Journal of Microbiology

Reviews

Synthetic biology strategies for sustainable bioplastic production by yeasts: Huong-Giang Le, Yongjae Lee, Sun-Mi Lee; J. Microbiol. 2025;63(3):e2501022. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501022

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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.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Harnessing organelle engineering to facilitate biofuels and biochemicals production in yeast: Phuong Hoang Nguyen Tran, Taek Soon Lee; J. Microbiol. 2025;63(3):e2501006. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501006

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Abstract PDF

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.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Journal Article

Non-Mitochondrial Aconitase-2 Mediates the Transcription of Nuclear-Encoded Electron Transport Chain Genes in Fission Yeast: Ho-Jung Kim, Soo-Yeon Cho, Soo-Jin Jung, Yong-Jun Cho, Jung-Hye Roe, Kyoung-Dong Kim; J. Microbiol. 2024;62(8):639-648. Published online June 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00147-8

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Abstract: Aconitase-2 (Aco2) is present in the mitochondria, cytosol, and nucleus of fission yeast. To explore its function beyond the well-known role in the mitochondrial tricarboxylic acid (TCA) cycle, we conducted genome-wide profiling using the aco2ΔNLS mutant, which lacks a nuclear localization signal (NLS). The RNA sequencing (RNA-seq) data showed a general downregulation of electron transport chain (ETC) genes in the aco2ΔNLS mutant, except for those in the complex II, leading to a growth defect in respiratory-prone media. Complementation analysis with non-catalytic Aco2 [aco2ΔNLS + aco2(3CS)], where three cysteines were substituted with serine, restored normal growth and typical ETC gene expression. This suggests that Aco2's catalytic activity is not essential for its role in ETC gene regulation. Our mRNA decay assay indicated that the decrease in ETC gene expression was due to transcriptional regulation rather than changes in mRNA stability. Additionally, we investigated the Php complex's role in ETC gene regulation and found that ETC genes, except those within complex II, were downregulated in php3Δ and php5Δ strains, similar to the aco2ΔNLS mutant. These findings highlight a novel role for nuclear aconitase in ETC gene regulation and suggest a potential connection between the Php complex and Aco2.

Review

Prions in Microbes: The Least in the Most: Moonil Son , Sia Han , Seyeon Lee; J. Microbiol. 2023;61(10):881-889. Published online September 5, 2023; DOI: https://doi.org/10.1007/s12275-023-00070-4

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Abstract

Prions are infectious proteins that mostly replicate in self-propagating amyloid conformations (filamentous protein polymers) and consist of structurally altered normal soluble proteins. Prions can arise spontaneously in the cell without any clear reason and are generally considered fatal disease-causing agents that are only present in mammals. However, after the seminal discovery of two prions, [PSI+] and [URE3], in the eukaryotic model microorganism Saccharomyces cerevisiae, at least ten more prions have been discovered, and their biological and pathological effects on the host, molecular structure, and the relationship between prions and cellular components have been studied. In a filamentous fungus model, Podospora anserina, a vegetative incomparability-related [Het-s] prion that directly triggers cell death during anastomosis (hyphal fusion) was discovered. These prions in eukaryotic microbes have extended our understanding to overcome most fatal human prion/amyloid diseases. A prokaryotic microorganism (Clostridium botulinum) was reported to have a prion analog. The transcriptional regulators of C. botulinum-Rho can be converted into the self-replicating prion form ([RHO-X-C+]), which may affect global transcription. Here, we outline the major issues with prions in microbes and the lessons learned from the relatively uncovered microbial prion world.

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A Story Between s and S: [Het-s] Prion of the Fungus Podospora anserina
Moonil Son
Mycobiology.2024; 52(2): 85. CrossRef

Journal Articles

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica: Mincheol Kim , Hyunjun Cho , Won Young Lee; J. Microbiol. 2020;58(12):1018-1026. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0524-3

