Computational protein sequence design has been widely applied in rational protein engineering and increasing the design accuracy and efficiency is highly desired. Here, we present ProDESIGN-LE, an accurate and efficient approach to protein sequence design. ProDESIGN-LE adopts a concise but informative representation of residue’s local environment and trains a transformer to learn the correlation between local environment of residues and their amino acid types. For a target backbone structure, ProDESIGN-LE uses the transformer to assign an appropriate residue type for each position based on its local environment within this structure, eventually acquiring a designed sequence with all residues fitting well with their local environments. We applied ProDESIGN-LE to design sequences for 68 naturally occurring and 129 hallucinated proteins within 20 seconds per protein on average. The designed proteins have their predicted structures perfectly resembling the target structures with a state-of-the-art average TM-score exceeding 0.80. We further experimentally validated ProDESIGN-LE by designing five sequences for an enzyme, chloramphenicol O-acetyltransferase type III (CAT III), and recombinantly expressing the proteins in E. coli. Of these proteins, three exhibited excellent solubility, and one yielded monomeric species with circular dichroism spectra consistent with the natural CAT III protein. The source code of ProDESIGN-LE is available through https://github.com/bigict/ProDESIGN-LE Supplementary data are available at Bioinformatics online.

2-Phenylethanol (2-PE), an aromatic alcohol with a rose-like fragrance, is widely used in the food, pharmaceutical, and high-end cosmetic industries. In this study, a high-yield 2-PE-producing strain was isolated and identified as Saccharomyces cerevisiae based on morphological characterization and taxonomic identification. Fermentation medium components (carbon and nitrogen sources) were optimized through single-factor experiments in shaking flasks, and fermentation medium with 40 g/L glucose, 5 g/L malt extract, 1.75 g/L corn steep liquor, 2.5 g/L yeast extract, 5 g/L malt extract, 1.75 g/L corn steep liquor was considered suitable for 2-PE production. RT-qPCR results indicated that corn steep liquor activates expression of genes related to the shikimate pathway and Ehrlich pathway (pha2, aro4, aro8, and aro9), thereby promoting the synthesis of 2-PE through these pathways. Excess yeast extract inhibited the expression of aro8 and aro9, while enhancing the expression of tdh3 and adh2, thus promoting the de novo synthesis of 2-PE. Furthermore, fermentation in a 5 L bioreactor was applied to investigate the effects of feeding strategies, inoculum proportion, and pH on 2-PE production. With a pH of 5.5 and10% inoculum proportion, the supplementation of the substrate L-Phe led to a 2-PE production of 4.81 g/L after 24 h of fermentation. Finally, in situ product recovery (ISPR) techniques was applied to alleviate 2-PE cytotoxicity, achieving a production of 6.41 g/L. This process offers a promising strategy for producing 2-PE efficiently and naturally, paving the way for further industrial applications in food, pharmaceutical, and cosmetic sectors.

Fatty acid alkyl esters have broad applications in biofuels, lubricant formulas, paints, coatings, and cosmetics. Traditionally, these esters are mostly produced through unsustainable and energy-intensive processes. In contrast, microbial production of esters from renewable and sustainable feedstocks may provide a promising alternative and has attracted widespread attention in recent years. At present, yeasts are used as ideal hosts for producing such esters, due to their availability for high-density fermentation, resistance to phage infection, and tolerance against toxic inhibitors. Here, we summarize recent development on the biosynthesis of alkyl esters, including fatty acid ethyl esters (FAEEs), fatty acid short-branched chain alkyl esters (FASBEs), and wax esters (WEs) by various yeast cell factories. We focus mainly on the enzyme engineering strategies of critical wax ester synthases, and the pathway engineering strategies employed for the biosynthesis of various ester products. The bottlenecks that limit productivity and their potential solutions are also discussed in this review.

Menaquinone-7 (MK-7) is an important bioactive form of vitamin K₂ that inhibits vascular calcification, maintains systemic calcium homeostasis, demonstrates high bioavailability, and possesses an extended plasma half-life. Bacillus subtilis naturally possesses the complete biosynthetic pathway for MK-7, benefits from a well-characterized genetic background and advanced genome-editing tools, and is regarded as a safe and efficient microbial chassis for industrial MK-7 fermentation. This review summarizes recent advances in the metabolic engineering of Bacillus subtilis for high-level MK-7 production, highlights pathway analyses, and discusses engineering strategies targeting four key modules: substrate utilization, secretion, spore/biofilm formation, and oxidative-stress defense.

The function of nuclear-localized mitochondria remains unknown. We found that mitochondria assembled dense particles to fragment and disperse into the particles, which reassembled to initiate nuclear formation and development. Individually-formed nuclei in one single cell were joined together by mitochondrial fragmentation concurrently partitioning cytoplasm to form an intranuclear inclusion (INC), whose creation was not related to herniation or invagination of the cytoplasm. Along with the nuclear transition of a mitochondrion and its neighboring counterparts, the organelle included itself in the nucleus to become nuclear mitochondrion through peripherally assembling of dense particles. New medium reversed the nuclear formation of the organelles to recovery and re-establishment via the return of the particles, which consisted of dense microvesicles (MIVs).

Traceless protein cleavage is a significant challenge in intein application, as most common inteins studied today are not both active and promiscuous. In this study, the intein gp41‐1 is engineered, which demonstrates the most efficient traceless cleavage reported to date and shows high compatibility to 1st amino acid. The evidence provided for the first time is that the unique THN motif, which is prevalent in class 3 inteins, is essential for achieving high‐efficiency traceless C‐terminal cleavage. The hydrogen bond between the hydroxyl group of Thr ₁₂₃ and the main chain of His ₁₂₄ is suggested to be indispensable for stabilizing the THN motif to separate Asp ₁₀₇ (the limiting factor for C‐cleavage) from Asn ₁₂₅ and the C‐extein residues from the active sites, which jointly lead to the highest traceless C‐cleavage activity. Both cleavage data and molecular dynamics (MD) simulations results demonstrate that mutating Thr ₁₂₃ greatly disturbed the THN motif, leading to inactivity. These findings reveal a pivotal motif for intein traceless cleavage efficiency, providing valuable insights for designing inteins with enhanced traceless C‐terminal cleavage capabilities in future applications.