Microbial Cell Factories最新文献

{"title":"Systematic approach for dissecting promoters and designing transform systems in microalgae.","authors":"Qinhua Gan, Xinjun Yu, Xiang Jiang, Xingwei Huang, Yi Xin, Yandu Lu","doi":"10.1186/s12934-025-02700-5","DOIUrl":"https://doi.org/10.1186/s12934-025-02700-5","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"127"},"PeriodicalIF":4.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic engineering of E. coli K-12 for heterologous carbohydrate antigen production.","authors":"Caixia Li, Hongxu Zha, Ziyan Jiao, Keyan Wei, Huaiyu Gao, Feiyi Lai, Zuoyong Zhou, Hongyan Luo, Pei Li","doi":"10.1186/s12934-025-02749-2","DOIUrl":"https://doi.org/10.1186/s12934-025-02749-2","url":null,"abstract":"<p><strong>Background: </strong>Carbohydrate-based vaccines have made a remarkable impact on public health over the past three decades. Efficient production of carbohydrate antigens is a crucial prerequisite for the development of such vaccines. The enzymes involved in the synthesis of bacterial surface carbohydrate antigens are usually encoded by large, uninterrupted gene clusters. Non-pathogenic E. coli glycoengineering starts with the genetic manipulation of these clusters. Heterologous gene cluster recombination through an expression plasmid has several drawbacks, including continuous antibiotic selection pressure, genetic instability, and metabolic burdens. In contrast, chromosome-level gene cluster expression can minimize the metabolic effects on the host and reduce industrial costs.</p><p><strong>Results: </strong>In this study, we employed the suicide vector-mediated allelic exchange method to directly replace the native polysaccharide gene clusters in E. coli with heterologous ones. Unlike previously strategies, this method does not rely on I-SceI endonuclease or CRISPR/Cas system to release the linearized DNA insert and λ-red recombinase to promote its homologous recombination. Meanwhile, the vectors could be conveniently constructed by assembling multiple large DNA fragments in order in vitro. The scarless chromosomal insertions were confirmed by whole-genome sequencing and the polysaccharide phenotypes of all glycoengineered E. coli mutants were evaluated through growth curves, silver staining, western blot, and flow cytometry. The data indicated that there was no obvious metabolic burden associated with the insertion of large gene clusters into the E. coli W3110 O-antigen locus, and the glycoengineered E. coli can produce LPS with a recovery rate around 1% of the bacterial dry weight. Moreover, the immunogenicity of the heterologously expressed carbohydrate antigens was analyzed by mice immunization experiments. The ELISA data demonstrated the successful induction of anti-polysaccharide IgM or IgG antibodies.</p><p><strong>Conclusions: </strong>We have provided a convenient and reliable genomic glycoengineering method to produce efficacious, durable, and cost-effective carbohydrate antigens in non-pathogenic E. coli. Non-pathogenic E. coli glycoengineering has great potential for the highly efficient synthesis of heterologous polysaccharides and can serve as a versatile platform to produce next-generation biomedical agents, including glycoconjugate vaccines, glycoengineered minicells or outer membrane vesicles (OMVs), polysaccharide-based diagnostic reagents, and more.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"126"},"PeriodicalIF":4.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the kinetics and mechanisms of tetramethrin biodegradation by the fungal strain Neocosmospora sp. AF3.","authors":"Wen-Juan Chen, Xiaofang Luo, Xuanrui Zhang, Kalpana Bhatt, Shao-Fang Chen, Mohamed A Ghorab, Xiaofan Zhou, Yaohua Huang","doi":"10.1186/s12934-025-02747-4","DOIUrl":"https://doi.org/10.1186/s12934-025-02747-4","url":null,"abstract":"<p><p>Tetramethrin is a common pyrethroid insecticide, but there is limited knowledge about its degradation kinetics and mechanisms. In this study, a novel fungal strain, Neocosmospora sp. AF3, was obtained from pesticide-contaminated fields and was shown to be highly effective for degrading tetramethrin and other widely used pyrethroids. The AF3 strain completely removed 10 mg/L of tetramethrin from mineral salt medium in 9 days. The first-order