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Abstract

The gut microbiome provides ecological information about host animals, but we still have limited knowledge of the gut microbiome, particularly for animals inhabiting remote locations, such as Antarctica. Here, we compared fecal microbiota between southern elephant seals (Mirounga leonina) and Weddell seals (Leptonychotes weddelli), that are top predatory marine mammals in the Antarctic ecosystem, using 16S rRNA amplicon sequencing and assessed the relationships of the gut microbial communities to functional profiles using gut metabolite analysis. The bacterial community did not differ significantly by host species or sex at the phylum level, but the distinction at the family level was obvious. The family Ruminococcaceae (Firmicutes) was more abundant in southern elephant seals than in Weddell seals, and the families Acidaminococcaceae (Firmicutes) and Pasteurellaceae (Gammaproteobacteria) were uniquely present in Weddell seals. The fecal bacterial community structure was distinctively clustered by host species, with only 6.7% of amplicon sequence variants (ASVs) shared between host species. This result implies that host phylogeny rather than other factors, such as diet or age, could be the major driver of fecal microbiotic diversification. Interestingly, there was no apparent sex effect on bacterial community structure in Weddell seals, but the effect of sex was pronounced in adult southern elephant seals mainly due to the prevalence of Edwardsiella sp., suggesting that extreme sexual dimorphism may modulate the gut microbiota of southern elephant seals. Unlike the clear distinction in the taxonomic composition of fecal bacterial communities, there were no discernible differences in the profiles of potential microbial functions and gut metabolites between host species or sexes, indicating that functional redundancy dominates the gut microbiota of seals surveyed in this study.

Citations

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Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices
Samuel Degregori, Xiaolin Wang, Akhil Kommala, Noah Schulhof, Sadaf Moradi, Allison MacDonald, Kaitlin Eblen, Sophia Jukovich, Emma Smith, Emily Kelleher, Kota Suzuki, Zoey Hall, Rob Knight, Katherine Ryan Amato
Biological Reviews.2024;[Epub] CrossRef
Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation
Aggeliki Dosi, Alexandra Meziti, Eleni Tounta, Kimon Koemtzopoulos, Anastasia Komnenou, Panagiotis Dendrinos, Konstantinos Kormas, Bernadette J. Connors
Microbiology Spectrum.2024;[Epub] CrossRef
Trait biases in microbial reference genomes
Sage Albright, Stilianos Louca
Scientific Data.2023;[Epub] CrossRef
Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project
Manuel Ochoa-Sánchez, Eliana Paola Acuña Gomez, Lia Ramírez-Fenández, Luis E. Eguiarte, Valeria Souza
PeerJ.2023; 11: e15978. CrossRef
Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean
Emanuela Buschi, Antonio Dell’Anno, Michael Tangherlini, Sergio Stefanni, Marco Lo Martire, Laura Núñez-Pons, Conxita Avila, Cinzia Corinaldesi
Frontiers in Microbiology.2023;[Epub] CrossRef
Age as a primary driver of the gut microbial composition and function in wild harbor seals
A. Pacheco-Sandoval, A. Lago-Lestón, A. Abadía-Cardoso, E. Solana-Arellano, Y. Schramm
Scientific Reports.2022;[Epub] CrossRef
Effect of Different Dietary Regimes on the Gut Microbiota and Fecal Metabolites of Père David’s Deer
Junai Zhen, Yijun Ren, Huidan Zhang, Xueli Yuan, Libo Wang, Hua Shen, Ping Liu, Yuqing Chen
Animals.2022; 12(5): 584. CrossRef
Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites
Jorge Doña, Stephany Virrueta Herrera, Tommi Nyman, Mervi Kunnasranta, Kevin P. Johnson
Frontiers in Microbiology.2021;[Epub] CrossRef
Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii)
Constanza Toro‐Valdivieso, Frederick Toro, Samuel Stubbs, Eduardo Castro‐Nallar, Barbara Blacklaws
MicrobiologyOpen.2021;[Epub] CrossRef

Roles of Dhh1 RNA helicase in yeast filamentous growth: Analysis of N-terminal phosphorylation residues and ATPase domains: Eunji Lee , Daehee Jung , Jinmi Kim; J. Microbiol. 2020;58(10):853-858. Published online September 29, 2020; DOI: https://doi.org/10.1007/s12275-020-0431-7

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Abstract

In yeast Saccharomyces cerevisiae, the Dhh1 protein, a member of the DEAD-box RNA helicase, stimulates Dcp2/Dcp1- mediated mRNA decapping and functions as a general translation repressor. Dhh1 also positively regulates translation of a selected set of mRNAs, including Ste12, a transcription factor for yeast mating and pseudohyphal growth. Given the diverse functions of Dhh1, we investigated whether the putative phosphorylation sites or the conserved motifs for the DEADbox RNA helicases were crucial in the regulatory roles of Dhh1 during pseudohyphal growth. Mutations in the ATPase A or B motif (DHH1-K96R or DHH1-D195A) showed significant defects in pseudohyphal colony morphology and agar invasive phenotypes. The N-terminal phospho-mimetic mutation, DHH1-T16E, showed defects in pseudohyphal phenotypes. Decreased levels of Ste12 protein were also observed in these pseudohyphal-defective mutant cells under filamentous- inducing low nitrogen conditions. We suggest that the ATPase motifs and the Thr16 phosphorylation site of Dhh1 are crucial to its regulatory roles in pseudohyphal growth under low nitrogen conditions.

