression to modulate mutation frequency in E. coli. By expressing the wild-type ε subunit under the control of the araBAD promoter (arabinose-inducible), and co-expressing the mutagenic D12A variant of the same protein, under the control of the lac promoter (inducible by isopropyl-thio-β-D-galactopyranoside, IPTG), we were able to alter the E. coli mutation frequency using appropriate concentrations of the inducers arabinose and IPTG. Finally, we discuss recent advances and future challenges of protein co-expression in E. coli.

Targeting divalent metal cations with Re(i) tetrazolato complexes

The design, preparation and characterization of four new Re(i) tetrazolato complexes together with the study of their luminescent sensing abilities toward Zn(ii), Cd(ii) and Cu(ii) are described herein.

Vemurafenib skin phototoxicity is indirectly linked to ultraviolet A minimal erythema dose decrease

BACKGROUND

Vemurafenib, an anti-rapidly accelerated fibrosarcoma kinase B (BRAF) molecule, improves survival among patients with metastatic BRAF-mutated melanoma. Photosensitivity, a frequent cutaneous adverse effect induced by vemurafenib, can lead to cessation of treatment.

OBJECTIVES

To investigate photosensitivity mechanisms in patients treated with vemurafenib for metastatic melanoma.

METHODS

In a prospective study of 12 patients, photobiological explorations with measurements of ultraviolet A (UVA) minimal erythema dose (MED) and polychromatic MED were performed over 3 days in all 12 patients. UVA MED and polychromatic MED were also assessed for four patients before treatment. We then performed spectrophotometric analyses of (i) serum and faeces in these four patients, before and after introduction of vemurafenib; (ii) the lyophilized form of vemurafenib without excipient added; and (iii) the lyophilized form of vemurafenib added to serum and faeces before treatment.

RESULTS

Photosensitivity was present in 92% of the patients. UVA MED was normal before treatment and decreased after treatment, while polychromatic MED remained normal. The same three peaks (210, 260 and 310 nm) were identified in the spectrum for UVB and UVC but not for UVA on spectrophotometric analyses for each condition (lyophilized vemurafenib; serum and faeces after introduction of vemurafenib; and lyophilized vemurafenib added to serum and faeces before treatment). The peaks were different before treatment.

CONCLUSIONS

Our study confirms that photosensitivity under vemurafenib treatment was a UVA phototoxicity reaction, and our results suggest that a metabolite of vemurafenib rather than the parent molecule is involved in this phototoxicity.