Deep learning-driven de novo design of ribosome binding sites in Paracoccus denitrificans
March 2027
Paracoccus denitrificans is a heterotrophic nitrifying–aerobic denitrifying bacterium widely used in wastewater treatment and as a model system for studying electron transport chains, making it a promising...
Gentamicin and d-serine selective pressure to improve the homogeneity of cells expressing target proteins
March 2027
In this work, selective pressure was applied in E. coli to enrich the population expressing recombinant proteins and suppress the emergence of low-expression phenotypes. To this end, plasmids were constructed...
Systems-level analysis of 1,6-hexanediol stress response and tolerance engineering in Escherichia coli
March 2027
1,6-Hexanediol (1,6-HDO) is an important chemical platform widely used in polymer and pharmaceutical industries, while its toxicity remains a major bottleneck limiting efficient microbial production....
Metabolic state-driven monitoring and control of abnormal pigment formation in sodium gluconate fermentation by Aspergillus niger
February 2027
Abnormal pigment formation during late-stage fungal fermentation poses a significant challenge to industrial product quality. This study established an integrated framework to understand and control...
A user-friendly strategy to engineer tailored intermediate strains for overcoming combined type I and type II restriction-modification barriers in Staphylococcus aureus
February 2027
A significant proportion of Staphylococcus aureus clinical isolates are refractory to plasmid transformation due to the combined action of type I and type II restriction-modification (RM) systems. Current...
Quorum sensing-driven riboflavin-hyperproducing electroactive bacteria for enhanced bioelectricity generation from sludge: From modular optimization to process performance
February 2027
Waste activated sludge (WAS) represents a significant byproduct of wastewater treatment and a renewable resource for bioenergy. Bioelectrochemical systems (BESs), which couple microbial metabolism with...
Lactiplantibacillus plantarum as a multifunctional probiotic for inflammatory bowel disease: Mechanisms, synbiotic strategies, and delivery systems
February 2027
Inflammatory bowel disease (IBD) encompasses a group of chronic inflammatory disorders of the bowel, characterized by complex etiologies that are closely associated with an imbalance in intestinal microbiota,...
High-level amyrin production in Yarrowia lipolytica via metabolic and enzyme engineering
February 2027
Amyrins arе pеntacyclic tritеrpеnoids with valuablе pharmacеutical and cosmеtic applications; howеvеr, thеir low abundancе in plants and complеx еxtraction procеssеs hindеr sustainablе supply. Hеrе,...
scYeast: a biological-knowledge-guided foundation model on yeast single-cell transcriptomics
February 2027
Though large-scale pre-trained models are vital for foundational cell modeling, most of them focus on human or mouse systems, with less emphasis on model organisms like yeast (Saccharomyces cerevisiae),...
Engineering nonconventional yeasts to produce carboxylic acids: Advances and Prospects
February 2027
Due to their versatile carboxy group, carboxylic acids can be used as bio-based monomers for high-value-added industrial products with great market demand. In recent years, metabolic engineering of...
Systematic enzyme and cofactor engineering for efficient ursolic acid biosynthesis in Yarrowia lipolytica
February 2027
Ursolic acid (UA) is a pharmaceutically valuable pentacyclic triterpenoid, but its microbial production is constrained by inefficient cytochrome P450 catalysis and limited cofactor availability. Here,...
Engineering short-sequence elements for condensate-like assemblies by de novo design
February 2027
Biomolecular condensates form through phase separation, playing a crucial role in cellular organization and gene regulation. However, native condensate elements often suffer from high molecular weight...
N-terminal fusion length: The key to reliable and context-preserving regulatory sequence characterization
February 2027
Regulatory sequences are commonly characterized using fluorescent reporters, yet how N-terminal coding context shapes these measurements has not been systematically quantified. Here, we evaluated the...
CodY constrains β-cypermethrin degradation by regulating physiological adaptation and soil ecological performance in Bacillus cereus GW-01
February 2027
β-cypermethrin (β-CY) is a widely used pyrethroid insecticide, yet the regulatory mechanisms that determine microbial degradation efficiency remain unclear. Here, we examined the role of the global...
Characterization of OsNrx3i1, the first intron of rice OsNrx3 gene, as a candidate intron-mediated enhancement element for synthetic promoter engineering
February 2027
Intron-mediated enhancement (IME) is a potent endogenous mechanism for boosting gene expression, yet few IME elements function efficiently across distantly related plant species. Here, we characterize...
Mining and engineering of active PB transposons in Hymenoptera
February 2027
PiggyBac (PB) transposons, such as the canonical transposon from Trichoplusia ni and the more recently discovered Mage from Lepidoptera, are “cut-and-paste” mobile genetic elements widely harnessed...
Artificial intelligence catalyzes antimicrobial peptide design
February 2027
With broad-spectrum, low resistance, and multifunctional properties, antimicrobial peptides (AMPs) are promising therapeutic agents against drug-resistant pathogens, yet their discovery and optimization...
Tailored biosynthesis of medium chain oleochemicals by engineering fatty acid synthase and β-oxidation
February 2027
Data-driven optimization of salt shock for high-efficiency ectoine production in Halomonas elongata
January 2027
Halomonas elongata stands as a highly promising industrial chassis, capable of low-cost fermentation under open, non-sterile conditions. However, precisely regulating the fermentation process to breach...
Key molecular networks underlying retinol's biphasic effects on cell proliferation through multi-omics integrative analysis using genome-scale metabolic modeling
January 2027
Retinol is widely used in skin anti-aging, yet its effects exhibit significant concentration dependence. However, the underlying biphasic mechanism, that is low concentrations promote cell proliferation...
Reprogramming the enduracidin NRPS assembly line via thioesterase domain relocation
January 2027
The rational engineering of multi-megadalton nonribosomal peptide synthetase (NRPS) assembly lines remains a formidable challenge due to their immense size and complexity. Conventional module deletion...
Improved catalytic efficiency of P450 OleP for converting lithocholic acid into murideoxycholic and ursodeoxycholic acids through semi-rational and rational design
January 2027
Cytochrome P450 enzymes are promising for synthesizing therapeutically beneficial bile acids murideoxycholic acid (MDCA) and ursodeoxycholic acid (UDCA) from lithocholic acid (LCA). However, the catalytic...
Development and characterization of a Cre/loxP toolkit for genome engineering in Komagataella phaffii
January 2027
The Cre/loxP system is a versatile tool for genome engineering, yet its application in the industrial yeast Komagataella phaffii has been limited primarily to marker recycling. This study reports a...