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Biological implications of decapping: beyond bulk mRNA decay
Fivos Borbolis, Popi Syntichaki
The FEBS Journal.2022; 289(6): 1457. CrossRef
The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth
Anuj Kumar
Annual Review of Genetics.2021; 55(1): 1. CrossRef

Omp16, a conserved peptidoglycan-associated lipoprotein, is involved in Brucella virulence in vitro: Feijie Zhi , Dong Zhou , Junmei Li , Lulu Tian , Guangdong Zhang , Yaping Jin , Aihua Wang; J. Microbiol. 2020;58(9):793-804. Published online September 1, 2020; DOI: https://doi.org/10.1007/s12275-020-0144-y

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Abstract

Brucella, the bacterial agent of common zoonotic brucellosis, primarily infects specific animal species. The Brucella outer membrane proteins (Omps) are particularly attractive for developing vaccine and improving diagnostic tests and are associated with the virulence of smooth Brucella strains. Omp16 is a homologue to peptidoglycan-associated lipoproteins (Pals), and an omp16 mutant has not been generated in any Brucella strain until now. Very little is known about the functions and pathogenic mechanisms of Omp16 in Brucella. Here, we confirmed that Omp16 has a conserved Pal domain and is highly conserved in Brucella. We attempted to delete omp16 in Brucella suis vaccine strain 2 (B. suis S2) without success, which shows that Omp16 is vital for Brucella survival. We acquired a B. suis S2 Omp16 mutant via conditional complementation. Omp16 deficiency impaired Brucella outer membrane integrity and activity in vitro. Moreover, inactivation of Omp16 decreased bacterial intracellular survival in macrophage RAW 264.7 cells. B. suis S2 and its derivatives induced marked expression of IL-1β, IL-6, and TNF-α mRNA in Raw 264.7 cells. Whereas inactivation of Omp16 in Brucella enhanced IL-1β and IL-6 expression in Raw 264.7 cells. Altogether, these findings show that the Brucella Omp16 mutant was obtained via conditional complementation and confirmed that Omp16 can maintain outer membrane integrity and be involved in bacterial virulence in Brucella in vitro and in vivo. These results will be important in uncovering the pathogenic mechanisms of Brucella.

