Engineering Microbiology最新文献

{"title":"Erratum regarding missing statements in previously published articles","authors":"","doi":"10.1016/j.engmic.2023.100125","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100125","url":null,"abstract":"","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 4","pages":"Article 100125"},"PeriodicalIF":0.0,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000577/pdfft?md5=d62ac2ff88fad76ed874a28dd3249ebf&pid=1-s2.0-S2667370323000577-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134832823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic engineering: Tools and applications","authors":"Yun Chen , Jiazhang Lian , Jin Hou","doi":"10.1016/j.engmic.2023.100126","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100126","url":null,"abstract":"","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 4","pages":"Article 100126"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000589/pdfft?md5=3e6761c3a40b7b699799a6a7089b770b&pid=1-s2.0-S2667370323000589-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134832824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the diversity of microbes and natural products from fungus-growing termite tripartite symbiosis","authors":"Muhammad Shoaib ,&nbsp;Ruining Bai ,&nbsp;Shuai Li ,&nbsp;Yan Xie ,&nbsp;Yulong Shen ,&nbsp;Jinfeng Ni","doi":"10.1016/j.engmic.2023.100124","DOIUrl":"10.1016/j.engmic.2023.100124","url":null,"abstract":"<div><p>The fungus-growing termite is considered a distinct ecological niche because it involves a tripartite symbiosis between the termite host, gut microflora, and the <em>in vitro</em> fungus <em>Termitomyces</em>, which has led to the expansion of highly organized and complex societies among termite colonies. Tripartite symbiosis in fungus-growing termites may promote unique microbes with distinctive metabolic pathways that may serve as valuable resources for developing novel antimicrobial therapeutic options. Recent research on complex tripartite symbioses has revealed a plethora of previously unknown natural products that may have ecological roles in signaling, communication, or defense responses. Natural products produced by symbionts may act as crucial intermediaries between termites and their pathogens by providing direct protection through their biological activities. Herein, we review the state-of-the-art research on both microbes and natural products originated from fungus-growing termite tripartite symbiosis, highlighting the diversity of microbes and the uniqueness of natural product classes and their bioactivities. Additionally, we emphasize future research prospects on fungus-growing termite related microorganisms, with a particular focus on their potential roles in bioactive product discovery.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100124"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000565/pdfft?md5=626d1e0eddd0b16494e5e73d294b7fe8&pid=1-s2.0-S2667370323000565-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135455640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances and applications of CRISPR/Cas-mediated interference in Escherichia coli","authors":"Xiaohui Lim,&nbsp;Congqiang Zhang,&nbsp;Xixian Chen","doi":"10.1016/j.engmic.2023.100123","DOIUrl":"10.1016/j.engmic.2023.100123","url":null,"abstract":"<div><p>The bacterium <em>Escherichia coli</em> (<em>E. coli</em>) is one of the most widely used chassis microbes employed for the biosynthesis of numerous valuable chemical compounds. In the past decade, the metabolic engineering of <em>E. coli</em> has undergone significant advances, although further productivity improvements will require extensive genome modification, multi-dimensional regulation, and multiple metabolic-pathway coordination. In this context, clustered regularly interspaced short palindromic repeats (CRISPR), along with CRISPR-associated protein (Cas) and its inactive variant (dCas), have emerged as notable recombination and transcriptional regulation tools that are particularly useful for multiplex metabolic engineering in <em>E. coli</em>. In this review, we briefly describe the CRISPR/Cas9 technology in <em>E. coli</em>, and then summarize the recent advances in CRISPR/dCas9 interference (CRISPRi) systems in <em>E. coli</em>, particularly the strategies designed to effectively regulate gene repression and overcome retroactivity during multiplexing. Moreover, we discuss recent applications of the CRISPRi system for enhancing metabolite production in <em>E. coli</em>, and finally highlight the major challenges and future perspectives of this technology.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100123"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000553/pdfft?md5=4d0cbb9f9fc0584a0733f98e22ad4832&pid=1-s2.0-S2667370323000553-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135371231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering Saccharomyces cerevisiae for efficient production of recombinant proteins","authors":"Shuo Yang ,&nbsp;Liyun Song ,&nbsp;Jing Wang ,&nbsp;Jianzhi Zhao ,&nbsp;Hongting Tang ,&nbsp;Xiaoming Bao","doi":"10.1016/j.engmic.2023.100122","DOIUrl":"10.1016/j.engmic.2023.100122","url":null,"abstract":"<div><p><em>Saccharomyces cerevisiae</em> is an excellent microbial cell factory for producing valuable recombinant proteins because of its fast growth rate, robustness, biosafety, ease of operability via mature genomic modification technologies, and the presence of a conserved post-translational modification pathway among eukaryotic