MOESM1 of Improving the specific activity and pH stability of xylanase XynHBN188A by directed evolution

Additional file 1: Figure S1. DNA sequence alignment and base mutation frequency detection of xylanase mutant library

Development of a Universal One-Step Purification and Activation Method to Engineer Protein-Glutaminase through Rational Design

Cytotoxic enzymes often exist as zymogens containing prodomains to keep them in an inactive state. Protein-glutaminase (PG), which can enhance various functional characteristics of food proteins, is an enzyme containing pro-PG and mature-PG (mPG). However, poor activity and stability limit its application while tedious purification and activation steps limit its high-throughput engineering. Here, based on structural analysis, we replaced the linker sequence between pro-PG and mPG with the HRV3C protease recognition sequence and then coexpressed it with HRV3C protease in Escherichia coli to develop an efficient one-step purification and activation method for PG. We then used this method to obtain several mutants designed by a combination of computer-aided approach and beneficial point mutations. The specific activity (131.6 U/mg) of the best variant D1 was 4.14-fold that of the wild type, and t1/2 and T5010 increased by 13 min and 7 °C, respectively. D1 could effectively improve the solubility and emulsification of wheat proteins, more than twice the effect of the wild type. We also discussed the mechanism underlying the improved properties of D1. In summary, we not only provide a universal one-step purification and activation method to facilitate zymogen engineering but also obtain an excellent PG mutant

MOESM1 of Tunnel engineering to accelerate product release for better biomass-degrading abilities in lignocellulolytic enzymes

Additional file 1: Table S1. The residues lining each tunnel in 2UWF. Table S2. The sequences of primers used to construct the saturated mutant library in this study. Figure S1. Schematic illustration of the library construction

MOESM1 of Metabolic engineering of Escherichia coli for the production of butyric acid at high titer and productivity

Additional file 1: Table S1. E. coli strains constructed and used in this study. Table S2. E. coli plasmids constructed and used in this study

The conserved residues in the catalytic domain.

<p>The conserved residues around the two catalytic Glu residues are shown in sticks and colored by elements. The rest of the catalytic domain is shown in ribbons and colored in blue.</p

Bacterial Surface-Assembled Chitinosome for Dismantling Chitin into <i>N</i>‑Acetyl Glucosamine

The construction of an efficient multienzyme catalyst for dismantling recalcitrant polymers into high-value-added chemicals is appealing in sustainable biomanufacturing. Colocalization of cascade enzymes has been broadly adopted by natural and synthetic multienzyme systems for chemical synthesis, while there has been rare research on the decomposition of polymeric substrates. In this study, we constructed an E. coli surface-assembly (ESA) system to colocalize a synthetic chitinosome composed of two chitin hydrolases, BpChiA and BlNagZ, via the SpyCatcher/SpyTag (SpyC/SpyT) conjugation. In the ESA–chitinosome complexes, the loading efficiency and specific activity of enzymes were improved by tuning the copies of SpyC and the linker lengths between the SpyT and enzymes, respectively. The ratio of BpChiA and BlNagZ was also optimized. The ESA–chitinosome complexes exhibited higher productivity of N-acetyl glucosamine than the mixture of separately assembled enzymes on cell surfaces. This work demonstrates that the enzyme colocalization and the formation of the ternary ESA–chitinosome–chitin complexes are critical for the catalytic synergism of cascade enzymes, providing new insights into the decomposition of recalcitrant polymeric substrates

Table_2_Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China.XLSX

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.</p

Table_6_Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China.XLSX

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.</p

Table_3_Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China.XLSX

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.</p

Data_Sheet_1_Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China.PDF

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson’s disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid–related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.</p