kinetic analysis indicated that the degradation rate constant of the AF3 strain on 50 mg/L tetramethrin was 0.2835 d^-1 (per day), and the half-life was 2.45 days. A response surface model analysis showed that the optimal degradation conditions for the AF3 strain are a temperature of 33.37 ℃, pH of 7.97, and inoculation amount of 0.22 g/L dry weight. The Andrews nonlinear fitting results suggested that the optimal concentration of tetramethrin metabolized by the AF3 strain is 12.6073 mg/L, and the q_max, K_i, and K_s values were 0.9919 d^-1, 20.1873 mg/L, and 7.8735 mg/L, respectively. The gas chromatography-mass spectrometry (GC-MS) analysis indicated that N-hydroxymethyl-3,4,5,6-tetrahydrophthalimide, chrysanthemic acid and tetrahydrophthalimide are the main intermediates involved in the metabolism of tetramethrin by the AF3 strain. Furthermore, this strain was shown to effectively degrade other pyrethroid pesticides including permethrin, beta-cypermethrin, chlorempenthrin, fenvalerate, D-cyphenothrin, bifenthrin, meperfluthrin, cyfluthrin, and deltamethrin within a short period, suggesting that Neocosmospora sp. AF3 can play an important role in the remediation of pyrethroid contamination. Taken together, these results shed a new light on uncovering the degradation mechanisms of tetramethrin and present useful agents for developing relevant pyrethroid bioremediation strategies.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"124"},"PeriodicalIF":4.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioactive protein hydrolysate from Sesamum indicum L. residue as a novel fat substitute by protease: production optimization and application in low-fat yogurt production.","authors":"Samia A Ahmed, Mohamed A A Abdella, Osama A Ibrahim","doi":"10.1186/s12934-025-02748-3","DOIUrl":"10.1186/s12934-025-02748-3","url":null,"abstract":"<p><strong>Background: </strong>Agricultural and industrial residues are renewable biomass sources present in large quantities causing pollution. Therefore, transforming these residues to eco-friendly products such as enzymes and bioactive materials reduces their quantity and impact on the environment, in addition to reducing the production costs.</p><p><strong>Results: </strong>Sesame cake is a by-product of the production of Sesame seed oil and is high in protein. The yield of Sesame cake protein hydrolysis (SH) improved by 4.2-fold through the optimization of conditions using Bacillus thuringiensis strain-MA8 protease via the Box-Behnken design (BBd). The average diameter of the particle size of SH was 677.10 nm. The application of SH (1-3%) in the production of low-fat yogurt (LSH) exhibited a fermentation time similar to that enriched with skim milk powder (LSMP). The total solids and protein levels in LSH-yogurt exceeded those in full fat yogurt (FFY). In addition, the acidity and overall acceptability ratings of LSH-yogurt were similar to FFY throughout the 15-day storage at 5 °C, without displaying any defects. Furthermore, the total essential amino acids (TEAA), total amino acids (TAA), and TEAA/TAA ratio of LSH (2%)-yogurt were approximately similar to FFY. Incorporating SH (2%) improved the chemical score of certain amino acids in LSH-yogurt. The hardness of LSH-yogurt exceeded that of FFY. Additionally, the springiness, gumminess, and cohesiveness of LSH-yogurt were similar to those of LSMP.</p><p><strong>Conclusions: </strong>Protein hydrolysate from Sesame cake is a new fat substitute for low-fat yogurt production without displaying any defects as well as reducing the risks associated with high-fat consumption and global obesity.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"123"},"PeriodicalIF":4.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A CRISPR-Cas9 system for knock-out and knock-in of high molecular weight DNA enables module-swapping of the pikromycin synthase in its native host.","authors":"Zhe-Chong Wang, Hayden Stegall, Takeshi Miyazawa, Adrian T Keatinge-Clay","doi":"10.1186/s12934-025-02741-w","DOIUrl":"10.1186/s12934-025-02741-w","url":null,"abstract":"<p><strong>Background: </strong>Engineers seeking to generate natural product analogs through altering modular polyketide synthases (PKSs) face significant challenges when genomically editing large stretches of DNA.