Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses.

Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated.

Weighted gene co-expression network analysis and drug-gene interaction bioinformatics uncover key genes associated with various presentations of malaria infection in African children and major drug candidates.

Malaria is a fatal parasitic disease with unelucidated pathogenetic mechanism. Herein, we aimed to uncover genes associated with different clinical aspects of malaria based on the GSE1124 dataset that is publicly accessible by using WGCNA. We obtained 16 co-expression modules and their correlations with clinical features.

Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19.

Coronavirus disease 2019 (COVID-19) has caused thousands of deaths worldwide and has become an urgent public health concern. The extraordinary interhuman transmission of this disease has urged scientists to examine the various facets of its pathogenic agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, based on publicly available genomic data, we analyzed the codon usage co-adaptation profiles of SARS-CoV-2 and other respiratory coronaviruses (CoVs) with their human host, identified CoV-responsive human genes and their functional roles on the basis of both the relative synonymous codon usage (RSCU)-based correlation of viral genes with human genes and differential gene expression analysis, and predicted potential drugs for COVID-19 treatment based on these genes.

Heterologous production of α-farnesene in metabolically engineered strains of Yarrowia lipolytica.

Herein, we studied the heterologous production of α-farnesene, a valuable sesquiterpene with various biotechnological applications, by metabolic engineering of Yarrowia lipolytica. Different overexpression vectors harboring combinations of tHMG1, IDI, ERG20 and codon-optimized α-farnesene synthase (OptFS) genes were constructed and integrated into the genome of Y. lipolytica Po1h.

Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica.

Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA) and Plackett-Burman design, we screened chemicals for lycopene production from a metabolically engineered strain of Y.

Metabolome analysis and pathway abundance profiling of Yarrowia lipolytica cultivated on different carbon sources.

Yarrowia lipolytica, a model microorganism of oleaginous yeasts with developed sophisticated genetic tools, is able to metabolize a wide range of substrates and accumulate large amounts of lipids. However, there is a lack of literature reporting the metabolic characteristics of Y. lipolytica metabolizing these substrates in a systematic view.

Improvement of ansamitocin P-3 production by Actinosynnema mirum with fructose as the sole carbon source.

Ansamitocin P-3 (AP-3) is an active and potent anti-tumor maytansinoid, which is usually produced by Actinosynnema spp. In this study, the effects of different carbon sources on biomass and AP-3 production by Actinosynnema mirum were investigated. The results showed great biomass production behavior of A.

Designing of a "cheap to run" fermentation platform for an enhanced production of single cell oil from Yarrowia lipolytica DSM3286 as a potential feedstock for biodiesel.

In this study, the culture medium components screening and filtering were undertaken in order to set up efficient and cost effective minimal culture media for lipid production from Yarrowia lipolytica DSM3286. The basal minimal culture medium (S2) designed yielded lipid content up to 35% of the microbial dry cell weight. A set of fermentation strategies based on this minimal medium was developed and the lipid content was raised to 51%.

Enhancement of ansamitocin P-3 production in Actinosynnema pretiosum by a synergistic effect of glycerol and glucose.

Ansamitocin P-3 (AP-3), a secondary metabolite produced by Actinosynnema pretiosum, is well known for its extraordinary antitumor properties and is broadly utilized in clinical research. Through this work, we found, for the first time, that the combination of glucose and glycerol as a mixed carbon source is an appropriate approach for enhancing the production of AP-3 by A. pretiosum.

Lycopene production in recombinant strains of Escherichia coli is improved by knockout of the central carbon metabolism gene coding for glucose-6-phosphate dehydrogenase.

Genetic manipulation was undertaken in order to understand the mechanism involved in the heterologous synthesis of lycopene in Escherichia coli. Knockout of the central carbon metabolic gene zwf (glucose-6-phosphate dehydrogenase) resulted in the enhancement of lycopene production (above 130 % relative to control). The amplification and overexpression of rate-limiting steps encoded by idi (isopentenyl diphosphate isomerase), dxs (1-deoxyxylulose-5-phosphate synthase) and ispDF (4-diphosphocytidyl-2C-methyl-D-erythritol synthase and 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase) genes improved lycopene synthesis from 0.