Applied Microbiology and Biotechnology最新文献

{"title":"Multiple regulators control the biosynthesis of brasilicardin in Nocardia terpenica.","authors":"Marcin Wolański, Michał Krawiec, Kay Nieselt, Tobias Schwarz, Dilek Dere, Bernhard Krismer, Carolina Cano-Prieto, Harald Gross, Jolanta Zakrzewska-Czerwińska","doi":"10.1007/s00253-025-13485-3","DOIUrl":"10.1007/s00253-025-13485-3","url":null,"abstract":"<p><p>Brasilicardin A, BraA, is a secondary metabolite produced by the bacterium Nocardia terpenica, and a promising drug due to its potent immunosuppressive activity and low cytotoxicity. Currently, a semisynthetic approach confers the production of a complete compound but suffers from limited heterologous biosynthesis of BraA intermediates used in the chemical semi-synthesis steps leading to only lab-scale quantities of the compound. A better understanding of the gene expression regulatory pathways involved within the brasilicardin biosynthetic gene cluster, Bra-BGC, is a prerequisite to improving production titers further. However, the transcriptional regulation of the Bra-BGC has only been superficially analyzed, till now. In this study, we comprehensively analyze the functions of several unstudied transcriptional regulators, KstR, SdpR, and OmpR, encoded within the close vicinity of the Bra-BGC, and delve into the role of the previously described cluster-situated activator Bra12. We present that Bra12 and the novel regulator SdpR bind several DNA sequences located in the promoter regions of the genes essential for BraA biosynthesis. Subsequently, we demonstrate the complex regulatory network through which both regulators can control the activity of those gene promoters and thus gene expression in Bra-BGC. Furthermore, using the heterologous producer strain Amycolatopsis japonicum, we present that Bra12 and SdpR regulators play opposite roles in brasilicardin congener biosynthesis. Finally, we propose a comprehensive model of multilevel gene expression regulation in Bra-BGC and propose the roles of locally encoded transcriptional regulators. KEY POINTS: • Multiple regulators bind within the brasilicardin gene cluster. • Bra12 and SdpR are key regulators of brasilicardin biosynthesis. • The bra0 - 1 intergenic region is likely a key regulatory \"hot-spot.\"</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"150"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.","authors":"Laurens Parret, Kenneth Simoens, Benjamin Horemans, Jo De Vrieze, Ilse Smets","doi":"10.1007/s00253-025-13522-1","DOIUrl":"10.1007/s00253-025-13522-1","url":null,"abstract":"<p><p>Biological flocculation is a complex phenomenon that is often treated as a black box. As a result, flocculation problems are usually remediated without knowledge of the exact causes. We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity to fundamentally study bioflocculation. Strong nitrifier microcolonies were formed during oxic/anoxic cycles in sequencing batch reactors, using alginate entrapment as a cell retention system. After the release of these aggregates into suspension, macroclusters with flocs of the denitrifier were observed. These results suggest that a living model of a full-scale activated sludge floc can be built through the use of this bottom-up approach. By eliminating shifts in the microbial community, the applied experimental conditions have a more direct effect on the observations. Key Points <math><mo>∙</mo></math> Studying flocculation with a model consortium is feasible <math><mo>∙</mo></math> Alginate entrapment leads to strong microcolony formation of nitrifiers <math><mo>∙</mo></math> FISH by itself is not suitable to study aggregation of a coculture.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"149"},"PeriodicalIF":3.9,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12178987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The RNF/NQR redox pumps: a versatile system for energy transduction in bacteria and archaea.","authors":"Wolfgang Buckel, Ulrich Ermler, Janet Vonck, Günter Fritz, Julia Steuber","doi":"10.1007/s00253-025-13531-0","DOIUrl":"10.1007/s00253-025-13531-0","url":null,"abstract":"<p><p>The Na⁺ (or H⁺)-translocating ferredoxin:NAD⁺ oxidoreductase (also called RNF, rhodobacter nitrogen fixation, complex) catalyzes the oxidation of reduced ferredoxin with NAD⁺, hereby generating an electrochemical gradient. In the reverse reaction driven by an electrochemical gradient, RNF provides reduced ferredoxin using NADH as electron donor. RNF plays a crucial role in the metabolism of many anaerobes, such as amino acid fermenters, acetogens, or aceticlastic methanogens. The Na⁺-translocating NADH:quinone oxidoreductase (NQR), which