Journal of Microbiology

Journal Article

Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces cerevisiae: Ju-Hee Choi, Oyungoo Bayarmagnai, Sung-Ho Bae; J. Microbiol. 2024;62(9):749-758. Published online July 12, 2024; DOI: https://doi.org/10.1007/s12275-024-00152-x

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Abstract: DNA double-strand break (DSB) repair is a fundamental cellular process crucial for maintaining genome stability, with homologous recombination and non-homologous end joining as the primary mechanisms, and various alternative pathways such as single-strand annealing (SSA) and microhomology-mediated end joining also playing significant roles under specific conditions. IRC genes were previously identified as part of a group of genes associated with increased levels of Rad52 foci in Saccharomyces cerevisiae. In this study, we investigated the effects of IRC gene mutations on DSB repair, focusing on uncharacterized IRC10, 19, 21, 22, 23, and 24. Gene conversion (GC) assay revealed that irc10Δ, 22Δ, 23Δ, and 24Δ mutants displayed modest increases in GC frequencies, while irc19Δ and irc21Δ mutants exhibited significant reductions. Further investigation revealed that deletion mutations in URA3 were not generated in irc19Δ mutant cells following HO-induced DSBs. Additionally, irc19Δ significantly reduced frequency of SSA, and a synergistic interaction between irc19Δ and rad52Δ was observed in DSB repair via SSA. Assays to determine the choice of DSB repair pathways indicated that Irc19 is necessary for generating both GC and deletion products. Overall, these results suggest a potential role of Irc19 in DSB repair pathways, particularly in end resection process.

Review

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

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In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Journal Articles

Prevalence of Indigenous Antibiotic‑Resistant Salmonella Isolates and Their Application to Explore a Lytic Phage vB_SalS_KFSSM with an Intra‑Broad Specificity: Jaein Choe , Su-Hyeon Kim , Ji Min Han , Jong-Hoon Kim , Mi-Sun Kwak , Do-Won Jeong , Mi-Kyung Park; J. Microbiol. 2023;61(12):1063-1073. Published online January 2, 2024; DOI: https://doi.org/10.1007/s12275-023-00098-6

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Abstract: The consumption of fresh produce has led to increase in antibiotic-resistant (AR) Salmonella outbreaks. In this study, indigenous Salmonella was isolated from a total of two hundred-two samples including fresh produce and agricultural environmental samples in Korea. After biochemical confirmation using the Indole, Methyl Red, Voges-Proskauer, Citrate tests, presumable Salmonella isolates were identified by 16S rRNA sequencing. Identified Salmonella isolates were evaluated for antibiotic susceptibility against twenty-two antibiotics. The specificity and the efficiency of plating (EOP) of vB_SalS_KFSSM were evaluated against fifty-three bacterial strains. Twenty-five suspected Salmonella were isolated and confirmed by the positive
result
for methyl red and citrate, of which ten were identified as Salmonella spp. through 16S rRNA gene sequencing. Eight Salmonella isolates (4.0%, n = 8/202) were resistant to at least one antibiotic, among which five were multi-drug resistant. As a lytic phage against Salmonella spp. CMGS-1, vB_SalS_KFSSM was isolated from cow manure. The phage was observed as a tailed phage belonging to the class Caudoviricetes. It exhibited an intra-broad specificity against four indigenous AR Salmonella isolates, two indigenous Salmonella isolates, and five other Salmonella serotypes with great efficiencies (EOP ≥ 0.75). Thus, this study suggested the potential of vB_SalS_KFSSM to combat indigenous AR Salmonella.

Characterization of antibiotic-resistant, coagulase-negative staphylococci from fresh produce and description of Staphylococcus shinii sp. nov. isolated from chives: Gyu-Sung Cho , Bo Li , Erik Brinks , Charles , M.A.P. Franz; J. Microbiol. 2022;60(9):877-889. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2100-5

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Abstract

Coagulase-negative Staphylococcus (CoNS) species may possess antibiotic resistance genes and have been associated with nosocomial infections. In this study, 91 CoNS with decreased susceptibility to oxacillin were isolated from fresh produce using oxacillin containing agar plates. Their antibiotic resistances were determined phenotypically and all isolates were identified by rep-PCR, 16S rRNA and rpoB gene sequencing. Furthermore, the genomes of representative strains were sequenced in order to confirm species identification by phylogenomics. The majority (64 of 91) of the CoNS strains could be identified as Mammaliicoccus (M.) fleurettii, while 13 were identified as M. sciuri, 8 as M. vitulinus, 2 as Staphylococcus (S.) epidermidis and single strains each as S. warneri, S. xylosus, Staphylococcus spp. and S. casei. Most of the strains were generally susceptible to clinically-relevant antibiotics, but only few (< 7%) strains possessed multiple resistances. Both oxacillin and cefoxitin resistant isolates were considered to be presumptive methicillin-resistant CoNS. From whole genome sequencing data of 6 representative strains, the mecA gene, accessory genes and the SCC loci were compared, which revealed high variability between some of the strains. The major fatty acids of K22-5MT strain included anteiso-C15:0, iso-C15:0, iso-C17:0, anteiso-C17:0, C18:0, and C20:0. Average nucleotide identity and digital DNA-DNA hybridization values indicated that Staphylococcus strain K22-5MT was below the species delineation cutoff values for ANI (less than 91%) and DDH (less than 44.4%), with the most closely related species being the S. pseudoxylosus S04009T type strain. Thus, strain K22- 5MT (=DSM 112532T, =LMG 32324T) represents a novel species, for which the name Staphylococcus shinii sp. nov. is proposed.