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Neurobrucellosis (Brucella ceti) in striped dolphins (Stenella coeruleoalba): Immunohistochemical studies on immune response and neuroinflammation
Agustín Rebollada-Merino, Federica Giorda, Martí Pumarola, Laura Martino, Alberto Gomez-Buendia, Umberto Romani-Cremaschi, Cristina Casalone, Virginia Mattioda, Fabio Di Nocera, Giuseppe Lucifora, Antonio Petrella, Lucas Domínguez, Mariano Domingo, Carla
Veterinary Pathology.2025; 62(2): 226. CrossRef
Enhancing host defense against Brucella: The immune effect exerted by anti-OMP16 monoclonal antibody
Yunyi Zhai, Hui Wang, Kaihui Sun, Ye Yuan, Shurong Yin, Jiaoyang Fang, Weifang Zheng, Gaowa Wudong, Xiaofang Liu, Yuanhao Yang, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
International Immunopharmacology.2025; 148: 114142. CrossRef
Brucella mediates autophagy, inflammation, and apoptosis to escape host killing
Yaqiong Qin, Gengxu Zhou, Fengyuan Jiao, Chuan Cheng, Chi Meng, Lingjie Wang, Shengping Wu, Cailiang Fan, Jixiang Li, Bo Zhou, Yuefeng Chu, Hanwei Jiao
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
A Thermosensitive and Degradable Chitin-Based Hydrogel as a Brucellosis Vaccine Adjuvant
Ruibao Ju, Yanjing Lu, Zhiwen Jiang, Jinhua Chi, Shuo Wang, Wanshun Liu, Yanbo Yin, Baoqin Han
Polymers.2024; 16(19): 2815. CrossRef
The (p)ppGpp synthetase Rsh promotes rifampicin tolerant persister cell formation in Brucella abortus by regulating the type II toxin-antitoxin module mbcTA
Xiaofang Liu, Pingping Wang, Ningqiu Yuan, Yunyi Zhai, Yuanhao Yang, Mingyue Hao, Mingxing Zhang, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
Frontiers in Microbiology.2024;[Epub] CrossRef
Pal Affects the Proliferation in Macrophages and Virulence of Brucella, and as Mucosal Adjuvants, Provides an Effective Protection to Mice Against Salmonella Enteritidis
Yubin Chen, Yanfang Fu, Lingcong Kong, Fengjie Wang, Xiaowei Peng, Zhiqiang Zhang, Qiumei Shi, Qingmin Wu, Tonglei Wu
Current Microbiology.2023;[Epub] CrossRef
Clearance of bacteria from lymph nodes in sheep immunized with Brucella suis S2 vaccine is associated with M1 macrophage activation
Si Chen, Yuanyuan Chen, Zizhuo Jiao, Chengqiang Wang, Dantong Zhao, Yongbin Liu, Wenguang Zhang, Shihua Zhao, Bin Yang, Qinan Zhao, Shaoyin Fu, Xiaolong He, Qiaoling Chen, Churiga Man, Guoying Liu, Xuefeng Wei, Li Du, Fengyang Wang
Veterinary Research.2023;[Epub] CrossRef
A Brucella Omp16 Conditional Deletion Strain Is Attenuated in BALB/c Mice
Feijie Zhi, Jiaoyang Fang, Weifang Zheng, Junmei Li, Guangdong Zhang, Dong Zhou, Yaping Jin, Aihua Wang
Journal of Microbiology and Biotechnology.2022; 32(1): 6. CrossRef
A designed peptide-based vaccine to combat Brucella melitensis, B. suis and B. abortus: Harnessing an epitope mapping and immunoinformatics approach
Hossein Tarrahimofrad, Javad Zamani, Michael R. Hamblin, Maryam Darvish, Hamed Mirzaei
Biomedicine & Pharmacotherapy.2022; 155: 113557. CrossRef
A LysR Transcriptional Regulator Manipulates Macrophage Autophagy Flux During Brucella Infection
Lu Zhang, Siyuan Yu, Xinnuan Ning, Hui Fang, Jie Li, Feijie Zhi, Junmei Li, Dong Zhou, Aihua Wang, Yaping Jin
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Uncovering the Hidden Credentials ofBrucellaVirulence
R. Martin Roop, Ian S. Barton, Dariel Hopersberger, Daniel W. Martin
Microbiology and Molecular Biology Reviews.2021;[Epub] CrossRef
RNA-Seq Analysis Reveals the Role of Omp16 in Brucella-Infected RAW264.7 Cells
Dong Zhou, Feijie Zhi, Jiaoyang Fang, Weifang Zheng, Junmei Li, Guangdong Zhang, Lei Chen, Yaping Jin, Aihua Wang
Frontiers in Veterinary Science.2021;[Epub] CrossRef

Reviews

The osmotic stress response operon betIBA is under the functional regulation of BetI and the quorum-sensing regulator AnoR in Acinetobacter nosocomialis: Bindu Subhadra , Surya Surendran , Bo Ra Lim , Jong Sung Yim , Dong Ho Kim , Kyungho Woo , Hwa-Jung Kim , Man Hwan Oh , Chul Hee Choi; J. Microbiol. 2020;58(6):519-529. Published online May 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0186-1

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Abstract

Adaptation to changing environmental conditions is crucial for the survival of microorganisms. Bacteria have evolved various mechanisms to cope with osmotic stress. Here, we report the identification and functional characterization of the osmotic stress response operon, betIBA, in Acinetobacter nosocomialis. The betIBA operon encodes enzymes that are important for the conversion of choline to the osmoprotectant, glycine betaine. The betIBA operon is polycistronic and is under the regulation of the first gene, betI, of the same operon. A bioinformatics analysis revealed the presence of a BetI-binding motif upstream of the betIBA operon, and electrophoretic mobility shift assays confirmed the specific binding of BetI. An mRNA expression analysis revealed that expression of betI, betB, and betA genes is elevated in a betIeletion mutant compared with the wild type, confirming that the autorepressor BetI represses the betIBA operon in A. nosocomialis. We further found that the betIBA operon is under the transcriptional control of the quorum-sensing (QS) regulator, AnoR in, A. nosocomialis. A subsequent analysis of the impact of BetI on expression of the QS genes, anoR and anoI, demonstrated that BetI acts as a repressor of anoR and anoI. In addition, it was noticed that the osmotic stress response regulator, OmpR might play an important role in controlling the expression of betIBA operon in A. nosocomialis. Collectively, these data demonstrate that QS and osmotic stress-response systems are correlated in A. nosocomialis and that the expression of genes in both systems is finely tuned by various feedback loops depending on osmolarity conditions.