has evolved from an RNF, is found in selected bacterial groups including anaerobic, marine, or pathogenic organisms. Since NQR and RNF are not related to eukaryotic respiratory complex I (NADH:quinone oxidoreductase), members of this oxidoreductase family are promising targets for novel antibiotics. RNF and NQR share a membrane-bound core complex consisting of four subunits, which represent an essential functional module for redox-driven cation transport. Several recent 3D structures of RNF and NQR in different states put forward conformational coupling of electron transfer and Na⁺ translocation reaction steps. Based on this common principle, putative reaction mechanisms of RNF and NQR redox pumps are compared. KEY POINTS: • Electrogenic ferredoxin:NAD⁺ oxidoreductases (RNF complexes) are found in bacteria and archaea. • The Na⁺ -translocating NADH:quinone oxidoreductase (NQR) is evolutionary related to RNF. • The mechanism of energy conversion by RNF/NQR complexes is based on conformational coupling of electron transfer and cation transport reactions.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"148"},"PeriodicalIF":3.9,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening signal peptides from Bacillus thuringiensis secretome for heterologous protein secretion.","authors":"Jianbo Yang, Yan Xia, Li Zhu, Zhiwen Wang, Fuping Song, Shuyuan Guo","doi":"10.1007/s00253-025-13533-y","DOIUrl":"10.1007/s00253-025-13533-y","url":null,"abstract":"<p><p>Efficient secretion of heterologous proteins is crucial for applications in industrial and biomedical fields. Selecting appropriate signal peptides and bacterial strains is critical for successful protein expression and export. Bacillus thuringiensis, known for its robust secretion capabilities within the Bacillus genus, shows promise as an ideal host for this purpose. We performed genome-based bioinformatic analysis of B. thuringiensis HD73. A total of 525 proteins were predicted to contain signal peptides, exceeding those in other Bacillus species. The extracellular proteome of B. thuringiensis HD73 was analyzed via LC-MS/MS, identifying 100 secreted proteins. A library of 30 signal peptides was constructed by integrating genome-based predictions with experimental secretome data. Using this library, green fluorescent protein secretory expression systems were developed in the acrystalliferous mutant strain B. thuringiensis HD73^-, and the strain carrying signal peptide S17 showed the highest secretion efficiency. Additionally, the top 10 performing signal peptides were used to express and secrete the convenient enzyme cutinase, with the S20 fusion strain exhibiting the highest cutinase activity (3.65 U/mL in the culture supernatant). This study provides the first combined bioinformatic and experimental characterization of the B. thuringiensis secretome. The developed secreted protein expression system and signal peptide library demonstrate effectiveness and offer potential for future heterologous protein secretion in B. thuringiensis. KEY POINTS: • Genome-based secretome and experimental secretome of B. thuringiensis were characterized. • A SP library comprising 30 SPs derived from B. thuringiensis was constructed. • GFP and cutinase were successfully secreted by B. thuringiensis.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"147"},"PeriodicalIF":3.9,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12167346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Redox regulation of hydrogen production in Escherichia coli during growth on by-products of the wine industry.","authors":"Lusine Baghdasaryan, Karen Trchounian, Gary Sawers, Anna Poladyan","doi":"10.1007/s00253-025-13535-w","DOIUrl":"10.1007/s00253-025-13535-w","url":null,"abstract":"<p><p>Lignocellulosic wine grape waste (WGW) is a cheap medium for Escherichia coli growth and H₂ production. The current study investigated the effect of initial redox potential (oxidation-reduction potential (ORP)) on the growth, H₂ production, ORP kinetics, and current generation of the E. coli BW25113 parental and a mutant strain optimized for hydrogen evolution when fermenting WGW (40 g L^-1) hydrolysate. Bacteria were cultivated anaerobically on pre-treated WGW hydrolysate with dilutions ranging from undiluted to fourfold dilution, at pH 7.5. Notably, a twofold diluted medium, with pH adjustment using K₂HPO₄, exhibited reduced acidification, prolonged H₂ production, and enhanced biomass formation (OD₆₀₀, 1.5). The addition of the redox reagent DL-dithiothreitol (DTT) was found to positively influence the H₂ production of both the E. coli BW25113 parental and mutant strains. H₂ production started after 24 h of growth, reaching