</p><p><strong>Results: </strong>We describe a CRISPR-Cas9 system that was employed to reprogram the PKS in Streptomyces venezuelae ATCC 15439 that helps biosynthesize the macrolide antibiotic pikromycin. We first demonstrate its precise editing ability by generating strains that lack megasynthase genes pikAI-pikAIV or the entire pikromycin biosynthetic gene cluster but produce pikromycin upon complementation. We then employ it to replace 4.4-kb modules in the pikromycin synthase with those of other synthases to yield two new macrolide antibiotics with activities similar to pikromycin.</p><p><strong>Conclusion: </strong>Our gene-editing tool has enabled the efficient replacement of extensive and repetitive DNA regions within streptomycetes.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"125"},"PeriodicalIF":4.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Further characterization and engineering of an 11-amino acid motif for enhancing recombinant soluble protein expression.","authors":"Jiawu Bi, Elaine Tiong, Ying Sin Koo, Weibiao Zhou, Fong Tian Wong","doi":"10.1186/s12934-025-02738-5","DOIUrl":"10.1186/s12934-025-02738-5","url":null,"abstract":"<p><strong>Background: </strong>Escherichia coli (E. coli) is a popular system for recombinant protein production, owing to its low cost and availability of genetic tools. However, the expression of soluble recombinant proteins remains an issue. As such, various solubility-enhancing and yield-improving methods such as the addition of fusion tags have been developed. This study focuses on a small solubility tag (NT11), derived from the N-terminal domain of a duplicated carbonic anhydrase from Dunaliella species. The small size of NT11 (< 10 kDa) lowers the chance of protein folding interference and post-translation removal requirement, which ultimately minimizes cost of production.</p><p><strong>Results: </strong>A comprehensive analysis was performed to improve the characteristics of the 11-amino acid tag. By investigating the alanine-scan library of NT11, we achieved at least a two-fold increase in protein yield for three different proteins and identified key residues for further development. We also demonstrated that the NT11 tag is not limited to the N-terminal position and can function at either the N- or C-terminal of the protein, providing flexibility in designing constructs. With these new insights, we have successfully doubled the recombinant soluble protein yields of valuable growth factors, such as fibroblast growth factor 2 (FGF2) and human epidermal growth factor (hEGF) in E. coli.</p><p><strong>Conclusion: </strong>The further characterisation and development of the NT11 tag have provided valuable insights into the optimisation process for such small tags and expanded our understanding of its potential applications. The ability of the NT11 tag to be positioned at either the N- or C- termini within the protein construct without compromising its effectiveness to enhance soluble recombinant protein yields, makes it a valuable tool across a diverse range of proteins. Collectively, these findings demonstrate a promising approach to simplify and enhance the efficiency of soluble recombinant protein production.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"122"},"PeriodicalIF":4.3,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineered biosynthesis and characterization of disaccharide-pimaricin.","authors":"Xiaoshan Zuo, Liqin Qiao, Yao Dong, Xing Jin, Zhongyuan Ren, Hao Cui","doi":"10.1186/s12934-025-02742-9","DOIUrl":"10.1186/s12934-025-02742-9","url":null,"abstract":"<p><strong>Background: </strong>Disaccharide polyene macrolides exhibit superior water solubility and significantly reduced hemolytic toxicity compared to their monosaccharide counterparts, making them promising candidates for safer antifungal therapeutics. In this study, we engineered a Streptomyces gilvosporeus (pSET152-nppY) capable of producing disaccharide-pimaricin (DSP) through heterologous expression of the nppY gene, which encodes a glycosyltransferase responsible for the second sugar extension in the biosynthetic pathway.