Characterization of recombinant E. coli expressing a novel fucosidase from Bacillus cereus 2-8 belonging to GH95 family

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron

Introduction

Research on the mechanism of marine polysaccharide utilization by Bacteroides thetaiotaomicron has drawn substantial attention in recent years. Derived from marine algae, the marine algae polysaccharides could serve as prebiotics to facilitate intestinal microecological balance and alleviate colonic diseases. Bacteroides thetaiotaomicron, considered the most efficient degrader of polysaccharides, relates to its capacity to degrade an extensive spectrum of complex polysaccharides. Polysaccharide utilization loci (PULs), a specialized organization of a collection of genes-encoded enzymes engaged in the breakdown and utilization of polysaccharides, make it possible for Bacteroides thetaiotaomicron to metabolize various polysaccharides. However, there is still a paucity of comprehensive studies on the procedure of polysaccharide degradation by Bacteroides thetaiotaomicron.

Methods

In the current study, the degradation of four kinds of marine algae polysaccharides, including sodium alginate, fucoidan, laminarin, and Pyropia haitanensis polysaccharides, and the underlying mechanism by Bacteroides thetaiotaomicron G4 were investigated. Pure culture of Bacteroides thetaiotaomicron G4 in a substrate supplemented with these polysaccharides were performed. The change of OD600, total carbohydrate contents, and molecular weight during this fermentation were determined. Genomic sequencing and bioinformatic analysis were further performed to elucidate the mechanisms involved. Specifically, Gene Ontology (GO) annotation, Clusters of Orthologous Groups (COG) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were utilized to identify potential target genes and pathways.

Results

Underlying target genes and pathways were recognized by employing bioinformatic analysis. Several PULs were found that are anticipated to participate in the breakdown of these four polysaccharides. These findings may help to understand the interactions between these marine seaweed polysaccharides and gut microorganisms.

Discussion

The elucidation of polysaccharide degradation mechanisms by Bacteroides thetaiotaomicron provides valuable insights into the utilization of marine polysaccharides as prebiotics and their potential impact on gut health. Further studies are warranted to explore the specific roles of individual PULs and their contributions to polysaccharide metabolism in the gut microbiota.

Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression in Bacillus subtilis DB104 through Transcriptome Analysis

Bacillus subtilis is widely employed for recombinant protein expression. B. subtilis DB104 offers a distinct advantage as a protein expression host because it is an extracellular protease-deficient derivative of B. subtilis 168. We have conducted a time-course transcriptome analysis of B. subtilis DB104 in a prior study. In the present study, we identified 10 genes that exhibited strong expression at each time point or all, based on transcriptome data. Subsequently, we assessed the strength of 12 promoters that transcribe these genes using enhanced green fluorescent protein (eGFP) as a reporter. Among these promoters, Psdp and PskfA had the highest expression levels. At 24 h, these two promoters exhibited 34.5- and 38.8-fold higher strength, respectively, than the strength of P43, the control promoter. Consequently, these two promoters were selected for further development. We enhanced these promoters by optimizing spacer length, promoter sequence, Shine-Dalgarno sequence, regulator binding sites, and terminator sequences. As a result, we successfully engineered the most potent protein expression cassette, Psdp-4, which exhibited a 3.84-fold increase in strength compared to the original Psdp promoter. Furthermore, we constructed an expression cassette for a human epidermal growth factor (hEGF) using Psdp-4 to evaluate its general application. The expression level of His tagged hEGF, quantified using ImageJ analysis and applied to SDS-PAGE, reached the highest yield of 103.9 μg/mL under the control of Psdp-4 at 24 h. The expressed hEGF protein was purified, and its bioactivity was confirmed through a cell proliferation assay using HT-29 cells. Our work demonstrates the construction of a highly efficient expression system for B. subtilis DB104 based on transcriptome data and promoter engineering. This system enables rapid, inducer-free protein expression within 24 h. It can be used as a valuable tool for various industrial applications.

Structure and function of microbial α-l-fucosidases: a mini review

Fucose is a monosaccharide commonly found in mammalian, insect, microbial and plant glycans. The removal of terminal α-l-fucosyl residues from oligosaccharides and glycoconjugates is catalysed by α-l-fucosidases. To date, glycoside hydrolases (GHs) with exo-fucosidase activity on α-l-fucosylated substrates (EC 3.2.1.51, EC 3.2.1.-) have been reported in the GH29, GH95, GH139, GH141 and GH151 families of the Carbohydrate Active Enzymes (CAZy) database. Microbes generally encode several fucosidases in their genomes, often from more than one GH family, reflecting the high diversity of naturally occuring fucosylated structures they encounter. Functionally characterised microbial α-l-fucosidases have been shown to act on a range of substrates with α-1,2, α-1,3, α-1,4 or α-1,6 fucosylated linkages depending on the GH family and microorganism. Fucosidases show a modular organisation with catalytic domains of GH29 and GH151 displaying a (β/α)8-barrel fold while GH95 and GH141 show a (α/α)6 barrel and parallel β-helix fold, respectively. A number of crystal structures have been solved in complex with ligands, providing structural basis for their substrate specificity. Fucosidases can also be used in transglycosylation reactions to synthesise oligosaccharides. This mini review provides an overview of the enzymatic and structural properties of microbial α-l-fucosidases and some insights into their biological function and biotechnological applications.