a maximum yield of 5.10 ± 0.02 mmol/L in the wild type and 5.3 ± 0.02 mmol/L in the septuple mutant strain, persisting until the end of the stationary growth phase. The introduction of 3 mM DTT induced H₂ production from the early-exponential phase, indicating that reducing conditions enhanced H₂ production. Furthermore, we assessed the efficacy of using intact E. coli cells (1.5 mg cell dry weight) as anode catalyst in a bio-electrochemical fuel-cell system. Whole cells of the septuple mutant grown under reduced ORP conditions yielded the highest electrical potential, reaching up to 0.7 V. The results highlight the potential of modifying medium buffering capacity and ORP as a tool to improve biomass yield and H₂ production during growth on WGW for biotechnological biocatalyst applications. KEY POINTS: • Grape pomace hydrolysate (GPH)'s pH positively impacts on biomass and H₂ yield • GPH with reduced ORP enhanced H₂ yield in bacterial early-exponential growth • GPH with reduced ORP facilitates microbial current generation in the system.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"146"},"PeriodicalIF":3.9,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12167259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent fermentation developments for improved rhamnolipid production.","authors":"Phavit Wongsirichot, James Winterburn","doi":"10.1007/s00253-025-13517-y","DOIUrl":"10.1007/s00253-025-13517-y","url":null,"abstract":"<p><p>Rhamnolipids (RL) are microbial amphiphilic molecules containing a hydrophilic rhamnose head and a hydrophobic fatty acid tail. RL are of interest to academia and industry due to their potential as a biosurfactant, being used to substitute petroleum-based surfactants in traditional applications or in novel bioremediation and biomedical applications. Currently, commercialization of RL is still in a nascent state, and improved RL production in terms of titers, yields, and productivities could benefit their techno-economic viability and market competitiveness. This review provides a detailed assessment of recent studies that have achieved higher RL production through improvements in microbial producers, media formulation, fermentation design, and operations. Key successes and areas for future work are identified and discussed in detail, as well as put into context with pilot-scale and techno-economic analysis of RL production from the wider literature. This review provides an updated perspective on the current status of RL production. The discussions and insights provided could potentially be used to improve future RL and biosurfactant commercialization efforts.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"145"},"PeriodicalIF":3.9,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144282235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"3C protease-independent production of foot-and-mouth disease virus-like particles in Pichia pastoris.","authors":"Zhiyao Li, Hu Dong, Shuanghui Yin, Manyuan Bai, Yun Zhang, Yaozhong Ding, Shiqi Sun, Huichen Guo","doi":"10.1007/s00253-025-13510-5","DOIUrl":"10.1007/s00253-025-13510-5","url":null,"abstract":"<p><p>The inactivated vaccines have played a pivotal role in the control and eradication of foot-and-mouth disease (FMD). However, certain safety concerns remain. Recently, virus-like particles (VLPs) have gradually become a research hotspot. As the eukaryotic expression system with the lowest production costs, the production of VLPs using Pichia pastoris has significant potential. During the natural infection process of FMD virus (FMDV), the polyprotein P1 is cleaved by 3C protease to form VP0, VP3, and VP1, which are subsequently assembled into VLPs. In this study, we adopted an alternative approach, co-expressing VP0, VP3, and VP1 without 3C protease for the production of FMDV VLPs in P. pastoris. The western blot (WB) assays showed variable protein expression on the same plasmid. VP0 was the highest, while VP3 and VP1 were similar. Furthermore, the order of proteins on the plasmid also mattered. The results indicated that His₆ tags at VP0, VP3, and VP1 N-termini significantly affected VLPs assembly. The three-dimensional structure of FMDV revealed that the N-terminus of VP3 and VP1, which are situated in the external space of VLPs, can be fused with His₆ tag. Inserting His₆ tags into the G-H loop region of VP1 did not hinder assembly, thus providing a reference for the affinity purification of capsid and VLPs assembly. Here, FMDV VLPs were successfully produced independently of 3C protease, avoiding the uncontrollable cleavage efficiency and toxicity of 3C protease in host cells and demonstrating the potential of P. pastoris for FMDV VLPs production. KEY POINTS: • FMDV VLPs could be produced in P. pastoris by a 3 C protease-independent approach • Optimal expression of FMDV VLPs in P. pastoris is achieved at pH 7 with 72-h induction • His₆ can be fused to the G-H region and C-terminus of VP1 and C-terminus of VP3 without affecting the VLPs assembly.