Comprehensive proteomic characterization of urethral stricture disease in the Chinese population.

Background: Male urethral stricture disease (USD) is predominantly characterized by scar formation. There are few effective therapeutic drugs, and comprehensive molecular characterizations of USD formation remain undefined. Methods: The proteomic profiling of twelve scar tissues and five matched normal adjacent tissues (NATs). Proteomic analysis methods were applied to explore the molecular characterizations of USD formation, including uncovering mechanistic pathways and providing novel biomarkers for scar formation. Results: Comparative proteomic analysis showed that the extracellular matrix (ECM) and complement cascade signaling were predominant in scar tissues. COL11A1 and CD248 significantly contributed to the accumulation of ECM components. Our study presented diverse molecular mechanisms of scar formation across different ages and suggested the potential effects of PXK in Age 1 (<45) patients. Furthermore, immune infiltration studies indicated the therapeutic potential of inhibiting the complement system (C4A, C4B) in Age 2 (≥45) patients, providing a potential clinical strategy for USD. Conclusion: This study illustrated the pathogenesis of USD formation and the diverse characteristics of USD patients with different ages, enhancing our understanding of the disease's pathogenesis and providing a valuable resource for USD treatment.

Harnessing microbes to pioneer environmental biophotoelectrochemistry.

In seeking sustainable environmental strategies, microbial biophotoelectrochemistry (BPEC) systems represent a significant advancement. In this review, we underscore the shift from conventional bioenergy systems to sophisticated BPEC applications, emphasizing their utility in leveraging solar energy for essential biochemical conversions. Recent progress in BPEC technology has facilitated improved photoelectron transfer and system stability, resulting in substantial advancements in carbon and nitrogen fixation, degradation of pollutants, and energy recovery from wastewater. Advances in system design and synthetic biology have expanded the potential of BPEC for environmental clean-up and sustainable energy generation. We also highlight the challenges of environmental BPEC systems, ranging from performance improvement to future applications.

Bioinformatic Approaches Identify Hybrid Antibiotics against Tuberculosis via d-Amino Acid-Activating Adenylation Domains from Cordyceps militaris.

The development of tuberculosis (TB) therapy has been marked by the discovery of natural-product-derived streptomycin, followed by the introduction of NP-derived rifampicin, representing a significant milestone in the history of TB management. However, TB remains a global challenge, with the emergence of multidrug-resistant Mycobacterium tuberculosis highlighting the need for novel therapeutic agents. In this study, a bioinformatic approach was employed to investigate d-amino acid-activating adenylation domains, leading to the identification of cordysetin A (1), a novel trans-decalin tetramic acid antibiotic from the ascomycete fungi Cordyceps militaris. Cordysetin A (1) exhibits considerable activity against M. tuberculosis in vitro and in vivo while maintaining low cytotoxicity. These results reveal that the d-configuration of the amino acid within this hybrid polyketide-nonribosomal antibiotic is crucial for preserving its anti-tuberculosis efficacy. These findings emphasize the significant translational potential of cordysetin A as a promising candidate for TB treatment, furthering our understanding of bioinformatic approaches in the development of effective anti-tuberculosis agents.

Enhancing the yield of Xenocoumacin 1 in Xenorhabdus nematophila YL001 by optimizing the fermentation process.

Xenocoumacin 1 (Xcn 1), antibiotic discovered from secondary metabolites of Xenorhabdus nematophila, had the potential to develop into a new pesticide due to its excellent activity against bacteria, oomycetes and fungi. However, the current low yield of Xcn1 limits its development and utilization. To improve the yield of Xcn1, response surface methodology was used to determine the optimal composition of fermentation medium and one factor at a time approach was utilized to optimize the fermentation process. The optimal medium composed of in g/L: proteose peptone 20.8; maltose 12.74; K2HPO4 3.77. The optimal fermentation conditions were that 25 °C, initial pH 7.0, inoculum size 10%, culture medium 75 mL in a 250 mL shake flask with an agitation rate of 150 rpm for 48 h. Xenorhabdus nematophila YL001 was produced the highest Xcn1 yield (173.99 mg/L) when arginine was added to the broth with 3 mmol/L at the 12th h. Compared with Tryptic Soy Broth medium, the optimized fermentation process resulted in a 243.38% increase in Xcn1 production. The obtained results confirmed that optimizing fermentation technology led to an increase in Xcn1 yield. This work would be helpful for efficient Xcn1 production and lay a foundation for its industrial production.

3-O-acylated bile acids: disrupters or harmonizers of metabolism?

Unveiling a metabolic mystery, this article explores how 3-O-acylated bile acids, specifically 3-O-succinylated cholic acid (3-sucCA) and 3-acetylated cholic acid (3-acetyCA), modified by gut microbes Bacteroides uniformis and Christensenella minuta, respectively, may either disrupt or harmonize our metabolic processes, offering novel therapeutic avenues for conditions such as metabolic dysfunction-associated steatohepatitis (MASH) and type 2 diabetes mellitus (T2D).

Clinical crusade: zosurabalpin's charge against antibiotic resistance.