organisms. However, meeting industrial and market requirements with the current low microbial production of recombinant proteins can be challenging. To address this issue, numerous efforts have been made to enhance the ability of yeast cell factories to efficiently produce proteins. In this review, we provide an overview of recent advances in <em>S. cerevisiae</em> engineering to improve recombinant protein production. This review focuses on the strategies that enhance protein production by regulating transcription through promoter engineering, codon optimization, and expression system optimization. Additionally, we describe modifications to the secretory pathway, including engineered protein translocation, protein folding, glycosylation modification, and vesicle trafficking. Furthermore, we discuss global metabolic pathway optimization and other relevant strategies, such as the disruption of protein degradation, cell wall engineering, and random mutagenesis. Finally, we provide an outlook on the developmental trends in this field, offering insights into future directions for improving recombinant protein production in <em>S. cerevisiae</em>.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100122"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000541/pdfft?md5=09024df4a0818d7b3b48953b72932856&pid=1-s2.0-S2667370323000541-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136118606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and application of a strong bidirectional acmN2p promoter from actinomycin D-producing streptomycetes","authors":"Sainan Li ,&nbsp;Danfeng Tang ,&nbsp;Xu Zhao ,&nbsp;Manxiang Zhu ,&nbsp;Xiangcheng Zhu ,&nbsp;Yanwen Duan ,&nbsp;Yong Huang","doi":"10.1016/j.engmic.2023.100121","DOIUrl":"10.1016/j.engmic.2023.100121","url":null,"abstract":"<div><p>Natural product biosynthesis is controlled at multiple levels. Characterization of naturally occurring promoters has facilitated the study of the synthetic biology of natural products. Herein, we report the discovery of two high-yield actinomycin D (ActD)-producing streptomycetes and the identification of a strong bidirectional acmN2p promoter from the ActD gene clusters and its application in heterologous expression of three core genes involved in the bacterial alkaloid bohemamine biosynthesis, providing a good example for identification of new promoters for synthetic biological applications.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100121"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S266737032300053X/pdfft?md5=d6c768acda89cc4d3e8c6348084fb5b6&pid=1-s2.0-S266737032300053X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135660811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Half a century after their discovery: Structural insights into exonuclease and annealase proteins catalyzing recombineering","authors":"Lucy J. Fitschen ,&nbsp;Timothy P. Newing ,&nbsp;Nikolas P. Johnston ,&nbsp;Charles E. Bell ,&nbsp;Gökhan Tolun","doi":"10.1016/j.engmic.2023.100120","DOIUrl":"10.1016/j.engmic.2023.100120","url":null,"abstract":"<div><p>Recombineering is an essential tool for molecular biologists, allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious <em>in vitro</em> manipulations involving restriction enzymes. The main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing (SSA) homologous recombination pathway to repair double-stranded DNA breaks. While there have been several reviews examining recombineering methods and applications, comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway: a 5′→3′ exonuclease and a single-strand annealing protein (SSAP or “annealase”). This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in <em>E. coli:</em> the RecET system from <em>E. coli</em> Rac prophage and the λRed system from bacteriophage λ. By comparing the structures of the RecT and Redβ annealases, and the RecE and λExo exonucleases, we provide new insights into how the structures of these proteins dictate their function. Examining the sequence conservation of the λExo and RecE exonucleases gives more profound insights into their critical functional features. Ultimately, as recombineering accelerates and evolves in the laboratory, a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100120"},"PeriodicalIF":0.0,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000528/pdfft?md5=42fa03ae2d300bd225539962db8c44f3&pid=1-s2.0-S2667370323000528-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135433168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent advances in genome-scale engineering in Escherichia coli and their applications","authors":"Hui Gao ,&nbsp;Zhichao Qiu ,&nbsp;Xuan Wang ,&nbsp;Xiyuan Zhang ,&nbsp;Yujia Zhang ,&nbsp;Junbiao Dai ,&nbsp;Zhuobin Liang","doi":"10.1016/j.engmic.2023.100115","DOIUrl":"10.1016/j.engmic.2023.100115","url":null,"abstract":"<div><p>Owing to the rapid advancement of genome engineering technologies, the scale of genome engineering has expanded dramatically. Genome editing has progressed from one genomic alteration at a time that could only be employed in few species, to the simultaneous generation of multiple modifications across many genomic loci in numerous species. The development and recent advances in multiplex automated genome engineering (MAGE)-associated technologies and clustered regularly interspaced short palindromic repeats and their associated protein (CRISPR-Cas)-based approaches, together with genome-scale synthesis technologies offer unprecedented opportunities for advancing genome-scale engineering in a broader range. These approaches provide new tools to generate strains with desired phenotypes, understand the complexity of biological systems, and directly evolve a genome with novel features. Here, we review the recent major advances in genome-scale engineering tools developed for <em>Escherichia coli</em>, focusing on their applications in identifying essential genes, genome reduction, recoding, and beyond.