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Metabolome analysis revealed the critical role of betaine for arsenobetaine biosynthesis in the marine medaka (Oryzias melastigma)
Qianyu Zhao, Qiao-Guo Tan, Wen-Xiong Wang, Peng Zhang, Zijun Ye, Liping Huang, Wei Zhang
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Yuyuan Cai, Xuehong Zhang, Michael J. Federle
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Sergey Peltek, Svetlana Bannikova, Tamara M. Khlebodarova, Yulia Uvarova, Aleksey M. Mukhin, Gennady Vasiliev, Mikhail Scheglov, Aleksandra Shipova, Asya Vasilieva, Dmitry Oshchepkov, Alla Bryanskaya, Vasily Popik
International Journal of Molecular Sciences.2024; 25(22): 12059. CrossRef
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Helen Park, Matthew Faulkner, Helen S Toogood, Guo-Qiang Chen, Nigel Scrutton
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The Effect of Proline on the Freeze-Drying Survival Rate of Bifidobacterium longum CCFM 1029 and Its Inherent Mechanism
Shumao Cui, Wenrui Zhou, Xin Tang, Qiuxiang Zhang, Bo Yang, Jianxin Zhao, Bingyong Mao, Hao Zhang
International Journal of Molecular Sciences.2022; 23(21): 13500. CrossRef
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Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
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Jia Guo, Xingmei Deng, Yu Zhang, Shengnan Song, Tianyi Zhao, Dexin Zhu, Shuzhu Cao, Peter Ivanovic Baryshnikov, Gang Cao, Hugh T. Blair, Chuangfu Chen, Xinli Gu, Liangbo Liu, Hui Zhang
International Journal of Molecular Sciences.2022; 23(17): 9905. CrossRef
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Gwendolyn J. Gregory, E. Fidelma Boyd
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MINIREVIEW] Fungi in salterns: Dawoon Chung† , Haryun Kim† , Hyun Seok Choi; J. Microbiol. 2019;57(9):717-724. Published online August 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9195-3

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Abstract

Salterns are hypersaline extreme environments with unique physicochemical properties such as a salinity gradient. Although the investigation of microbiota in salterns has focused on archaea and bacteria, diverse fungi also thrive in the brine and soil of salterns. Fungi isolated from salterns are represented by black yeasts (Hortaea werneckii, Phaeotheca triangularis, Aureobasidium pullulans, and Trimmatostroma salinum), Cladosporium, Aspergillus, and Penicillium species. Most studies on saltern-derived fungi gave attention to black yeasts and their physiological characteristics, including growth under various culture conditions. Since then, biochemical and molecular tools have been employed to explore adaptation of these fungi to salt stress. Genome databases of several fungi in salterns are now publicly available and being used to elucidate salt tolerance mechanisms and discover the target genes for agricultural and industrial applications. Notably, the number of enzymes and novel metabolites known to be produced by diverse saltern-derived fungi has increased significantly. Therefore, fungi in salterns are not only interesting and important subjects to study fungal biodiversity and adaptive mechanisms in extreme environments, but also valuable bioresources with potential for biotechnological applications.

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Eman H. Zaghloul, Hala H. Abdel-Latif, Asmaa Elsayis, Sahar W.M. Hassan
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[MINIREVIEW] The nature of meiotic chromosome dynamics and recombination in budding yeast: Soogil Hong , Jeong Hwan Joo , Hyeseon Yun , Keunpil Kim; J. Microbiol. 2019;57(4):221-231. Published online January 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8541-9

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Abstract

During meiosis, crossing over allows for the exchange of genes between homologous chromosomes, enabling their segregation and leading to genetic variation in the resulting gametes. Spo11, a topoisomerase-like protein expressed in eukaryotes, and diverse accessory factors induce programmed doublestrand breaks (DSBs) to initiate meiotic recombination during the early phase of meiosis after DNA replication. DSBs are further repaired via meiosis-specific homologous recombination. Studies on budding yeast have provided insights into meiosis and genetic recombination and have improved our understanding of higher eukaryotic systems. Cohesin, a chromosome-associated multiprotein complex, mediates sister chromatid cohesion (SCC), and is conserved from yeast to humans. Diverse cohesin subunits in budding yeast have been identified in DNA metabolic pathways, such as DNA replication, chromosome segregation, recombination, DNA repair, and gene regulation. During cell cycle, SCC is established by multiple cohesin subunits, which physically bind sister chromatids together and modulate proteins that involve in the capturing and separation of sister chromatids. Cohesin components include at least four core subunits that establish and maintain SCC: two structural maintenance chromosome subunits (Smc1 and Smc3), an α-kleisin subunit (Mcd1/Scc1 during mitosis and Rec8 during meiosis), and Scc3/Irr1 (SA1 and SA2). In addition, the cohesin-associated factors Pds5 and Rad61 regulate structural modifications and cell cyclespecific dynamics of chromatin to ensure accurate chromosome segregation. In this review, we discuss SCC and the recombination pathway, as well as the relationship between the two processes in budding yeast, and we suggest a possible conserved mechanism for meiotic chromosome dynamics from yeast to humans.

