Microbial platform to synthesize chorismate derivatives via metabolic engineering approach

A synthetic metabolic pathway suitable for the production of chorismate derivatives was designed in Escherichia coli. An L-phenylalanine-overproducing E. coli strain was engineered to enhance the availability of phosphoenolpyruvate (PEP), which is a key precursor in the biosynthesis of aromatic compounds in microbes. Two major reactions converting PEP to pyruvate were inactivated. Using this modified E.coli as a base strain, we tested our system by carrying out the production of salicylate, a high-demand aromatic chemical. The titer of salicylate reached 11.5 g/L in batch culture after 48 h cultivation in a 1-liter jar fermentor, and the yield from glucose as the sole carbon source exceeded 40% (mol/mol). In this test case, we found that pyruvate was synthesized primarily via salicylate formation and the reaction converting oxaloacetate to pyruvate. In order to demonstrate the generality of our designed strain, we employed this platform for the production of each of 7 different chorismate derivatives. Each of these industrially important chemicals was successfully produced to levels of 1-3 g/L in test tube-scale culture. In addition, by extending chorismate pathway, we successfully achieved maleate production, which is one of significant dicarboxylic acid as well as succinate and malate. A novel synthetic pathway of maleate was constructed in our base strain, and the productivity reached 7.1 g/L. This is the first report about maleate production using genetically engineered micro-organisms

Metabolic design of Escherichia coli for muconic acid production

Adipic acid(AA) is a versatile bulk chemical to be used for raw materials such as nylon 6,6. Currently, AA biosynthesis from bio-resources have received a lot of attention in recent years as environment-friendly and renewable AA production process. Muconic acid(MA), also known as 2,4-hexadienedioic acid, is expected as a biosynthesis precursor of AA. There are Several studies on MA biosynthesis using Escherichia coli introduced foreign genes. In those studies, MA is synthesized from intermediate products of shikimate pathway. However, the production volume is not sufficient and it is a hindrance to industrialization. In this study, we aimed to the high efficiency biosynthesis of MA using metabolic designed Escherichia coli. First, we designed the metabolism to increase the accumulation of phosphoenolpyruvic acid (PEP), which is one of the starting materials of the shikimate pathway. Next, we determined the optimal MA synthetic pathway branched from the shikimate pathway. Specifically, we examined three types of MA production pathway with PEP accumulation strain as parent and selected the pathway with the highest MA production. Finally, we examined efficient production of MA using fusion proteins. Shikimate pathway protein and MA production pathway protein were combined to direct carbon flux into MA production

Effect of rhegmatogenous retinal detachment on preoperative and postoperative retinal sensitivities

This retrospective study investigated foveal and perifoveal retinal sensitivities using microperimetry before and after surgery for rhegmatogenous retinal detachment (RRD). Consecutive patients with RRD who underwent vitrectomy or scleral buckling were included. Comprehensive ophthalmological examinations, including microperimetry and swept-source optical coherence tomography, were performed before and 6 months after surgery. Pre- and postoperative retinal sensitivities at the fovea and 4 perifoveal measurement points farthest from the fixation point, both vertically and horizontally (superior, inferior, nasal, and temporal) were examined. A total of 34 foveal and 136 perifoveal measurement points in 34 eyes of 34 patients were evaluated. The postoperative retinal sensitivity was significantly higher than the preoperative value at foveal and perifoveal points with (P<0.001 for both) and without (fovea: P=0.005, perifovea: P<0.001) RRD. The postoperative retinal sensitivity was significantly lower at foveal (P<0.01) and perifoveal (P<0.001) points with preoperative RRD than at points without preoperative RRD; furthermore, it was significantly better at points with ellipsoid zone (Ez) continuity than at points with Ez discontinuity (fovea: P<0.01, perifovea: P<0.001). RRD deteriorates retinal sensitivity, regardless of its presence or absence at the measurement point before surgery. Postoperative Ez continuity is important for good postoperative retinal sensitivity

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

Identification of Triple Flame Based on Numerical Data for Laminar Lifted Flames

The flame base structures of laminar lifted flames are numerically investigated in order to develop a model of triple flame applicable to the flamelet model. The lifted flames formed in the downstream expanded duct developed by Kioni et al. are calculated systematically in terms of the fuel concentration gradient at the inlet using a variant of the HSMAC method, modified so as to deal with variations of density. The triple flame is formed at the flame base of lifted nonpremixed flame for every case, even the case which does not initially have partial mixing. The diffusion flame appears to be supported by the enhancement of the surrounding premixed flames, resulting in a temperature rise. All scalar quantities along the premixed flames of the triple flame decline along a similar profile in mixture fraction space, and scalar quantities in the region surrounded by the premixed flames are almost completely conserved. On the basis of the results, we developed a model of triple flame that is applicable to the flamelet model. In the model, the region without reaction upstream of the flame base is referred to as the unburned region (frozen flow structure region), followed by the transition region outside the premixed flames, in which the flame changes from the frozen structure to the fully burning diffusion structure. The region surrounded by the premixed flames is referred to as the triple flame structure region. The region following the triple flame structure region is the fully burning diffusion flame structure region.・rights：日本機械学会・rights：本文データは学協会の許諾に基づきCiNiiから複製したものである・relation：isVersionOf：http://ci.nii.ac.jp/naid/110004773161

Population Dynamics in the Biogenesis of Single-/Multi-Layered Membrane Vesicles Revealed by Encapsulated GFP-Monitoring Analysis

Various generations of membrane vesicles (MV) have been observed in Escherichia coli in terms of triggering events and populations of single-layered (s)/multi-layered (m) forms. Previously, we proposed a novel mechanism for MV generation triggered by the intracellular accumulation of biopolyester polyhydroxybutyrate (PHB). This was designated as the Polymer Intracellular Accumulation-triggered system for Membrane Vesicle Production (PIA-MVP). Herein, we attempted to determine the conditions for the change in the population between s-MV and m-MV using glucose concentration-dependent PIA-MVP. PIA-MVP was established using the good correlation between the glucose concentration-dependent PHB accumulation and MV generation. Thus, we assumed the presence of a critical glucose concentration could determine the population ratio of s-MV to m-MV, indicating that s-MV generation is a dominant component in the extracellular environment. Cytoplasmic green fluorescent protein (GFP) was used to evaluate the glucose concentration, enabling the selective generation of s-MV. The glucose concentration was determined to be 15 g/L to satisfy this purpose under the culture conditions. In conclusion, we established a biological system allowing us to selectively generate both single- and multi-layered MVs based on PIA-VIP encapsulation of GFP, providing a versatile toolkit to gain insights into the MV generation mechanism and achieve progress in various engineering applications