Journal of Microbiology最新文献

Advancements in the production of value-added products via methane biotransformation by methanotrophs: Current status and future perspectives.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2412024

Ok Kyung Lee, Jong Seok Lee, Yoonyong Yang, Moonsuk Hur, Kyung Jin Lee, Eun Yeol Lee

引用次数: 0

Progress and challenges in CRISPR/Cas applications in microalgae.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501028

Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee

{"title":"Progress and challenges in CRISPR/Cas applications in microalgae.","authors":"Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee","doi":"10.71150/jm.2501028","DOIUrl":"10.71150/jm.2501028","url":null,"abstract":"Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 3","pages":"e2501028"},"PeriodicalIF":3.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advancing microbial engineering through synthetic biology.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2503100

Ki Jun Jeong

引用次数: 0

Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501033

Jun Ren, So Hee Oh, Dokyun Na

引用次数: 0

Synthetic biology strategies for sustainable bioplastic production by yeasts. 利用酵母生产可持续生物塑料的合成生物学战略。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501022

Huong-Giang Le, Yongjae Lee, Sun-Mi Lee

{"title":"Synthetic biology strategies for sustainable bioplastic production by yeasts.","authors":"Huong-Giang Le, Yongjae Lee, Sun-Mi Lee","doi":"10.71150/jm.2501022","DOIUrl":"10.71150/jm.2501022","url":null,"abstract":"The increasing environmental concerns regarding conventional plastics have led to a growing demand for sustainable alternatives, such as biodegradable plastics. Yeast cell factories, specifically Saccharomyces cerevisiae and Yarrowia lipolytica, have emerged as promising platforms for bioplastic production due to their scalability, robustness, and ease of manipulation. This review highlights synthetic biology approaches aimed at developing yeast cell factories to produce key biodegradable plastics, including polylactic acid (PLA), polyhydroxyalkanoates (PHAs), and poly (butylene adipate-co-terephthalate) (PBAT). We explore recent advancements in engineered yeast strains that utilize various synthetic biology strategies, such as the incorporation of new genetic elements at the gene, pathway, and cellular system levels. The combined efforts of metabolic engineering, protein engineering, and adaptive evolution have enhanced strain efficiency and maximized product yields. Additionally, this review addresses the importance of integrating computational tools and machine learning into the Design-Build-Test-Learn cycle for strain development. This integration aims to facilitate strain development while minimizing effort and maximizing performance. However, challenges remain in improving strain robustness and scaling up industrial production processes. By combining advanced synthetic biology techniques with computational approaches, yeast cell factories hold significant potential for the sustainable and scalable production of bioplastics, thus contributing to a greener bioeconomy.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 3","pages":"e2501022"},"PeriodicalIF":3.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recent advances in targeted mutagenesis to expedite the evolution of biological systems.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501008

Seungjin Kim, Seungwon Lee, Hyun Gyu Lim

引用次数: 0

Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501006

Phuong Hoang Nguyen Tran, Taek Soon Lee

{"title":"Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast.","authors":"Phuong Hoang Nguyen Tran, Taek Soon Lee","doi":"10.71150/jm.2501006","DOIUrl":"10.71150/jm.2501006","url":null,"abstract":"Microbial biosynthesis using yeast species offers numerous advantages to produce industrially relevant biofuels and biochemicals. Conventional metabolic engineering approaches in yeast focus on biosynthetic pathways in the cytoplasm, but these approaches are disturbed by various undesired factors including metabolic crosstalk, competing pathways and insufficient precursors. Given that eukaryotic cells contain subcellular organelles with distinct physicochemical properties, an emerging strategy to overcome cytosolic pathway engineering bottlenecks is through repurposing these organelles as specialized microbial cell factories for enhanced production of valuable chemicals. Here, we review recent progress and significant outcomes of harnessing organelle engineering for biofuels and biochemicals production in both conventional and non-conventional yeasts. We highlight key engineering strategies for the compartmentalization of biosynthetic pathways within specific organelles such as mitochondria, peroxisomes, and endoplasmic reticulum; involved in engineering of signal peptide, cofactor and energy enhancement, organelle biogenesis and dual subcellular engineering. Finally, we discuss the potential and challenges of organelle engineering for future studies and propose an automated pipeline to fully exploit this approach.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 3","pages":"e2501006"},"PeriodicalIF":3.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recent advances in the Design-Build-Test-Learn (DBTL) cycle for systems metabolic engineering of Corynebacterium glutamicum.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501021

Subeen Jeon, Yu Jung Sohn, Haeyoung Lee, Ji Young Park, Dojin Kim, Eun Seo Lee, Si Jae Park