Citations

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RPA interacts with Rad52 to promote meiotic crossover and noncrossover recombination
Jeong H Joo, Soogil Hong, Mika T Higashide, Eui-Hwan Choi, Seobin Yoon, Min-Su Lee, Hyun Ah Kang, Akira Shinohara, Nancy Kleckner, Keun P Kim
Nucleic Acids Research.2024; 52(7): 3794. CrossRef
Elevated expression of exogenous RAD51 enhances the CRISPR/Cas9-mediated genome editing efficiency
Seo Jung Park, Seobin Yoon, Eui-Hwan Choi, Hana Hyeon, Kangseok Lee, Keun Pil Kim
BMB Reports.2023; 56(2): 102. CrossRef
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B. Aravind, Kutubuddin Molla, Satendra K. Mangrauthia, Gireesha Mohannath
Journal of Plant Biochemistry and Biotechnology.2023; 32(4): 661. CrossRef
A Method for Physical Analysis of Recombination Intermediates in Saccharomyces cerevisiae
Kiwon Rhee, Hyungseok Choi, Keun P. Kim, Jeong H. Joo
Journal of Microbiology.2023; 61(11): 939. CrossRef
The Kleisin Subunits of Cohesin Are Involved in the Fate Determination of Embryonic Stem Cells
Young Eun Koh, Eui-Hwan Choi, Jung-Woong Kim, Keun Pil Kim
Molecules and Cells.2022; 45(11): 820. CrossRef
Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control
Tina L. Sing, Gloria A. Brar, Elçin Ünal
Annual Review of Genetics.2022; 56(1): 89. CrossRef
Yeast polyubiquitin unit regulates synaptonemal complex formation and recombination during meiosis
Min-Kyung Jo, Kiwon Rhee, Keun Pil Kim, Soogil Hong
Journal of Microbiology.2022; 60(7): 705. CrossRef
Histone variant H2A.Z promotes meiotic chromosome axis organization in Saccharomyces cerevisiae
Lorencia Chigweshe, Amy J MacQueen, Scott G Holmes, J Berman
G3 Genes|Genomes|Genetics.2022;[Epub] CrossRef
Meiosis-specific cohesin complexes display essential and distinct roles in mitotic embryonic stem cell chromosomes
Eui-Hwan Choi, Seobin Yoon, Young Eun Koh, Tae Kyung Hong, Jeong Tae Do, Bum-Kyu Lee, Yoonsoo Hahn, Keun P. Kim
Genome Biology.2022;[Epub] CrossRef
Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast
Jeong Hwan Joo, Hyun Ah Kang, Keun Pil Kim, Soogil Hong
Journal of Microbiology.2022; 60(2): 177. CrossRef
The multiple roles of RAB GTPases in female and male meiosis
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The synaptonemal complex central region modulates crossover pathways and feedback control of meiotic double-strand break formation
Min-Su Lee, Mika T Higashide, Hyungseok Choi, Ke Li, Soogil Hong, Kangseok Lee, Akira Shinohara, Miki Shinohara, Keun P Kim
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From coins to cancer therapy: Gold, silver and copper complexes targeting human topoisomerases
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E2F1 facilitates DNA break repair by localizing to break sites and enhancing the expression of homologous recombination factors
Eui-Hwan Choi, Keun Pil Kim
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Recruitment of Rec8, Pds5 and Rad61/Wapl to meiotic homolog pairing, recombination, axis formation and S-phase
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Journal Articles

Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables: Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh; J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-019-8487-y