</p><p><strong>Results: </strong>The novel compound was structurally characterized and designated disaccharide-pimaricin (DSP), featuring an aglycone identical to pimaricin and a unique disaccharide moiety (mycosaminyl-α1-4-N-acetylglucosamine). A purification protocol for DSP was established. Compared to pimaricin, DSP demonstrated a 50% reduction in antifungal activity, a 12.6-fold decrease in hemolytic toxicity, and a remarkable 107.6-fold increase in water solubility. Growth analysis revealed a delayed growth cycle in the mutant strain, suggesting that nppY expression may impose additional metabolic burden. Optimization of the fermentation medium using a statistical design identified an optimal formulation, with a maximum DSP titer of 138.168 mg/L.</p><p><strong>Conclusions: </strong>This study underscores the potential of disaccharide polyene macrolides as safer antifungal agents and establishes a robust framework for engineering strains to produce these compounds. The findings provide critical insights into balancing biosynthetic efficiency and strain fitness, advancing the development of next-generation polyene antibiotics.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"121"},"PeriodicalIF":4.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional insights from recombinant production of bacterial proteases in Saccharomyces cerevisiae.","authors":"Tova Lindh, Mattias Collin, Rolf Lood, Magnus Carlquist","doi":"10.1186/s12934-025-02732-x","DOIUrl":"10.1186/s12934-025-02732-x","url":null,"abstract":"<p><strong>Background: </strong>Proteases are important enzymes in food and pharmaceutical industries, but challenges persist in their recombinant production due to host cell proteome hydrolysis and fitness loss. The development of recombinant expression systems for directed evolution of proteolytic enzymes, and industrial production are desirable. This study evaluated Saccharomyces cerevisiae as expression host for three bacterial proteases: BdpK (from Bdellovibrio bacteriovorus), IdeS, and SpeB (both from Streptococcus pyogenes), each with distinct peptide substrate scopes.</p><p><strong>Results: </strong>We developed an experimental pipeline for analysis of protease gene expression levels and fitness effects on yeast cultures. Heterologous genes were fused with green fluorescent protein and their expression and effects on cell viability was monitored at the single-cell level by flow cytometry. IdeS-GFP fusion was produced efficiently with a gaussian distribution within the population and without compromising cell growth or viability. BdpK, on the other hand, displayed lower expression level and a more heterogenous distribution that was less stable over time. Production of SpeB was not feasible. Inserting the speB-GFP fusion gene resulted in complete growth inhibition and a significantly higher frequency of cells with compromised membrane integrity. Plasmid-based expression was compared with integrated-based expression, revealing higher total expression levels and lower degree of population heterogeneity for the latter.</p><p><strong>Conclusions: </strong>S. cerevisiae was found to be an efficient expression host for the bacterial protease IdeS. In contrast, the expression of BdpK and SpeB faced significant challenges, including lack of activity for BdpK, or imposing a substantial fitness burden on the cells for SpeB, likely due to its broad substrate scope resulting in native protein degradation. The findings of this study provide valuable insights into the limitations and possibilities of yeast as an expression host for bacterial protease production and for studying their physiological effects using yeast as a model eukaryote.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"119"},"PeriodicalIF":4.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Region-based segmental swapping of homologous enzymes for higher cadaverine production.","authors":"Seungjin Kim, Dae-Yeol Ye, Hyun Gyu Lim, Myung Hyun Noh, Jae-Seong Yang, Gyoo Yeol Jung","doi":"10.1186/s12934-025-02739-4","DOIUrl":"10.1186/s12934-025-02739-4","url":null,"abstract":"<p><strong>Background: </strong>Cadaverine, displaying potential in medicine, agriculture and polyamide production, is biologically produced through L-lysine decarboxylation. Considering the potential of the polyamide market, its biological production has been focused on with following diverse efforts to improve the production. In Escherichia coli, lysine decarboxylase exists in two forms: CadA and LdcC, and it is known that CadA exhibits superior catalytic activity compared to LdcC. Despite its potential, cadaverine production is limited due to increased intracellular pH, which destabilizes the decameric structure of CadA and inhibits its activity.