Evolution. Changing the cofactor diet of an enzyme

Enzymatic Characterization of the Isocitrate Dehydrogenase with Dual Coenzyme Specificity from the Marine Bacterium Umbonibacter marinipuiceus

Isocitrate dehydrogenase (IDH) can be divided into NAD⁺-dependent and NADP⁺-dependent types based on the coenzyme specificity. It is worth noting that some IDHs exhibit dual coenzyme specificity characteristics. Herein, a dual coenzyme-dependent IDH from Umbonibacter Marinipuiceus (UmIDH) was expressed, purified, and identified in detail for the first time. SDS-PAGE and Gel filtration chromatography analyses showed that UmIDH is an 84.7 kDa homodimer in solution. The K_m values for NAD⁺ and NADP⁺ are 1800.0 ± 64.4 μM and 1167.7 ± 113.0 μM in the presence of Mn²⁺, respectively. Meanwhile, the catalytic efficiency (k_cat/K_m) of UmIDH is only 2.3-fold greater for NADP⁺ than NAD⁺. The maximal activity for UmIDH occurred at pH 8.5 (with Mn²⁺) or pH 8.7 (with Mg²⁺) and at 35 °C (with Mn²⁺ or Mg²⁺). Heat inactivation assay revealed that UmIDH sustained 50% of maximal activity after incubation at 57 °C for 20 min with either Mn²⁺ or Mg²⁺. Moreover, three putative core coenzyme binding residues (R345, L346, and V352) of UmIDH were evaluated by site-directed mutagenesis. This recent work identified a unique dual coenzyme-dependent IDH and achieved the groundbreaking bidirectional modification of this specific IDH's coenzyme dependence for the first time. This provides not only a reference for the study of dual coenzyme-dependent IDH, but also a basis for the investigation of the coenzyme-specific evolutionary mechanisms of IDH.

Proteomic study of plaque fluid in high caries and caries free children

BACKGROUND:

The occurrence and development of caries is a complex process affected by multiple factor.

OBJECTIVE:

The present study was envisaged to evaluate the plaque fluid in caries free children and children with high caries, in order to establish a data set of bacterial secretion proteomics. A non-labeled quantitative technique based on two-dimensional liquid chromatography-series mass spectroscopy was employed to detect plaque fluid. Based on the proteomics data, the database search, data processing and pathway analysis illuminated the function of these proteins, and clarified the role of plaque microecology in caries occurrence and development.

METHODS:

The study enrolled 8 caries free (CF) children, whose decayed-missed-filled surface of teeth is 0 (dmfs = 0), and caries sensitive (CS) children, whose decayed-missed-filled surface of teeth is > 10(dmfs > 10) (3 ∼ 5 years old) for the smooth tooth plaque and the plaque in the high caries group. The plaque protein was extracted using the unlabeled quantitative technique like liquid chromatography-series mass spectrometry, using DeCyderTM MS Differential Analysis Software (version 1.0, GE Healthcare) that detected and compared the spectra, and quantified the full scanning before series mass spectroscopy. After obtaining all peptides with quantitative information, significantly differential polypeptide molecules were obtained (p< 0.05), and a metabolic pathway analysis was performed.

RESULTS:

We identified 1,804 peptides with quantitative information, including 39 in CF, 30 in CS, and 1,735 similarly expressing peptides. After statistical analysis, 603 statistically different expression peptide data sets were obtained, including 202 high-expressed peptides in Group CF, 33 greater than 1.5 fold peptides, 401 high-expressed in Group CS and 199 greater than 1.5 fold peptide (173 nonredundant proteins).

CONCLUSION:

Our study obtained the largest known dataset of the bacterial secretion protein in children with high caries, and screened the data set of high caries state. 603 peptides were statistically rich in 101 pathways, including glycolysis pyruvate acid metabolism, tricarboxylic acid cycle, pentyl phosphate pathway, fructose mannose metabolism, starch and sucrose metabolism, and ABC transporters.

Metabolic anchor reactions for robust biorefining

Microbial cell factories based on renewable carbon sources are fundamental to a sustainable bio-economy. The economic feasibility of producer cells requires robust performance balancing growth and production. However, the inherent competition between these two objectives often leads to instability and reduces productivity. While algorithms exist to design metabolic network reduction strategies for aligning these objectives, the biochemical basis of the growth-product coupling has remained unresolved. Here, we reveal key reactions in the cellular biochemical repertoire as universal anchor reactions for aligning cell growth and production. A necessary condition for a reaction to be an anchor is that it splits a substrate into two or more molecules. By searching the currently known biochemical reaction space, we identify 62 C-C cleaving anchor reactions, such as isocitrate lyase (EC 4.1.3.1) and L-tryptophan indole-lyase (EC 4.1.99.1), which are relevant for biorefining. The here identified anchor reactions mark network nodes for basing growth-coupled metabolic engineering and novel pathway designs.

Creation of bioorthogonal redox systems depending on nicotinamide flucytosine dinucleotide

Many enzymes catalyzing biological redox chemistry depend on the omnipresent cofactor, nicotinamide adenine dinucleotide (NAD). NAD is also involved in various nonredox processes. It remains challenging to disconnect one particular NAD-dependent reaction from all others. Here we present a bioorthogonal system that catalyzes the oxidative decarboxylation of l-malate with a dedicated abiotic cofactor, nicotinamide flucytosine dinucleotide (NFCD). By screening the multisite saturated mutagenesis libraries of the NAD-dependent malic enzyme (ME), we identified the mutant ME-L310R/Q401C, which showed excellent activity with NFCD, yet marginal activity with NAD. We found that another synthetic cofactor, nicotinamide cytosine dinucleotide (NCD), also displayed similar activity with the ME mutants. Inspired by these observations, we mutated d-lactate dehydrogenase (DLDH) and malate dehydrogenase (MDH) to DLDH-V152R and MDH-L6R, respectively, and both mutants showed fully active with NFCD. When coupled with DLDH-V152R, ME-L310R/Q401C required only a catalytic amount of NFCD to convert l-malate. Our results opened the window to engineer bioorthogonal redox systems for a wide variety of applications in systems biology and synthetic biology.

Direct electrochemistry of lactate dehydrogenase immobilized on silica sol–gel modified gold electrode and its application

The direct electrochemistry of lactate dehydrogenase (LDH) immobilized in silica sol-gel film on gold electrode was investigated, and an obvious cathodic peak at about -200 mV (versus SCE) was found for the first time. The LDH-modified electrode showed a surface controlled irreversible electrode process involving a one electron transfer reaction with the charge-transfer coefficient (alpha) of 0.79 and the apparent heterogeneous electron transfer rate constant (K(s)) of 3.2 s(-1). The activated voltammetric response and decreased charge-transfer resistance of Ru(NH(3))(6)(2+/3+) on the LDH-modified electrode provided further evidence. The surface morphologies of silica sol-gel and the LDH embedded in silica sol-gel film were characterized by SEM. A potential application of the LDH-modified electrode as a biosensor for determination of lactic acid was also investigated. The calibration range of lactic acid was from 2.0 x 10(-6) to 3.0 x 10(-5) mol L(-1) and the detection limit was 8.0 x 10(-7) mol L(-1) at a signal-to-noise ratio of 3. Finally, the effect of environmental pollutant resorcinol on the direct electrochemical behavior of LDH was studied. The experimental results of voltammetry indicated that the conformation of LDH molecule was altered by the interaction between LDH and resorcinol. The modified electrode can be applied as a biomarker to study the pollution effect in the environment.