Youming Zhang

PTEN and p53 are two pivotal tumor suppressors that synergistically restrain tumor progression but are frequently inactivated in cancer. Restoring their functions is a promising therapeutic strategy but remains limited by unsustainable protein production and off-target effects. Here, we report a biohybrid platform integrating engineered attenuated Salmonella typhimurium VNP20009 with nanotechnology to enable durable restoration of PTEN and p53 functions in tumors. The bacteria are engineered with a quorum-sensing-regulated lysis circuit coupled to PTEN expression, enabling controlled proliferation and sustained PTEN production and release. Their intrinsic tumor tropism and long-term intracellular parasitism allow them to function as exogenous organelle mimics, providing continuous PTEN supplementation. Surface-conjugated nanoparticles further deliver the MDM2 inhibitor to stabilize p53 and synergistically restore the PTEN-p53 network. This platform achieves 94.9% tumor inhibition in murine melanoma and confers durable survival in all treated mice when combined with anti-PD-1 therapy, highlighting its strong therapeutic potential for cancer treatment.

Genome mining of the marine-derived Streptomyces sp. S42 uncovered a type II polyketide synthetase (T2 PKS) biosynthetic gene cluster (BGC) harboring a gene for 3-ketoacyl-ACP synthase III (KAS III), a hallmark of non-acetate starter unit incorporation, suggesting that the BGC may produce previously unidentified aromatic polyketides. Heterologous expression and promoter engineering of this prioritized BGC in host Streptomyces albus J1074 activated the biosynthetic pathway, leading to the isolation of eight new polycyclic aromatic derivatives, verrucones A–H (1–8). Comprehensive structural elucidation via NMR and HRESIMS revealed that these compounds feature either a 2-methylbutyryl or an isobutyryl starter unit and can be classified into three distinct skeletal types. Based on these findings and bioinformatic analysis, a plausible biosynthetic pathway for 1–8 involving divergent spontaneous cyclization from a common nascent polyketide intermediate was proposed. Among the isolated compounds, 1–5 exhibited inhibitory activity against several protein tyrosine phosphatases (PTPs) with IC₅₀ values ranging from 1.84 μM to 24.82 μM. This study presents a successful case study demonstrating that combining KAS III-targeted genome mining with heterologous expression is a viable approach for discovering non-acetate-primed aromatic polyketides.

Myxobacteria are renowned producers of structurally diverse bioactive natural products. Motivated by a comprehensive inventory of myxobacterial biosynthetic gene clusters (BGCs), we develop efficient genetic toolkits and construct a robust heterologous expression chassis. We identify a pair of Myxococcus -derived recombinases, designated MxRecET, that enables efficient genome editing in the model strain Myxococcus xanthus DK1622. The synergistic combination of MxRecET recombineering with the transposon-associated nuclease TnpB (ISDra2) enables versatile genetic manipulations, including seamless deletion of large DNA fragments (up to 200 kb), tandem editing of dual loci, and flexible single-nucleotide substitutions within a streamlined two-week workflow. This integrated technology, termed MxDIRECT, facilitates the rational engineering of DK1622 into a plug-and-play chassis designated MxPKS, featuring enhanced growth properties, elimination of competing pathways, an improved precursor supply, and increased robustness. The effectiveness of MxPKS is demonstrated through heterologous expression of four polyketide synthase BGCs, leading to the discovery of multiple unknown polyketides. This work establishes a foundation for accelerated bioprospecting of myxobacteria.

Despite the considerable potential of lactic acid bacteria (LAB) as probiotics, there is a fundamental gap between the functional limitations of wild-type strains and the complex demands of aquaculture. Modular and intelligent engineering strategies are the primary avenues for bridging this gap. This article systematically reviews the strategies and advances in the application of genetically engineered LAB. Technologies, including clustered regularly interspaced short palindromic repeat (CRISPR)/Cas systems, Red/ET recombination, and functional modifications have significantly enhanced the targeted delivery, environmental tolerance, and multiple probiotic functions of LAB, successfully yielding engineered strains such as oral vaccine strains expressing pathogen antigens, antimicrobial peptide-high-yielding antibacterial strains, and nitrite-degrading water-improving strains. These engineered strains have demonstrated superior performance in disease prevention, growth promotion, and environmental remediation compared to wild-type strains in the farming of tilapia, shrimp, and shellfish. However, challenges, such as plasmid instability, biosafety risks, and regulatory barriers, remain unresolved. Future research should focus on multi-omics-guided precision design, development of environmentally responsive genetic circuits, and full-cycle risk assessment, promoting engineered LAB as a core solution for sustainable aquaculture through collaboration across industries, academia, and research.

The probiotic strain Escherichia coli Nissle 1917 (EcN), a potential member of tumor-targeting bacteria, shows great promise for cancer treatment. By leveraging engineered EcN, we can design a bacteria-assisted, tumor-targeted therapy for the biosynthesis and targeted delivery of small-molecule anticancer agents. In this study, we aimed to use EcN as a base for synthesizing Romidepsin (FK228), an FDA-approved drug originally made by Chromobacterium violaceum No. 96. Through gene cluster reconstruction, promoter optimization, and genome modification, we created FK228-producing strains to boost anticancer efficacy. The engineered strain achieved a maximum in vitro yield of 1.5 mg/L. In 4T1 tumor-bearing BALB/c mouse xenograft models, six recombinant strains outperformed the wild-type EcN. Proteome showed that inflammatory response induced by EcN combined with intratumoral FK228 production improved treatment results. Also, targeted synthesis reduced FK228's cardiotoxicity and mortality. Engineered EcN enables drug biosynthesis and precise delivery, offering powerful anticancer activity.