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100115"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000474/pdfft?md5=967c43434767d6e9eae7f04f34e86a01&pid=1-s2.0-S2667370323000474-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135347943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidation and engineering mitochondrial respiratory-related genes for improving bioethanol production at high temperature in Saccharomyces cerevisiae","authors":"Xianni Qi ,&nbsp;Zhen Wang ,&nbsp;Yuping Lin ,&nbsp;Yufeng Guo ,&nbsp;Zongjie Dai ,&nbsp;Qinhong Wang","doi":"10.1016/j.engmic.2023.100108","DOIUrl":"10.1016/j.engmic.2023.100108","url":null,"abstract":"<div><p>Industrial manufacturing of bioproducts, especially bioethanol, can benefit from high-temperature fermentation, which requires the use of thermotolerant yeast strains. Mitochondrial activity in yeast is closely related to its overall metabolism. However, the mitochondrial respiratory changes in response to adaptive thermotolerance are still poorly understood and have been rarely utilized for developing thermotolerant yeast cell factories. Here, adaptive evolution and transcriptional sequencing, as well as whole-genome-level gene knockout, were used to obtain a thermotolerant strain of <em>Saccharomyces cerevisiae</em>. Furthermore, thermotolerance and bioethanol production efficiency of the engineered strain were examined. Physiological evaluation showed the boosted fermentation capacity and suppressed mitochondrial respiratory activity in the thermotolerant strain. The improved fermentation produced an increased supply of adenosine triphosphate required for more active energy-consuming pathways. Transcriptome analysis revealed significant changes in the expression of the genes involved in the mitochondrial respiratory chain. Evaluation of mitochondria-associated gene knockout confirmed that <em>ADK1, DOC1,</em> or <em>MET7</em> were the key factors for the adaptive evolution of thermotolerance in the engineered yeast strain. Intriguingly, overexpression of <em>DOC1</em> with <em>TEF1</em> promoter regulation led to a 10.1% increase in ethanol production at 42 °C. The relationships between thermotolerance, mitochondrial activity, and respiration were explored, and a thermotolerant yeast strain was developed by altering the expression of mitochondrial respiration-related genes. This study provides a better understanding on the physiological mechanism of adaptive evolution of thermotolerance in yeast.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 2","pages":"Article 100108"},"PeriodicalIF":0.0,"publicationDate":"2023-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000401/pdfft?md5=fc8f07d0ab59477e3894e1846ec85ed5&pid=1-s2.0-S2667370323000401-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135248195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recombineering enables genome mining of novel siderophores in a non-model Burkholderiales strain","authors":"Xingyan Wang,&nbsp;Haibo Zhou,&nbsp;Xiangmei Ren,&nbsp;Hanna Chen,&nbsp;Lin Zhong,&nbsp;Xianping Bai,&nbsp;Xiaoying Bian","doi":"10.1016/j.engmic.2023.100106","DOIUrl":"https://doi.org/10.1016/j.engmic.2023.100106","url":null,"abstract":"<div><p>Iron is essential for bacterial survival, and most bacteria capture iron by producing siderophores. <em>Burkholderiales</em> bacteria produce various types of bioactive secondary metabolites, such as ornibactin and malleobactin siderophores. In this study, the genome analysis of <em>Burkholderiales</em> genomes showed a putative novel siderophore gene cluster <em>crb</em>, which is highly similar to the ornibactin and malleobactin gene clusters but does not have <em>pvdF</em>, a gene encoding a formyltransferase for N-<em>δ</em>‑hydroxy-ornithine formylation. Establishing the bacteriophage recombinase Redγ-Redαβ7029 mediated genome editing system in a non-model <em>Burkholderiales</em> strain <em>Paraburkholderia caribensis</em> CICC 10960 allowed the rapid identification of the products of <em>crb</em> gene cluster, caribactins A-F (<strong>1–6</strong>). Caribactins contain a special amino acid residue N-<em>δ</em>‑hydroxy-N-<em>δ</em>-acetylornithine (haOrn), which differs from the counterpart N-<em>δ</em>‑hydroxy-N-<em>δ</em>-formylornithine (hfOrn) in ornibactin and malleobactin, owing to the absence of <em>pvdF</em>. Gene inactivation showed that the acetylation of hOrn is catalyzed by CrbK, whose homologs probably not be involved in the biosynthesis of ornibactin and malleobactin, showing possible evolutionary clues of these siderophore biosynthetic pathways from different genera. Caribactins promote biofilm production and enhance swarming and swimming abilities, suggesting that they may play crucial roles in biofilm formation. This study also revealed that recombineering has the capability to mine novel secondary metabolites from non-model <em>Burkholderiales</em> species.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"3 3","pages":"Article 100106"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49891302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}