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Microbial agents for the control of ticks Rhipicephalus microplus
Edgar Castro-Saines, Rodolfo Lagunes-Quintanilla, Rubén Hernández-Ortiz
Parasitology Research.2024;[Epub] CrossRef
Scandinavium lactucae sp. nov. Isolated from Healthy Lettuce in South Korea
Jiwon Park, Sieun Park, Kwang-Kyo Oh, Charles M. A. P. Franz, Gyu-Sung Cho
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Efficacy of Entomopathogenic Staphylococcus Bacteria as a Biocontrol Agent against Rhipicephalus microplus Ticks: Assessing Reproductive Inhibition and Mortality Rates
Raquel Cossio-Bayugar, Cesar A. Arreguin-Perez, Hugo Aguilar-Diaz, Estefan Miranda-Miranda
Microorganisms.2024; 12(3): 551. CrossRef
Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites
Ana Sosa-Fajardo, Cristian Díaz-Muñoz, David Van der Veken, Inés Pradal, Marko Verce, Stefan Weckx, Frédéric Leroy
BMC Genomics.2024;[Epub] CrossRef
Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk
Yu-Ting Wang, Yu-Chun Lin, Yi-Huei Hsieh, Yu-Tzu Lin, Moriyuki Hamada, Chih-Chieh Chen, Jong-Shian Liou, Ai-Yun Lee, Wei-Ling Zhang, Yung-Tsung Chen, Chien-Hsun Huang
Pathogens.2024; 13(4): 343. CrossRef
Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge: Yaya Zhou† , Jianchu Zhang† , Dongmei Zhang , Wan-Li Ma , Xiaorong Wang; J. Microbiol. 2021;59(10):941-948. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1206-5

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Abstract

Several follow-up studies have found that COVID-19 (coronavirus disease 2019) patients had persistent symptoms after discharge. Gut microbiota play an important role in human health and immune responses. Therefore, this study investigated the gut microbiota of recovered COVID-19 patients and the correlations between gut microbiota and persistent symptoms after discharge. Stool samples were collected from 15 recovered healthcare workers (HCWs) with COVID-19 at three months after discharge, in addition, stool samples were collected from 14 healthy controls (HCs) to perform 16S rRNA gene sequencing between May and July 2020. Compared with HCs, recovered HCWs had reduced bacterial diversity at three months after discharge, with a significantly higher relative abundance of opportunistic pathogens, and a significantly lower relative abundance of beneficial bacteria. In addition, Escherichia unclassified was positively correlated with persistent symptoms at three months after discharge, including fatigue (r = 0.567, p = 0.028), chest tightness after activity (r = 0.687, p = 0.005), and myalgia (r = 0.523, p = 0.045). Intestinibacter bartlettii was positively correlated with anorexia (r = 0.629, p = 0.012) and fatigue (r = 0.545, p = 0.036). However, Faecalibacterium prausnitzii was negatively correlated with chest tightness after activity (r = -0.591, p = 0.02), and Intestinimonas butyriciproducens was negatively correlated with cough (r = -0.635, p = 0.011). In conclusion, the gut microbiota of recovered HCWs with COVID-19 at three months after discharge was different from that of HCs, and altered gut microbiota was correlated with persistent symptoms after discharge, highlighting that gut microbiota may play an important role in the recovery of patients with COVID-19.

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Molecular characterization of the Saccharomycopsis fibuligera ATF genes, encoding alcohol acetyltransferase for volatile acetate ester formation: Hye Yun Moon , Hyeon Jin Kim , Ki Seung Kim , Su Jin Yoo , Dong Wook Lee , Hee Je Shin , Jeong Ah Seo , Hyun Ah Kang; J. Microbiol. 2021;59(6):598-608. Published online May 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1159-8