{"title":"Recent advances in the Design-Build-Test-Learn (DBTL) cycle for systems metabolic engineering of Corynebacterium glutamicum.","authors":"Subeen Jeon, Yu Jung Sohn, Haeyoung Lee, Ji Young Park, Dojin Kim, Eun Seo Lee, Si Jae Park","doi":"10.71150/jm.2501021","DOIUrl":"10.71150/jm.2501021","url":null,"abstract":"Existing microbial engineering strategies-encompassing metabolic engineering, systems biology, and systems metabolic engineering-have significantly enhanced the potential of microbial cell factories as sustainable alternatives to the petrochemical industry by optimizing metabolic pathways. Recently, systems metabolic engineering, which integrates tools from synthetic biology, enzyme engineering, omics technology, and evolutionary engineering, has been successfully developed. By leveraging modern engineering strategies within the Design-Build-Test-Learn (DBTL) cycle framework, these advancements have revolutionized the biosynthesis of valuable compounds. This review highlights recent progress in the metabolic engineering of Corynebacterium glutamicum, a versatile microbial platform, achieved through various approaches from traditional metabolic engineering to advanced systems metabolic engineering, all within the DBTL cycle. A particular focus is placed C5 platform chemicals derived from L-lysine, one of the key amino acid production pathways of C. glutamicum. The development of DBTL cycle-based metabolic engineering strategies for this process is discussed.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 3","pages":"e2501021"},"PeriodicalIF":3.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expanding the genetic code: In vivo approaches for incorporating non-proteinogenic monomers.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501005

Dongheon Lee, Suk Min Yun, Jong-Il Choi

{"title":"Expanding the genetic code: In vivo approaches for incorporating non-proteinogenic monomers.","authors":"Dongheon Lee, Suk Min Yun, Jong-Il Choi","doi":"10.71150/jm.2501005","DOIUrl":"10.71150/jm.2501005","url":null,"abstract":"The application of genetic code expansion has enabled the incorporation of non-canonical amino acids (ncAAs) into proteins, introducing novel functional groups and significantly broadening the scope of protein engineering. Over the past decade, this approach has extended beyond ncAAs to include non-proteinogenic monomers (npMs), such as β-amino acids and hydroxy acids. In vivo incorporation of these monomers requires maintaining orthogonality between endogenous and engineered aminoacyl-tRNA synthetase (aaRS)/tRNA pairs while optimizing the use of the translational machinery. This review introduces the fundamental principles of genetic code expansion and highlights the development of orthogonal aaRS/tRNA pairs and ribosomal engineering to incorporate npMs. Despite these advancements, challenges remain in engineering aaRS/tRNA pairs to accommodate npMs, especially monomers that differ significantly from L-α-amino acids due to their incompatibility with existing translational machinery. This review also introduces recent methodologies that allow aaRSs to recognize and aminoacylate npMs without reliance on the ribosomal translation system, thereby unlocking new possibilities for synthesizing biopolymers with chemically diverse monomers.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 3","pages":"e2501005"},"PeriodicalIF":3.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition.

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-02-01 Epub Date: 2025-02-27 DOI: 10.71150/jm.2411019

Seohyun Ahn, Min Cho, Michael J Sadowsky, Jeonghwan Jang

{"title":"Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition.","authors":"Seohyun Ahn, Min Cho, Michael J Sadowsky, Jeonghwan Jang","doi":"10.71150/jm.2411019","DOIUrl":"https://doi.org/10.71150/jm.2411019","url":null,"abstract":"Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were thought to be carried-out by anaerobic bacteria constrained to anoxic conditions as they use nitrate (NO3-) as a terminal electron acceptor instead of molecular O2. Three soil bacilli, Neobacillus spp. strains PS2-9 and PS3-12 and Bacillus salipaludis PS3-36, were isolated from rice paddy field soil in Korea. The bacterial strains were selected as possible candidates performing aerobic denitrification and DNRA as they observed to reduce NO3- and produce extracellular NH4+ regardless of oxygen presence at the initial screening. Whole genome sequencing revealed that these strains possessed all the denitrification and DNRA functional genes in their genomes, including the nirK, nosZ, nirB, and nrfA genes, which were simultaneously cotranscribed under aerobic condition. The ratio between the assimilatory and dissimilatory NO3- reduction pathways depended on the availability of a nitrogen source for cell growth, other than NO3-. Based on the phenotypic and transcriptional analyses of the NO3- reductions, all three of the facultative anaerobic strains reduced NO3- likely in both assimilatory and dissimilatory pathways under both aerobic and anoxic conditions. To our knowledge, this is the first report that describes coexistence of NO3- assimilation, denitrification, and DNRA in a Bacillus or Neobacillus strain under aerobic condition. These strains may play a pivotal role in the soil nitrogen cycle.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 2","pages":"e2411019"},"PeriodicalIF":3.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0