In a recent report, Zampaloni et al. describe a novel tethered macrocyclic peptide (MCP) antibiotic, zosurabalpin, that disrupts the essential function of the LptB2FGC complex in Gram-negative bacteria and demonstrates efficacy against carbapenem-resistant Acinetobacter baumannii (CRAB). Its preclinical success suggests a substantial shift in treating antibiotic resistance, pending clinical trials to validate its effectiveness, pharmacokinetics, and resistance management.

Microbial gatekeepers: unraveling the role of the gut microbiota enzyme DPP4 in diabetes management.

Wang et al. identified dipeptidyl peptidase 4 (DPP4) as a gut microbe-derived enzyme that impacts on host glucose metabolism. They further introduced a novel therapeutic, daurisoline-d4 (Dau-d4), a selective microbial DPP4 (mDPP4) inhibitor that shows promise in improving glucose tolerance, highlighting the potential of therapies that target both host enzymes and gut microbial enzymes.

Genomics refined: AI-powered perspectives on structural analysis.

Understanding protein function by deciphering 3D structure has distinct limitations. A recent study by Huang et al. used AlphaFold2, an artificial intelligence (AI) protein-folding prediction model, to predict and classify deaminase proteins based on structural similarities, highlighting the untapped potential of AI in functional genomics and protein engineering.

Intellectual property and funding: fueling Chinese synbio.

As China emerges as a synthetic biology (synbio) global leader, it faces distinct science-society challenges. Our series offers a snapshot of China's synbio state, emphasizing the intersection and its policy implications. The debut piece elucidates the intellectual property rights (IPR)-funding interplay in China's expanding synbio territory, underlining its key role in driving innovation and commercialization.

Biosafety and biosecurity: treading China's synbio tightrope.

Our second piece dissects China's intricate balancing act in synthetic biology (synbio), analyzing its adept maneuvering between fostering innovation and imposing strict regulations. The priority is enhancing biosecurity, biosafety, and public trust, crucial for sustainable gene editing advancements and preventing potential misuse of synthetic viruses.

The gut-Snhg9 interplay as a new path to metabolic health.

Parsing the intricate interplay between gut microbiota, gene modulation, and host metabolism remains challenging. Wang et al. employed diverse methods to uncover how the gut microbiota reshapes intestinal lipid metabolism through the lncRNA Snhg9, underscoring the value of systems biology approaches in dissecting host-microbiome relationships involved in metabolic disorders.

Exploring the antibiotic potential of cultured 'unculturable' bacteria.

In response to the severe global antibiotic resistance crisis, this forum delves into 'unculturable' bacteria, believed to be a promising source of novel antibiotics. We propose remarkable drug discovery strategies that leverage these bacteria's diversity, aspiring to transform resistance management. The urgent call for new antibiotics accentuates the essentiality of further research.

Ethics and engagement: steering China's synbio future.

In the final article of the series, we delve into the crucial role of public engagement and ethical guidelines in shaping the trajectory of synthetic biology (synbio) within China's evolving scientific landscape. We discuss the interconnectedness of enhanced public discourse, stronger ethics, and responsible, transparent advancements in the field.

Redefining the Glyphosate Sector: Harmonizing Inventiveness and Sustainable Practices for a Better World.

The glyphosate industry has long been a critical player in global agriculture, providing effective and economical solutions for weed control. However, growing concerns over environmental and health impacts have led to increased scrutiny and calls for more sustainable practices. This Viewpoint focuses on the scientific aspects of greener glyphosate synthesis strategies, discussing recent advancements in biobased pathways and catalytic methods, challenges such as scalability and technical hurdles, and future prospects for the herbicide industry. By embracing these new techniques, we can ensure a more sustainable future for herbicide production and contribute to a healthier world.

Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks.

Cyclic peptide natural products represent an important class of bioactive compounds and clinical drugs. Enzymatic side-chain macrocyclization of ribosomal peptides is a major strategy developed by nature to generate these chemotypes, as exemplified by the superfamily of ribosomally synthesized and post-translational modified peptides. Despite the diverse types of side-chain crosslinks in this superfamily, the participation of histidine residues is rare. Herein, we report the discovery and biosynthesis of bacteria-derived tricyclic lanthipeptide noursin, which is constrained by a tri amino acid labionin crosslink and an unprecedented histidine-to-butyrine crosslink, named histidinobutyrine. Noursin displays copper-binding ability that requires the histidinobutyrine crosslink and represents the first copper-binding lanthipeptide. A subgroup of lanthipeptide synthetases, named LanKCHbt, were identified to catalyze the formation of both the labionin and the histidinobutyrine crosslinks in precursor peptides and produce noursin-like compounds. The discovery of the histidinobutyrine-containing lanthipeptides expands the scope of post-translational modifications, structural diversity and bioactivity of ribosomally synthesized and post-translational modified peptides.

Concise Biosynthesis of Tropone-Containing Spiromaterpenes by a Sesquiterpene Cyclase and a Multifunctional P450 from a Deep-Sea-Derived Spiromastix sp. Fungus.

