Biology subjects

Liang, Z.-X.

Publications and source records attributed to Liang, Z.-X..

3 recordsLinked to original sources

bioRxiv2026

Characterization and Optimization of Streptomyces albidoflavus MD102 as a heterologous expression chassis

We report the isolation and characterization of Streptomyces albidoflavus MD102, a strain that can be used as a microbial chassis for the heterologous production of secondary metabolites. This strain, closely related to the widely used S. albidoflavus J1074, exhibits a compact genome, exceptional genetic tractability, rapid growth, and susceptibility to antibiotics. Whole-genome sequencing revealed the metabolic capabilities of S. albidoflavus MD102, highlighting its versatility in supporting the production of diverse secondary metabolites. Employing CRISPR/Cas9-assisted genome editing tools, we created mutant strains with reduced genome and cleaner chromatographic background. In addition to the deletion of several biosynthetic gene clusters (BGC), we inserted the global regulator bldA gene and geranyl diphosphate synthase (gpps) genes and an additional {Phi}BT1-attB attachment site into the chromosome to enhance the strains capability in producing secondary metabolites. S. albidoflavus MD102 will be a new addition to the repertoire of existing Streptomyces chassis, contributing to the advancement of secondary metabolite discovery and synthetic microbiology. IMPORTANCEThe pursuit of a universal Streptomyces microbial chassis for the heterologous production of secondary metabolites has proven elusive, prompting a more pragmatic approach to develop a suite of Streptomyces chassis. The current study introduces Streptomyces albidoflavus MD102 as a promising heterologous chassis with rapid growth, susceptibility to common antibiotics, and genetic tractability. Its close phylogenetic relation with the widely used versatile S. albidoflavus J1074 chassis and the traits gained from strain improvement place the engineered S. albidoflavus MD102 strains as useful chassis for the heterologous production of microbial secondary metabolites. A notable feature of S. albidoflavus MD102 that distinguishes it from J1074 and other Streptomyces chassis is the presence of metabolic genes in its genome putatively responsible for the degradation of aromatic compounds. This characteristic may endow the strain with the capability to convert petrogenic polycyclic aromatic hydrocarbons (PAHs) and substituted aromatics into valuable secondary metabolites.

microbiology↗

bioRxiv2020

High-throughput 3D tracking reveals the importance of near wall swimming and initial attachment behaviors of P. aeruginosa for biofilm formation on a vertical wall

Studying the swimming behaviour of bacteria in 3 dimensions (3D) allows us to understand critical biological processes, such as biofilm formation. It is still unclear how near wall swimming behaviour may regulate the initial attachment and biofilm formation. It is challenging to address this as visualizing the movement of bacteria with reasonable spatial and temporal resolution in a high-throughput manner is technically difficult. Here, we compared the near wall (vertical) swimming behaviour of P. aeruginosa (PAO1) and its mutants {Delta}dipA (reduced in swarming motility and increased in biofilm formation) and {Delta}fimX (deficient in twitching motility and reduced in biofilm formation) using our new imaging technique based on light sheet microscopy. We found that P. aeruginosa (PAO1) increases its speed and changes its swimming angle drastically when it gets closer to a wall. In contrast, {Delta}dipA mutant moves toward the wall with steady speed without changing of swimming angle. The near wall behavior of {Delta}dipA allows it to be more effective to interact with the wall or wall-attached cells, thus leading to more capture events and a larger biofilm volume during initial attachment when compared with PAO1. Furthermore, we found that {Delta}fimX has a similar near wall swimming behavior as PAO1, however, it has a higher dispersal frequency and smaller biofilm formation when compared with PAO1 which can be explained by its poor twitching motility. Together, we propose that near wall swimming behavior of P. aeruginosa plays an important role in the regulation of initial attachment and biofilm formation. ImportanceBacterial biofilm is a community of bacteria on surfaces which leads to serious problems in medical devices, food industry, and aquaculture. The initial attachment and subsequent microcolony formation play critical roles in bacterial biofilm formation. However, it is unclear how the initial attachment is regulated, in particular, on a vertical surface. To study this, we have developed a novel imaging technique based on light sheet microscopy, which overcame the limitations of other imaging techniques, to understand how 3D bacterial motility near a wall may regulate initial attachment during biofilm formation. Using our technique, we discovered that near wall swimming behavior of the bacteria, P. aeruginosa, plays an important role in the regulation of biofilm formation during initial attachment.

microbiology↗

bioRxiv2020

Large-scale sequence similarity analysis reveals the scope of sequence and function divergence in PilZ domain proteins

PilZ domain-containing proteins constitute a superfamily of widely distributed bacterial signalling proteins. Although studies have established the canonical PilZ domain as an adaptor protein domain evolved to specifically bind the second messenger c-di-GMP, mounting evidence suggest that the PilZ domain has undergone enormous divergent evolution to generate a superfamily of proteins that are characterized by a wide range of c-di-GMP-binding affinity, binding partners and cellular functions. The divergent evolution has even generated families of non-canonical PilZ domains that completely lack c-di-GMP binding ability. In this study, we performed a large-scale sequence analysis on more than 28,000 single- and di-domain PilZ proteins using the sequence similarity networking tool created originally to analyse functionally diverse enzyme superfamilies. The sequence similarity networks (SSN) generated by the analysis feature a large number of putative isofunctional protein clusters, and thus, provide an unprecedented panoramic view of the sequence-function relationship and function diversification in PilZ proteins. Some of the protein clusters in the networks are considered as unexplored clusters that contain proteins with completely unknown biological function; whereas others contain one, two or a few functionally known proteins, and therefore, enabling us to infer the cellular function of uncharacterized homologs or orthologs. With the ultimate goal of elucidating the diverse roles played by PilZ proteins in bacterial signal transduction, the work described here will facilitate the annotation of the vast number of PilZ proteins encoded by bacterial genome and help to prioritize functionally unknown PilZ proteins for future studies. ImportanceAlthough PilZ domain is best known as the protein domain evolved specifically for the binding of the second messenger c-di-GMP, divergent evolution has generated a superfamily of PilZ proteins with a diversity of ligand or protein-binding properties and cellular functions. We analysed the sequences of more than 28,000 PilZ proteins using the sequence similarity networking (SSN) tool to yield a global view of the sequence-function relationship and function diversification in PilZ proteins. The results will facilitate the annotation of the vast number of PilZ proteins encoded by bacterial genomes and help us prioritize PilZ proteins for future studies.

biochemistry↗