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Abstract

White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

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Effects of total microbiota-containing backslop from 450-day-fermented kimchi on microbe and metabolite dynamics
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Food Chemistry.2025; 468: 142420. CrossRef
Effects of storage temperature on the diversity of white colony-forming yeast and correlations between bacterial and yeast communities in salted kimchi cabbage
Chan-Il Bae, Yoon-Soo Gwak, Su-Jeong Eom, Shinyoung Lee, Mi-Ju Kim
Food Science and Biotechnology.2025; 34(4): 1001. CrossRef
Effects of white colony-forming yeast on microbial communities and metabolites in kimchi
Yoon-Soo Gwak, Shinyoung Lee, Chan-Il Bae, Su-Jeong Eom, Mi-Ju Kim
Food Chemistry.2025; 465: 142059. CrossRef
D-Limonene Inhibits Pichia kluyveri Y-11519 in Sichuan Pickles by Disrupting Metabolism
Chaoyi Zeng, Yue Sun, Haoran Lin, Ziyu Li, Qing Zhang, Ting Cai, Wenliang Xiang, Jie Tang, Patchanee Yasurin
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Ting Mi, Yao Jin, Yulan Che, Jun Huang, Rongqing Zhou, Chongde Wu
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Joon Yong Kim, Seong-Eun Park, Eun-Ju Kim, Seung-Ho Seo, Tae Woong Whon, Kwang-Moon Cho, Sun Jae Kwon, Seong Woon Roh, Hong-Seok Son
Food Research International.2022; 154: 111044. CrossRef
Safety assessment of white colony-forming yeasts in kimchi
Chang Hee Jeong, Joon Yong Kim, Young Joon Oh, Hye In Ko, Seong Woon Roh, Sung Wook Hong, Hyuk Cheol Kwon, Sung Gu Han, Tae Woon Kim
Food Microbiology.2022; 106: 104057. CrossRef
Safety Assessment of White Colony-Forming Yeasts in Kimchi
Chang Hee Jeong, Joon Yong Kim, Young Joon Oh, Hye In Ko, Seong Woon Roh, Sung Wook Hong, Hyuk Cheol Kwon, Sung Gu Han, Tae-Woon Kim
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Real-time PCR assays for the quantitative detection of Kazachstania servazzii and Candida sake related to undesirable white colony on kimchi
Mi-Ju Kim, Sung-gi Min, So Won Shin, Jiyong Shin, Hae-Yeong Kim
Food Control.2021; 125: 107984. CrossRef
Yarrowia lipolytica: a multitalented yeast species of ecological significance
Dmitry Mamaev, Renata Zvyagilskaya
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Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
Scientific Data.2021;[Epub] CrossRef
Growth Inhibitory Effect of Garlic Powder and Cinnamon Extract on White Colony-Forming Yeast in Kimchi
Mi-Ju Kim, Seong-Eun Kang, Chang Hee Jeong, Sung-Gi Min, Sung Wook Hong, Seong Woon Roh, Deok-Young Jhon, Tae-Woon Kim
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Impact of fermentation conditions on the diversity of white colony-forming yeast and analysis of metabolite changes by white colony-forming yeast in kimchi
Mi-Ju Kim, Hae-Won Lee, Joon Yong Kim, Seong Eun Kang, Seong Woon Roh, Sung Wook Hong, Seung Ran Yoo, Tae-Woon Kim
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Se Hee Lee, Tae Woong Whon, Seong Woon Roh, Che Ok Jeon
Applied Microbiology and Biotechnology.2020; 104(18): 7731. CrossRef
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Lynne Faherty, Clifton Lewis, Matt McElheron, Niall Garvey, Róisín Duggan, Ben Shovlin, Tadhg Ó Cróinín, Kevin P. Byrne, Caoimhe E. O’Brien, Kenneth H. Wolfe, Geraldine Butler, Antonis Rokas
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Sera Jung, Hyelyeon Hwang, Jong-Hee Lee
Food Control.2019; 106: 106701. CrossRef

[PROTOCOL] Structural analysis of N-/O-glycans assembled on proteins in yeasts: Eun Jung Thak , Jungho Kim , Dong-Jik Lee , Jeong Yoon Kim , Hyun Ah Kang; J. Microbiol. 2018;56(1):11-23. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7468-x

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Abstract

Protein glycosylation, the most universal and diverse posttranslational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species- and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N- and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.

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NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N‐LINKED GLYCANS
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Yeast synthetic biology for designed cell factories producing secretory recombinant proteins
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The protein and neutral lipid composition of lipid droplets isolated from the fission yeast, Schizosaccharomyces pombe: Alex Meyers , Karuna Chourey , Taylor M. Weiskittel , Susan Pfiffner , John R. Dunlap , Robert L. Hettich , Paul Dalhaimer; J. Microbiol. 2017;55(2):112-122. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6205-1

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Abstract

Lipid droplets consist of a core of neutral lipids surrounded by a phospholipid monolayer with bound proteins. Much of the information on lipid droplet function comes from proteomic and lipodomic studies that identify the components of droplets isolated from organisms throughout the phylogenetic tree. Here, we add to that important inventory by reporting lipid droplet factors from the fission yeast, Schizosaccharomyces pombe. Unique to this study was the fact that cells were cultured in three different environments: 1) late log growth phase in glucose-based media, 2) stationary phase in glucosebased media, and 3) late log growth phase in media containing oleic acid. We confirmed colocalization of major factors with lipid droplets using live-cell fluorescent microscopy. We also analyzed droplets from each of the three conditions for sterol ester (SE) and triacylglycerol (TAG) content, along with their respective fatty acid compositions. We identified a previously undiscovered lipid droplet protein, Vip1p, which affects droplet size distribution. The results provide further insight into the workings of these ubiquitous organelles.

