Rewiring of metabolic pathways in yeasts for sustainable production of biofuels.

The ever-increasing global energy demand has led world towards negative repercussions such as depletion of fossil fuels, pollution, global warming and climate change. Designing microbial cell factories for the sustainable production of biofuels is therefore an active area of research. Different yeast cells have been successfully engineered using synthetic biology and metabolic engineering approaches for the production of various biofuels.

Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has been identified to be a mutation hot spot, with the P323L mutation being commonly observed in viral genomes isolated from North America. RdRp forms a complex with nonstructural proteins nsp7 and nsp8 to form the minimal replication/transcription machinery required for genome replication. As mutations in RdRp may affect formation of the RdRp-nsp7-nsp8 supercomplex, we analyzed viral genomes to identify mutations in nsp7 and nsp8 protein sequences.

Utilization of Bacillus subtilis cells displaying a glucose-tolerant β-glucosidase for whole-cell biocatalysis.

The microbial production of industrial enzymes requires a large number of complex biochemical steps for purification which increases their production cost. Additionally, poor thermo-stability of the purified enzymes under the operational conditions along with the challenges in their recovery and subsequent reuse, limit their usage in an industrial bioprocess. Surface display of heterologous enzymes on bacterial cells appear to be a suitable alternative.

Evaluation of autoantibody signatures in meningioma patients using human proteome arrays.

Meningiomas are one of the most common tumors of the Central nervous system (CNS). This study aims to identify the autoantibody biomarkers in meningiomas using high-density human proteome arrays (~17,000 full-length recombinant human proteins). Screening of sera from 15 unaffected healthy individuals, 10 individuals with meningioma grade I and 5 with meningioma grade II was performed.

Prediction of Loops in G Protein-Coupled Receptor Homology Models: Effect of Imprecise Surroundings and Constraints.

In the present study, we explored the extent to which inaccuracies inherent in homology models of the transmembrane helical cores of G protein-coupled receptors (GPCRs) can impact loop prediction. We demonstrate that loop prediction in homology models is much more difficult than loop reconstruction in crystal structures because of the imprecise positioning of loop anchors. Deriving information from 17 recently available GPCR crystal structures, we estimated all of the possible errors that could occur in loop anchors as the result of comparative modeling.

Evaluation of risedronate as an antibiofilm agent.

Escherichia coli cra null mutants have been reported in the literature to be impaired in biofilm formation. To develop E. coli biofilm-inhibiting agents for prevention and control of adherent behaviour, analogues of a natural Cra ligand, fructose-1,6-bisphosphate, were identified based on two-dimensional similarity to the natural ligand.

Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays.

The heterogeneity and poor prognosis associated with gliomas, makes biomarker identification imperative. Here, we report autoantibody signatures across various grades of glioma serum samples and sub-categories of glioblastoma multiforme using Human Proteome chips containing ~17000 full-length human proteins. The deduced sets of classifier proteins helped to distinguish Grade II, III and IV samples from the healthy subjects with 88, 89 and 94% sensitivity and 87, 100 and 73% specificity, respectively.

Engineering of yeast pyruvate decarboxylase for enhanced selectivity towards carboligation.

The aim of the study was to increase production of (R)-PAC by altering carboligation activity of Pdc in Saccharomyces cerevisiae. Pdc1 activity was modified by over-expression as well as changing the rate of decarboxylation and carboligation by site specific mutation in Pdc1. Over-expression of mutant Pdc1 resulted in 50 ± 2.

(R)-PAC biosynthesis in [BMIM][PF₆]/aqueous biphasic system using Saccharomyces cerevisiae BY4741 cells.

(R)-phenylacetylcarbinol or (R)-PAC is a pharmaceutical precursor of (1R, 2S) ephedrine and (1S, 2S) pseudoephedrine. Biotransformation of benzaldehyde and glucose by pyruvate decarboxylase produces (R)-PAC. This biotransformation suffers from toxicity of the substrate, product [(R)-PAC] and by-product (benzyl alcohol).

Production, characterization, and immunogenicity of a secreted form of Plasmodium falciparum merozoite surface protein 4 produced in Bacillus subtilis.

Plasmodium falciparum is the causative agent of the most serious form of malaria. Although a combination of control measures has significantly limited malaria morbidity and mortality in the last few years, it is generally agreed that sustained control or even eradication will require additional tools including an effective malaria vaccine. Merozoite surface protein 4, MSP4, which is present during the asexual stage of P.

Comparison of pyruvate decarboxylases from Saccharomyces cerevisiae and Komagataella pastoris (Pichia pastoris).

Pyruvate decarboxylases (PDCs) are a class of enzymes which carry out the non-oxidative decarboxylation of pyruvate to acetaldehyde. These enzymes are also capable of carboligation reactions and can generate chiral intermediates of substantial pharmaceutical interest. Typically, the decarboxylation and carboligation processes are carried out using whole cell systems.

Co-production of two recombinant proteins in Escherichia coli using the promoter region of the divergently expressed curli genes.

Expression of multiple proteins in a single host is desirable in biotechnological processes. The curli intergenic region in Escherichia coli contains promoter elements for the expression of the divergent csgBAC and csgDEFG operons. Using this bidirectionally active promoter region, we demonstrate high level production of two different recombinant proteins.

Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis.

Cra is a pleiotropic regulatory protein that controls carbon and energy flux in enteric bacteria. Recent studies have shown that Cra also regulates other cell processes and influences biofilm formation. The purpose of the present study was to investigate the role of Cra in biofilm formation in Escherichia coli.

Analyzing metabolic variations in different bacterial strains, historical perspectives and current trends--example E. coli.

The analysis of metabolic differences in bacterial strains is a useful tool for the development of strains with desired growth and production properties. Several methods are available for the evaluation and understanding of the differences: Biochemical methods to measure metabolites concentration and enzyme activity, mathematical methods to analyze metabolic fluxes through the various pathways, proteomic methods to identify expressed proteins, and genomic methods to detect and measure gene expression. A combination of the various methods is required to obtain a comprehensive understanding of metabolic activities.

Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and Northern blot analyses.

In a series of previous reports it was established by implementing metabolic flux, NMR/MS, and Northern blot analysis that the glyoxylate shunt, the TCA cycle, and acetate uptake by acetyl-CoA synthetase are more active in Escherichia coli BL21 than in Escherichia coli JM109. These differences were accepted as the reason for the differences in the glucose metabolism and acetate excretion of these two strains. Examination of the bacterial metabolism by microarrays and time course Northern blot showed that in addition to the glyoxylate shunt, the TCA cycle and the acetate uptake, other metabolic pathways are active differently in the two strains.