Synthetic and Systems Biotechnology最新文献

{"title":"Promoter engineering enables precise metabolic regulation towards efficient β-elemene production in Ogataea polymorpha","authors":"Min Ye ,&nbsp;Jiaoqi Gao ,&nbsp;Jingjing Li ,&nbsp;Wei Yu ,&nbsp;Fan Bai ,&nbsp;Yongjin J. Zhou","doi":"10.1016/j.synbio.2024.02.001","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.02.001","url":null,"abstract":"<div><p>Precisely controlling gene expression is beneficial for optimizing biosynthetic pathways for improving the production. However, promoters in nonconventional yeasts such as <em>Ogataea polymorpha</em> are always limited, which results in incompatible gene modulation. Here, we expanded the promoter library in <em>O. polymorpha</em> based on transcriptional data, among which 13 constitutive promoters had the strengths ranging from 0–55% of P_<em>GAP</em>, the commonly used strong constitutive promoter, and 2 were growth phase-dependent promoters. Subsequently, 2 hybrid growth phase-dependent promoters were constructed and characterized, which had 2-fold higher activities. Finally, promoter engineering was applied to precisely regulate cellular metabolism for efficient production of β-elemene. The glyceraldehyde-3-phosphate dehydrogenase gene <em>GAP</em> was downregulated to drive more flux into pentose phosphate pathway (PPP) and then to enhance the supply of acetyl-CoA by using phosphoketolase-phosphotransacetylase (PK-PTA) pathway. Coupled with the phase-dependent expression of synthase module (<em>ERG20</em>∼<em>LsLTC2</em> fusion), the highest titer of 5.24 g/L with a yield of 0.037 g/(g glucose) was achieved in strain YY150U under fed-batch fermentation in shake flasks. This work characterized and engineered a series of promoters, that can be used to fine-tune genes for constructing efficient yeast cell factories.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000164/pdfft?md5=30fe479323455d722c88b67e37cd6ce9&pid=1-s2.0-S2405805X24000164-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139738552","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-based visual toolkit enabling multiplex integration at specific genomic loci in Aspergillus niger","authors":"Yangyang Li ,&nbsp;Cen Li ,&nbsp;Yishan Fu ,&nbsp;Quan Zhang ,&nbsp;Jianing Ma ,&nbsp;Jingwen Zhou ,&nbsp;Jianghua Li ,&nbsp;Guocheng Du ,&nbsp;Song Liu","doi":"10.1016/j.synbio.2024.01.014","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.014","url":null,"abstract":"<div><p><em>Aspergillus niger</em> is a highly versatile fungal strain utilized in industrial production. The expression levels of recombinant genes in <em>A. niger</em> can be enhanced by increasing the copy number. Nevertheless, given the prolonged gene editing cycle of <em>A. niger</em>, a “one-step” strategy facilitating the simultaneous integration of recombinant genes into multiple genomic loci would provide a definitive advantage. In our previous study, a visual multigene editing system (VMS) was designed to knock out five genes, employing a tRNA-sgRNA array that includes the pigment gene <em>albA</em> and the target genes. Building upon this system, hybrid donor DNAs (dDNAs) were introduced to establish a clustered regularly interspaced short palindromic repeats (CRISPR)-based multiplex integration toolkit. Firstly, a CRISPR-Cas9 homology-directed repair (CRISPR-HDR) system was constructed in <em>A. niger</em> by co-transforming the CRISPR-Cas9 plasmid (with a highly efficient sgRNA) and the dDNA, resulting in precise integration of recombinant xylanase gene <em>xynA</em> into the target loci (the β-glucosidase gene <em>bgl</em>, the amylase gene <em>amyA</em>, and the acid amylase gene <em>ammA</em>). Subsequently, the length of homology arms in the dDNA was optimized to achieve 100% editing efficiency at each of the three gene loci. To achieve efficient multiplex integration in <em>A. niger</em>, the CRISPR plasmid pLM2 carrying a sgRNA-tRNA array was employed for concurrent double-strand breaks at multiple loci (<em>bgl</em>, <em>amyA</em>, <em>ammA</em>, and <em>albA</em>). Hybrid dDNAs were then employed for repair, including dDNA1-3 (containing <em>xynA</em> expression cassettes without selection markers) and dDNA_albA (for <em>albA</em> knockout). Among the obtained white colonies (RLM2′), 23.5% exhibited concurrent replacement of the <em>bgl</em>, <em>amyA</em>, and <em>ammA</em> genes with <em>xynA</em> (three copies). Notably, the xynA activity obtained by simultaneous insertion into three loci was 48.6% higher compared to that obtained by insertion into only the <em>bgl</em> locus. Furthermore, this multiple integration toolkit successfully enhanced the expression of endogenous pectinase pelA and <em>Candida antarctica</em> lipase CALB. Hence, the combined application of VMS and the CRISPR-HDR system enabled the simultaneous application of multiple selection markers, facilitating the rapid generation in the <em>A. niger</em> cell factories.