</p><p><strong>Results: </strong>In this study, based on the structural analysis, a chimeric CadA enzyme, CL2, was engineered by replacing its pH-sensitive region with a structurally stable counterpart derived from LdcC. The resulting BLCL2 strain with CL2 produced 1.12 g/L of cadaverine-1.96 times higher than BLC strain with the wild type CadA in flask culture. Compared to the wild type CadA, structural modifications enhanced pH stability and improved the affinity of CadA toward pyridoxal 5-phosphate (PLP), its cofactor.</p><p><strong>Conclusions: </strong>This study developed the improved strains for cadaverine production by creating the new enzyme, which is validated by enhanced amount of cadaverine. In addition, the segmental swapping guided by structure analysis was exhibited as the one of effective method in protein engineering strategies. These advancements offer a promising approach to optimizing cadaverine biosynthesis for industrial applications.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"120"},"PeriodicalIF":4.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization.","authors":"Jeffrey J Czajka, Ziyu Dai, Tijana Radivojević, Joonhoon Kim, Shuang Deng, Teresa Lemmon, Marie Swita, Meagan C Burnet, Nathalie Munoz, Yuqian Gao, Young-Mo Kim, Beth Hofstad, Jon K Magnuson, Hector Garcia Martin, Kristin E Burnum-Johnson, Kyle R Pomraning","doi":"10.1186/s12934-025-02705-0","DOIUrl":"10.1186/s12934-025-02705-0","url":null,"abstract":"<p><strong>Background: </strong>Lipomyces starkeyi is an oleaginous yeast with a native metabolism well-suited for production of lipids and biofuels from complex lignocellulosic and waste feedstocks. Recent advances in genetic engineering tools have facilitated the development of L. starkeyi into a microbial chassis for biofuel and chemical production. However, the feasibility of redirecting L. starkeyi lipid flux away from lipids and towards other products remains relatively unexplored. Here, we engineer the native metabolism to produce malic acid by introducing the reductive TCA pathway and a C4-dicarboxylic acid transporter to the yeast.</p><p><strong>Results: </strong>Heterogeneous expression of two genes, the Aspergillus oryzae malate transporter and malate dehydrogenase, enabled L. starkeyi malic acid production. Overexpression of a third gene, the native pyruvate carboxylase, allowed titers to reach approximately 10 g/L during shaking flasks cultivations, with production of malic acid inhibited at pH values less than 4. Corn-stover hydrolysates were found to be well-tolerated, and controlled bioreactor fermentations on the real hydrolysate produced 26.5 g/L of malic acid. Proteomic, transcriptomic and metabolomic data from real and mock hydrolysate fermentations indicated increased levels of a S. cerevisiae hsp9/hsp12 homolog (proteinID: 101453), glutathione dependent formaldehyde dehydrogenases (proteinIDs: 2047, 278215), oxidoreductases, and expression of efflux pumps and permeases during growth on the real hydrolysate. Simultaneously, machine learning based medium optimization improved production dynamics by 18% on mock hydrolysate and revealed lower tolerance to boron (a trace element included in the standard cultivation medium) than other yeasts.</p><p><strong>Conclusions: </strong>Together, this work demonstrated the ability to produce organic acids in L. starkeyi with minimal byproducts. The fermentation characterization and omic analyses provide a rich dataset for understanding L. starkeyi physiology and metabolic response to growth in hydrolysates. Identified upregulated genes and proteins provide potential targets for overexpression for improving growth and tolerance to concentrated hydrolysates, as well as valuable information for future L. starkeyi engineering work.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":"24 1","pages":"117"},"PeriodicalIF":4.3,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}