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Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast
Anna Marešová, Michaela Grulyová, Miluše Hradilová, Viacheslav Zemlianski, Jarmila Princová, Martin Převorovský, Cathy Savage-Dunn
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Mild Heat Stress Alters the Physical State and Structure of Membranes in Triacylglycerol-Deficient Fission Yeast, Schizosaccharomyces pombe
Péter Gudmann, Imre Gombos, Mária Péter, Gábor Balogh, Zsolt Török, László Vígh, Attila Glatz
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Yi Jin, Yanjie Tan, Jian Wu, Zhuqing Ren
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Oleaginous yeasts: Time to rethink the definition?
José Manuel Salvador López, Meriam Vandeputte, Inge N. A. Van Bogaert
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Proteomic and lipidomic analyses of lipid droplets in Aurantiochytrium limacinum ATCC MYA-1381
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ER-localized phosphatidylethanolamine synthase plays a conserved role in lipid droplet formation
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Lipid Droplet Nucleation
Abdou Rachid Thiam, Elina Ikonen
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Metabolism of Storage Lipids and the Role of Lipid Droplets in the Yeast Schizosaccharomyces pombe
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Lipid Droplets in Neurodegenerative Disorders
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The Peroxygenase Activity of the Aspergillus flavus Caleosin, AfPXG, Modulates the Biosynthesis of Aflatoxins and Their Trafficking and Extracellular Secretion via Lipid Droplets
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Application of high-resolution melting analysis for differentiation of spoilage yeasts: Mine Erdem , Zülal Kesmen , Esra Özbekar , Bülent Çetin , Hasan Yetim; J. Microbiol. 2016;54(9):618-625. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6017-8

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Abstract

A new method based on high resolution melting (HRM) analysis was developed for the differentiation and classification of the yeast species that cause food spoilage. A total 134 strains belonging to 21 different yeast species were examined to evaluate the discriminative power of HRM analysis. Two different highly variable DNA regions on the 26 rRNA gene were targeted to produce the HRM profiles of each strain. HRMbased grouping was compared and confirmed by (GTG)5 rep- PCR fingerprinting analysis. All of the yeast species belonging to the genera Pichia, Candida, Kazachstania, Kluyveromyces, Debaryomyces, Dekkera, Saccharomyces, Torulaspora, Ustilago, and Yarrowia, which were produced as species-specific HRM profiles, allowed discrimination at species and/or strain level. The HRM analysis of both target regions provided successful discrimination that correlated with rep-PCR fingerprinting analysis. Consequently, the HRM analysis has the potential for use in the rapid and accurate classification and typing of yeast species isolated from different foods to determine their sources and routes as well as to prevent contamination.

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Review

REVIEW] Hgc1-Cdc28–how much does a single protein kinase do in the regulation of hyphal development in Candida albicans?: Yue Wang; J. Microbiol. 2016;54(3):170-177. Published online February 27, 2016; DOI: https://doi.org/10.1007/s12275-016-5550-9

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Abstract

The fungal human pathogen Candida albicans can cause invasive infection with high mortality rates. A key virulence factor is its ability to switch between three morphologies: yeast, pseudohyphae and hyphae. In contrast to the ovalshaped unicellular yeast cells, hyphae are highly elongated, tube-like, and multicellular. A long-standing question is what coordinates all the cellular machines to construct cells with distinct shapes. Hyphal-specific genes (HSGs) are thought to hold the answer. Among the numerous HSGs found, only UME6 and HGC1 are required for hyphal development. UME6 encodes a transcription factor that regulates many HSGs including HGC1. HGC1 encodes a G1 cyclin which partners with the Cdc28 cyclin-dependent kinase. Hgc1- Cdc28 simultaneously phosphorylates and regulates multiple substrates, thus controlling multiple cellular apparatuses for morphogenesis. This review is focused on major progresses made in the past decade on Hgc1’s roles and regulation in C. albicans hyphal development and other traits important for infection.

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