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000140/pdfft?md5=837ddfea7b86bd9e3d04b25f4df547a0&pid=1-s2.0-S2405805X24000140-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139733189","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":"Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology","authors":"Anqi Peng ,&nbsp;Guobin Yin ,&nbsp;Wenjie Zuo ,&nbsp;Luyao Zhang ,&nbsp;Guocheng Du ,&nbsp;Jian Chen ,&nbsp;Yang Wang ,&nbsp;Zhen Kang","doi":"10.1016/j.synbio.2024.01.013","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.013","url":null,"abstract":"<div><p>Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as <em>Escherichia coli</em> and <em>Salmonella enterica</em>, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably <em>Bacillus subtilis</em>. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing <em>B. subtilis</em> as a foundational chassis.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000139/pdfft?md5=9961fe8dfbfe06bc8e20ae8ac72eaefc&pid=1-s2.0-S2405805X24000139-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139738551","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":"DIProT: A deep learning based interactive toolkit for efficient and effective Protein design","authors":"Jieling He ,&nbsp;Wenxu Wu ,&nbsp;Xiaowo Wang","doi":"10.1016/j.synbio.2024.01.011","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.011","url":null,"abstract":"<div><p>The protein inverse folding problem, designing amino acid sequences that fold into desired protein structures, is a critical challenge in biological sciences. Despite numerous data-driven and knowledge-driven methods, there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein design. In this paper, we present DIProT, an interactive protein design toolkit. DIProT leverages a non-autoregressive deep generative model to solve the inverse folding problem, combined with a protein structure prediction model. This integration allows users to incorporate prior knowledge into the design process, evaluate designs in silico, and form a virtual design loop with human feedback. Our inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets, with promising sequence recovery and inference time. Case studies further illustrate how DIProT can facilitate user-guided protein design.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000115/pdfft?md5=5b3ed4052e1bca3e811b5172802c4dcb&pid=1-s2.0-S2405805X24000115-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139731528","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 statistical approach to enhance the productivity of Streptomyces baarensis MH-133 for bioactive compounds","authors":"Mohamed H. Kalaba ,&nbsp;Gamal M. El-Sherbiny ,&nbsp;Osama M. Darwesh ,&nbsp;Saad A. Moghannem","doi":"10.1016/j.synbio.2024.01.012","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.012","url":null,"abstract":"<div><p>The goal of this study was to use statistical optimization to change the nutritional and environmental conditions so that <em>Streptomyces baarensis</em> MH-133 could make more active metabolites. Twelve trials were used to screen for critical variables influencing productivity using the Placket-Burman Design method. <em>S. baarensis</em> MH-133 is significantly influenced by elicitation, yeast extract, inoculum size, and incubation period in terms of antibacterial activity. A total of 27 experimental trials with various combinations of these factors were used to carry out the response surface technique using the Box-Behnken design. The analyses revealed that the model was highly significant (p &lt; 0.001), with a lack-of-fit of 0.212 and a coefficient determination (R2) of 0.9224. Additionally, the model predicted that the response as inhibition zone diameter would reach a value of 27 mm. Under optimal conditions, <em>S. baarensis</em> MH-133 produced 18.0 g of crude extract to each 35L and was purified with column chromatography. The active fraction exhibiting antibacterial activity was characterized using spectroscopic analysis. The MIC and MBC values varied between 37.5 and 300 μg/ml and 75 and 300 μg/ml, respectively. In conclusion, the biostatistical optimization of the active fraction critical variables, including environmental and nutritional conditions, enhances the production of bioactive molecules by <em>Streptomyces</em> species.