Environmental metagenomics and microbial taxonomy provide essential frameworks to evaluate how population structures shape the evolution of antimicrobial resistance and microbial community dynamics within densely populated environments. To evaluate microbial community composition and pathogenic potential, high-touch surfaces at high-traffic sites on and off campus were analyzed using metagenomics and characterization of 188 bacterial isolates, including antibiotic susceptibility testing, hemolytic assays, and whole-genome sequencing. Off-campus sites showed significantly higher bacterial richness and more complex communities enriched with diverse potential pathogens. Notably, high-risk carbapenemase genes were predominantly identified in these off-campus urban environments. In contrast, on-campus environments harbored less diverse communities dominated by opportunistic, antibiotic-resistant Staphylococcus species, with metagenomic analysis confirming a concentrated enrichment of β-lactam resistance determinants associated with methicillin-resistant staphylococci. Phenotypic profiling revealed extensive antimicrobial resistance, with 84.7% of isolates exhibiting resistance to at least one antibiotic and 35.1% of Staphylococcus showing hemolytic activity. Whole-genome sequencing further revealed that these resistance and pathogenic traits are predominantly localized on mobile plasmids, highlighting a high potential for horizontal gene transfer. These findings indicate that population activities shape distinct microbial communities in closely adjacent environments and highlight the importance of monitoring high-risk resistance determinants in densely populated university settings.

PTEN and p53 are two pivotal tumor suppressor proteins that act synergistically to restrain tumor progression but are frequently inactivated in tumors. Restoration of their tumor suppressor functions holds promise for fundamentally inhibiting tumor growth. However, it is hampered by unsustainable protein production, insufficient intracellular delivery, and off-target side effects. Here, we report a biohybrid therapeutic platform that integrates engineered attenuated Salmonella typhimurium VNP20009 (VNP) with nanotechnology to enable durable restoration of PTEN and p53 functions in tumors. The VNP strain was genetically engineered with a quorum-sensing (QS)-regulated lysis and PTEN-expression system, thereby maintaining bacterial density within a controllable range, markedly improving in vivo safety, and enhancing PTEN release by 5.2-fold. Notably, VNP exhibits intrinsic tumor-targeting capability and long-term intracellular parasitism over 7 days, functioning as an exogenous organelle mimic in tumor cells that enables sustained PTEN delivery and restoration of tumor suppressor activity. Moreover, RG7388-loaded nanoparticles (RG-NPs) were conjugated onto the bacterial surface, allowing efficient intracellular delivery and sustained release of an MDM2 inhibitor to elevate p53 levels and synergize with PTEN-mediated tumor suppression. This biohybrid platform achieved up to 94.9% tumor inhibition in a murine melanoma model and conferred long-term survival in 100% of mice when combined with anti-PD-1 therapy, highlighting its strong therapeutic promise for cancer therapy and the potential of engineering VNP as a programmable exogenous organelle mimic.

Efficient engineering of nonribosomal peptide synthetases (NRPSs) is a key strategy for expanding valuable peptide natural products. Current bioinformatics-guided approaches are often constrained by a set of predefined fusion sites, remaining experimentally challenging in most NRPS systems. Here we present the Recombineering Accelerated Evolution (RACE), which harnesses Red/ET recombineering mediated partially matched homologous recombination to recapitulate recombination-driven NRPS evolution on a highly accelerated timescale. Application of RACE to six known NRPS gene clusters generated 830 recombinants and yielded over 600 novel peptides including novel bis-lipopeptides. These recombinants reveal 112 previously unrecognized recombination fusion sites, providing an extensive landscape for NRPS evolution and more useful resources for guiding NRPS engineering. The RACE establishes a new paradigm for programmable NRPS evolution and enables rapid discovery of bioactive peptides.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause significant morbidity and mortality despite the end of its pandemic phase. The emergence of highly mutated SARS-CoV-2 variants of concern highlights the requirement of broad-spectrum antiviral countermeasures which possess both prophylactic and therapeutic efficacies. Here, we obtain a macrocyclic peptide, 6L3-3P11K, that effectively inhibits a wide range of SARS-CoV-2 variants and subvariants. Structural studies show that 6L3-3P11K forms homotrimers that lock the spike protein (S) trimer into a “closed” conformation by engaging a conserved non-receptor binding motif (non-RBM) of S. This interaction disrupts the binding between S and ACE2 receptor. Structure-guided modifications result in a thermostable and trypsin-resistant macrocyclic peptide, 6L3-1F3P11hR, that exhibits prophylactic and therapeutic effects against SARS-CoV-2 infection in a male hACE2 transgenic mouse model after intranasal administration. Our results provide a drug candidate for the control and prevention of COVID-19 and may stimulate further research on macrocyclic broad-spectrum anti-coronavirus drug development.