Spiromaterpenes are a group of rare tropone-containing sesquiterpenes with antineuroinflammatory activity. Herein, we elucidate their biosynthetic pathway in a deep-sea-derived Spiromastix sp. fungus by heterologous expression, biochemical characterization, and incubation experiments. The sesquiterpene cyclase SptA was first characterized to catalyze the production of guaia-1(5),6-diene, and a multifunctional cytochrome P450 catalyzed the tropone ring formation. These results provide important clues for the rational mining of bioactive guaiane-type sesquiterpenes and expand the repertoire of P450 activities to synthesize unique building blocks of natural products.

Hijacking a Linaridin Biosynthetic Intermediate for Lanthipeptide Production.

Linaridins and lanthipeptides are two classes of natural products belonging to the ribosomally synthesized and posttranslationally modified peptide (RiPP) superfamily. Although these two RiPP classes share similar structural motifs such as dehydroamino acids and thioether-based cross-links, the biosynthesis of linaridins and lanthipeptides involved distinct sets of enzymes. Here, we report the identification of a novel lanthipeptide cypepeptin from a recombinant strain of Streptomyces lividans, which harbors most of the cypemycin (a prototypic linaridin) biosynthetic gene cluster but lacks the decarboxylase gene cypD. In contrast to the generally believed structure of cypemycin, multiple d-amino acids and Z-dehydrobutyrines were observed in both cypepeptin and cypemycin, and the stereochemistry of each amino acid was established by the extensive structural analysis in combination with genetic knockout and mutagenesis studies. Comparative analysis of cypemycin and cypepeptin showed that the aminovinyl-cysteine (AviCys) moiety of cypemycin plays an essential role in disrupting the cell integrity of M. luteus, which cannot be functionally substituted by the structurally similar lanthionine moiety.

Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate.

Glyphosate is a widely used herbicide with an annual production of more than one million tons globally. Current commercialized production processes of glyphosate are generally associated with manufacturing hazards and toxic wastes. Recently, many countries have strengthened environmental supervision and law enforcement on glyphosate manufacturing. Therefore, a green source of glyphosate is required. Here, we characterize the genes required for producing aminomethylphosphonate (AMP), one of the intermediates in the biosynthesis of the potent antibiotics argolaphos. We apply a synthetic biology strategy to improve AMP production in Streptomyces lividans, with fermentation titers of 52 mg L-1, a 500-fold improvement over the original strain. Furthermore, we develop an efficient and practical chemical process for converting AMP to glyphosate. Our findings highlight one greenness-driven alternative in the production of glyphosate.

Heterologous expression and characterization of glycoside hydrolase with its potential applications in hyperthermic environment.

With the progressive focus on renewable energy via biofuels production from lignocellulosic biomass, cellulases are the key enzymes that play a fundamental role in this regard. This study aims to unravel the characteristics of Thermotoga maritima MSB8 (Tma) (a hyperthermophile from hot springs) thermostable glycoside hydrolase enzyme. Here, a glycoside hydrolase gene of Thermotoga maritima (Tma) was heterologously expressed and characterized. The gene was placed in the pQE-30 expression vector under the T5 promotor, and the construct pQE-30-Gh was then successfully integrated into Escherichia coli BL21 (DH5α) genome by transformation. Sequence of the glycoside hydrolase contained an open reading frame of 2.124 kbp, encoded a polypeptide of 721 amino acid residues. The molecular weight of the recombinant protein estimated was 79 kDa. The glycoside hydrolase was purified by Ni+2-NTA affinity chromatography and its enzymatic activity was investigated. The recombinant enzyme is highly stable within an extreme pH range (2.0-7.0) and highly thermostable at 80 °C for 72 h indicating its viability in hyperthermic environment and acidic nature. Moreover, the Ca2+ and Mn2+ introduction stimulated the residual activity of recombinant enzyme. Conclusively, the thermostable glycoside hydrolase possesses potential to be exploited for industrial applications at hyperthermic environment.

Effective removal of the herbicide glyphosate by the kelp Saccharina japonica female gametophytes from saline waters and its mechanism elucidation.

Glyphosate has been widely and extensively used for weed control because of its excellent herbicidal profile and low costs. However, more than 750 glyphosate products are on the market and are increasingly regarded as water pollutants as they cause adverse effects on aquatic life. Dry cell weight and photosynthesis of Saccharina japonica female gametophytes increased when glyphosate was used as the sole phosphorus source at the concentration of less than 20 mg L-1. Nuclear magnetic resonance (NMR) analysis unambiguously confirmed that female gametophytes of the brown alga Saccharina japonica have the capability of breaking the C-P bond of glyphosate to orthophosphate, which finds the enormous potential of the most common seaweed to degrade the most widely used herbicide in the world. Furthermore, this is the first report on the use of glyphosate as the sole phosphorus source for the growth of eukaryotic cells. Because of the wide distribution and relatively easy cultivation of the fast-growing brown alga Saccharina japonica on the coast, our results set a promising stage for developing large macroalgae-based biotechnologies that can be applied for the remediation of contaminated seawater, which is greener and more cost-effective than conventional treatment methods.