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000127/pdfft?md5=768b4ab7df25b863d27da3068bee31d4&pid=1-s2.0-S2405805X24000127-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139731526","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":"Efficient conversion of aromatic and phenylpropanoid alcohols to acids by the cascade biocatalysis of alcohol and aldehyde dehydrogenases","authors":"Zetian Qiu ,&nbsp;Xiaohui Liu ,&nbsp;Jie Yu ,&nbsp;Yushuo Zhao ,&nbsp;Guang-Rong Zhao ,&nbsp;Shengying Li ,&nbsp;Kun Liu ,&nbsp;Lei Du ,&nbsp;Li Ma","doi":"10.1016/j.synbio.2024.01.008","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.008","url":null,"abstract":"<div><p>Benzyl and phenylpropanoid acids are widely used in organic synthesis of fine chemicals, such as pharmaceuticals and condiments. However, biocatalysis of these acids has received less attention than chemical synthesis. One of the main challenges for biological production is the limited availability of alcohol dehydrogenases and aldehyde dehydrogenases. Environmental microorganisms are potential sources of these enzymes. In this study, 129 alcohol dehydrogenases and 42 aldehyde dehydrogenases from <em>Corynebacterium glutamicum</em>, <em>Pseudomonas aeruginosa</em>, and <em>Bacillus subtilis</em> were identified and explored with various benzyl and phenylpropanoid alcohol and aldehyde substrates, among which four alcohol dehydrogenases and four aldehyde dehydrogenases with broad substrate specificity and high catalytic activity were obtained. Moreover, a cascade whole-cell catalytic system including ADH-90, ALDH-40, and the NAD(P)H oxidase LreNox was established, which showed high efficiency in converting cinnamyl alcohol and <em>p</em>-methylbenzyl alcohol into the respective carboxylic acids. Remarkably, this biocatalytic system can be easily scaled up to gram-level production, facilitating preparation purposes.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000085/pdfft?md5=abf03745517cb60e65a89be5b84ed786&pid=1-s2.0-S2405805X24000085-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139731527","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":"Development of Zn2+-controlled expression system for lactic acid bacteria and its application in engineered probiotics","authors":"Xiaoning Xu ,&nbsp;Lingwen Zhang ,&nbsp;Yue Cui,&nbsp;Jian Kong,&nbsp;Tingting Guo","doi":"10.1016/j.synbio.2024.01.009","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.009","url":null,"abstract":"<div><p><em>Lactococcus lactis</em> and <em>Streptococcus thermophilus</em> are considered as ideal chassis of engineered probiotics, while food-grade genetic tools are limited in those strains. Here, a Zn²⁺-controlled gene expression (ZICE) system was identified in the genome of <em>S</em>. <em>thermophilus</em> CGMCC7.179, including a transcriptional regulator <em>sczA</em>_<em>st</em> and a promoter region of cation transporter <em>czcD</em> (P_{<em>czcDst</em>}). Specific binding of the SczA_st to the palindromic sequences in P_{<em>czcDst</em>} was demonstrated by EMSA analysis, suggesting the regulation role of SczA_st on P_{<em>czcDst</em>}. To evaluate their possibility to control gene expression <em>in vivo</em>, the <em>sczA</em>_<em>st</em>-P_{<em>czcDst</em>} was employed to drive the expression of green fluorescence protein (GFP) gene in <em>L</em>. <em>lactis</em> NZ9000 and <em>S. thermophilus</em> CGMCC7.179, respectively. Both of the transformants could express GFP under Zn²⁺ induction, while no fluorescence without Zn²⁺ addition. For optimal conditions, Zn²⁺ was used at a final concentration of 0.8 mM in <em>L</em>. <em>lactis</em> and 0.16 mM in <em>S</em>. <em>thermophilus</em> at OD₆₀₀ close to 0.4, and omitting yeast extract powder in the medium unexpectedly improved GFP expression level by 2.2-fold. With the help of the ZICE system, engineered <em>L</em>. <em>lactis</em> and <em>S</em>. <em>thermophilus</em> strains were constructed to secret cytokine interleukin-10 (IL-10) with immunogenicity, and the IL-10 content in the supernatant of the engineered <em>L</em>. <em>lactis</em> was 59.37 % of that under the nisin controlled expression system. This study provided a tightly controlled expression system by the food-grade inducer Zn²⁺, having potential in development of engineered probiotics.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000097/pdfft?md5=c5abfefcff8bbbf09a148db249a223d7&pid=1-s2.0-S2405805X24000097-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675536","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":"Establishment of a selectable marker recycling system for iterative gene editing in Fusarium fujikuroi","authors":"Tian-Qiong Shi ,&nbsp;Cai-Ling Yang ,&nbsp;Dong-Xun Li ,&nbsp;Yue-Tong Wang ,&nbsp;Zhi-Kui Nie","doi":"10.1016/j.synbio.2024.01.010","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.010","url":null,"abstract":"<div><p>Gibberellic acid (GA3) is a vital plant growth hormone widely used in agriculture. Currently, GA3 production relies on liquid fermentation by the filamentous fungus <em>Fusarium fujikuroi</em>. However, the lack of an effective selection marker recycling system hampers the application of metabolic engineering technology in <em>F. fujikuroi</em>, as multiple-gene editing and positive-strain screening still rely on a limited number of antibiotics. In this study, we developed a strategy using pyr4-blaster and CRISPR/Cas9 tools for recycling orotidine-5′-phosphate decarboxylase (Pyr4) selection markers. We demonstrated the effectiveness of this method for iterative gene integration and large gene-cluster deletion. We also successfully improved GA3 titers by overexpressing geranylgeranyl pyrophosphate synthase and truncated 3-hydroxy-3-methyl glutaryl coenzyme A reductase, which rewired the GA3 biosynthesis pathway. These results highlight the efficiency of our established system in recycling selection markers during iterative gene editing events. Moreover, the selection marker recycling system lays the foundation for further research on metabolic engineering for GA3 industrial production.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000103/pdfft?md5=263ce68a4e92b98b20bf2ba0ea5b0a9b&pid=1-s2.0-S2405805X24000103-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139682434","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":"Enhancement of polymyxin B1 production by an artificial microbial consortium of Paenibacillus polymyxa and recombinant Corynebacterium glutamicum producing precursor amino acids","authors":"Hui-Zhong Sun ,&nbsp;Si-Yu Wei ,&nbsp;Qiu-Man Xu ,&nbsp;Wei Shang ,&nbsp;Qing Li ,&nbsp;Jing-Sheng Cheng ,&nbsp;Ying-Jin Yuan","doi":"10.1016/j.synbio.2024.01.015","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.01.015","url":null,"abstract":"<div><p>Polymyxin B, produced by <em>Paenibacillus polymyxa,</em> is used as the last line of defense clinically. In this study, exogenous mixture of precursor amino acids increased the level and proportion of polymyxin B1 in the total of polymyxin B analogs of <em>P. polymyxa</em> CJX518-AC (PPAC) from 0.15 g/L and 61.8 % to 0.33 g/L and 79.9 %, respectively. The co-culture of strain PPAC and recombinant <em>Corynebacterium glutamicum</em>-leu01, which produces high levels of threonine, leucine, and isoleucine, increased polymyxin B1 production to 0.64 g/L. When strains PPAC and <em>C. glu</em>-leu01 simultaneously inoculated into an optimized medium with 20 g/L peptone, polymyxin B1 production was increased to 0.97 g/L. Furthermore, the polymyxin B1 production in the co-culture of strains PPAC and <em>C. glu</em>-leu01 increased to 2.21 g/L after optimized inoculation ratios and fermentation medium with 60 g/L peptone. This study provides a new strategy to improve polymyxin B1 production.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000152/pdfft?md5=02c2b4278f602f462013bc252610def3&pid=1-s2.0-S2405805X24000152-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139694699","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":"Identification of crucial roles of transcription factor IhfA on high production of free fatty acids in Escherichia coli","authors":"Lixia Fang ,&nbsp;Ziyi Han ,&nbsp;Xueru Feng ,&nbsp;Xueyan Hao ,&nbsp;Mengxiao Liu ,&nbsp;Hao Song ,&nbsp;Yingxiu Cao","doi":"10.1016/j.synbio.2024.01.007","DOIUrl":"10.1016/j.synbio.2024.01.007","url":null,"abstract":"<div><p>Transcription factor engineering has unique advantages in improving the performance of microbial cell factories due to the global regulation of gene transcription. Omics analyses and reverse engineering enable learning and subsequent incorporation of novel design strategies for further engineering. Here, we identify the role of the global regulator IhfA for overproduction of free fatty acids (FFAs) using CRISPRi-facilitated reverse engineering and cellular physiological characterization. From the differentially expressed genes in the <em>ihfA</em>^L− strain, a total of 14 beneficial targets that enhance FFAs production by above 20 % are identified, which involve membrane function, oxidative stress, and others. For membrane-related genes, the engineered strains obtain lower cell surface hydrophobicity and increased average length of membrane lipid tails. For oxidative stress-related genes, the engineered strains present decreased reactive oxygen species (ROS) levels. These gene modulations enhance cellular robustness and save cellular resources, contributing to FFAs production. This study provides novel targets and strategies for engineering microbial cell factories with improved FFAs bioproduction.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000073/pdfft?md5=5f9028642b74a6570cdf7c188df29636&pid=1-s2.0-S2405805X24000073-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139634234","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}