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"144"},"PeriodicalIF":3.9,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144274111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced production of ergothioneine in Aspergillus oryzae.","authors":"Lihong Wang, Xueqin Tian, Pinghong Xue, Yunhong Deng, Rui Gao, Zhihong Hu","doi":"10.1007/s00253-025-13505-2","DOIUrl":"10.1007/s00253-025-13505-2","url":null,"abstract":"<p><p>Ergothioneine (EGT) is a rare amino acid with potent antioxidant and anti-inflammatory properties, with a wide range of applications in food, cosmetics, and medicine. In the present study, Aspergillus oryzae, a common edible fungus, was engineered as an optimal host for EGT production. Moreover, two endogenous genes involved in EGT biosynthesis were characterized. The homolog AoEgt1 was shown to be localized in the vacuoles, whereas the homolog AoEgt2 was found in the peroxisomes. Overexpression of EGT biosynthetic genes from different organisms enhanced EGT production, yielding 15.17 mg EGT/g of dry weight. Using glucose as the carbon source and supplementing methionine (Met) as a precursor further increased EGT production to 20.03 mg EGT/g of dry weight, constituting an eight-fold increase compared to the wild-type strain. This study discusses the successful construction of a high-yielding A. oryzae strain for EGT biosynthesis, providing a novel strategy for efficient EGT synthesis. KEY POINTS: • Two newly described homologs, AoEgt1 and AoEgt2, were identified in A. oryzae. • AoEgt1 and AoEgt2 were found to contribute to EGT biosynthesis. • EGT production was significantly increased by overexpression of Egt1 and Egt2. • Glucose and Met supplementation in the medium increased EGT production.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"143"},"PeriodicalIF":3.9,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Anxiety of microbially synthesized Fe3O4-SPIONs on embryonic/larval ontogeny in red tilapia (Oreochromis sp.).","authors":"Samia S Abouelkheir, Mona M Mourad","doi":"10.1007/s00253-025-13499-x","DOIUrl":"10.1007/s00253-025-13499-x","url":null,"abstract":"","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"142"},"PeriodicalIF":3.9,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphoproteomics analysis of acid stress response of Alicyclobacillus acidoterrestris in response to acid stress.","authors":"Yingli Liu, Kunrun Wu, Lingxia Jiao, Rui Shen, Junjian Ran, Youzhi Wu","doi":"10.1007/s00253-025-13525-y","DOIUrl":"10.1007/s00253-025-13525-y","url":null,"abstract":"<p><p>Alicyclobacillus acidoterrestris causes pasteurized acidic juices spoilage, resulting in a significant decline in juice quality and causing economic losses. Exploration of A. acidoterrestris in response to acid stress could help control contamination caused by the bacteria. In this study, the mechanism of A. acidoterrestris in response to acid stress was studied by quantitative phosphoproteomics technique. Results showed that the phosphorylation of 40 proteins in A. acidoterrestris was closely related to the regulation of acid stress. The KEGG pathway enrichment analysis showed that the quorum sensing pathway, which might be involved in the perception of A. acidoterrestris, was mainly enriched. We found that the upregulation of Spo0A and YidC phosphorylationmay resist acid stress by forming spores. The phosphorylation level of pyruvate kinase increased, which may improve bacterial acid stress resistance through the formation of energy supply. The phosphorylation level of ABC transporter permease was significantly upregulated, which may be part of the cell adaptation adjustment and contribute to the survival of A. acidoterrestris under acid stress. In summary, the molecular mechanism of acid stress regulation of A. acidoterrestris was proposed via quantitative phosphoproteomics, which provided a theoretical and experimental basis for further investigation of the acid resistance mechanism of A. acidoterrestris. KEY POINTS: • Spo0 A, Yidc proteins may be the key regulatory proteins for acid stress response. • ABC transporters are beneficial to the survival of the bacteria under acidic stress. • A. acidoterrestris may sense and transmit pH signal through quorum sensing pathway.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":"141"},"PeriodicalIF":3.9,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}