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Abstract

Aroma ester components produced by fermenting yeast cells via alcohol acetyltransferase (AATase)-catalyzed intracellular reactions are responsible for the fruity character of fermented alcoholic beverages, such as beer and wine. Acetate esters are reportedly produced at relatively high concentrations by non-Saccharomyces species. Here, we identified 12 ATF orthologues (SfATFs) encoding putative AATases, in the diploid genome of Saccharomycopsis fibuligera KJJ81, an isolate from wheat-based Nuruk in Korea. The identified SfATF proteins (SfAtfp) display low sequence identities with S. cerevisiae Atf1p (between 13.3 and 27.0%). All SfAtfp identified, except SfAtf(A)4p and SfAtf(B)4p, contained the activation domain (HXXXD) conserved in other Atf proteins. Culture supernatant analysis using headspace gas chromatography mass spectrometry confirmed that the recombinant S. cerevisiae strains expressing SfAtf(A)2p, SfAtf(B)2p, and SfAtf(B)6p produced high levels of isoamyl and phenethyl acetates. The volatile aroma profiles generated by the SfAtf proteins were distinctive from that of S. cerevisiae Atf1p, implying difference in the substrate preference. Cellular localization analysis using GFP fusion revealed the localization of SfAtf proteins proximal to the lipid particles, consistent with the presence of amphipathic helices at their N- and C-termini. This is the first report that systematically characterizes the S. fibuligera ATF genes encoding functional AATases responsible for acetate ester formation using higher alcohols as substrate, demonstrating their biotechnological potential for volatile ester production.

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Genome-Wide Identification and Biochemical Characterization of Alcohol Acyltransferases for Aroma Generation in Wickerhamomyces subpelliculosus Isolates from Fermented Food
Su Jin Yoo, Hyeon Jin Kim, Hye Yun Moon, Min-Seung Jeon, Yong Uk Cho, Che Ok Jeon, Seong-Il Eyun, Hyun Ah Kang
Journal of Agricultural and Food Chemistry.2024; 72(50): 28194. CrossRef
Characterization and phylogenetic analysis of the complete mitochondrial genome of Saccharomycopsis fibuligera (lindner) Klocker 1907 (saccharomycetales: saccharomycopsidaceae)
Yue Deng, Guangjiu Chen, Xuedong Bao, Jie He
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Optimization of High-Density Fermentation Conditions for Saccharomycopsis fibuligera Y1402 through Response Surface Analysis
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Foods.2024; 13(10): 1546. CrossRef
Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products
Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-joo Jeon, Che Ok Jeon, Seong-il Eyun, Hyun Ah Kang
FEMS Yeast Research.2023;[Epub] CrossRef
Beer fermentation performance and sugar uptake of Saccharomycopsis fibuligera–A novel option for low-alcohol beer
Yvonne Methner, Frederico Magalhães, Luis Raihofer, Martin Zarnkow, Fritz Jacob, Mathias Hutzler
Frontiers in Microbiology.2022;[Epub] CrossRef
Comparative analysis of aroma components and quality of Geotrichum candidum after space mutation breeding
Junjie Chen, Qianying Li, Jie Wang, Weizhe Chen, Qikai Zheng, Qingping Zhong, Xiang Fang, Zhenlin Liao
Frontiers in Microbiology.2022;[Epub] CrossRef

Review

Microbial phenomics linking the phenotype to function: The potential of Raman spectroscopy: Jin-Kyung Hong , Soo Bin Kim , Eun Sun Lyou , Tae Kwon Lee; J. Microbiol. 2021;59(3):249-258. Published online January 26, 2021; DOI: https://doi.org/10.1007/s12275-021-0590-1

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Abstract

Raman spectroscopy is a promising tool for identifying microbial phenotypes based on single cell Raman spectra reflecting cellular biochemical biomolecules. Recent studies using Raman spectroscopy have mainly analyzed phenotypic changes caused by microbial interactions or stress responses (e.g., antibiotics) and evaluated the microbial activity or substrate specificity under a given experimental condition using stable isotopes. Lack of labelling and the nondestructive pretreatment and measurement process of Raman spectroscopy have also aided in the sorting of microbial cells with interesting phenotypes for subsequently conducting physiology experiments through cultivation or genome analysis. In this review, we provide an overview of the principles, advantages, and status of utilization of Raman spectroscopy for studies linking microbial phenotypes and functions. We expect Raman spectroscopy to become a next-generation phenotyping tool that will greatly contribute in enhancing our understanding of microbial functions in natural and engineered systems.

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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.

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Characteristic and role of chromosomal type II toxin-antitoxin systems locus in Enterococcus faecalis ATCC29212: Zhen Li , Chao Shi , Shanjun Gao , Xiulei Zhang , Di Lu , Guangzhi Liu; J. Microbiol. 2020;58(12):1027-1036. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0079-3

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Abstract

The Gram-positive bacterium Enterococcus faecalis is currently one of the major pathogens of nosocomial infections. The lifestyle of E. faecalis relies primarily on its remarkable capacity to face and survive in harsh environmental conditions. Toxin-antitoxin (TA) systems have been linked to the growth control of bacteria in response to adverse environments but have rarely been reported in Enterococcus. Three functional type II TA systems were identified among the 10 putative TA systems encoded by E. faecalis ATCC29212. These toxin genes have conserved domains homologous to MazF (DR75_ 1948) and ImmA/IrrE family metallo-endopeptidases (DR75_ 1673 and DR75_2160). Overexpression of toxin genes could inhibit the growth of Escherichia coli. However, the toxin DR75_1673 could not inhibit bacterial growth, and the bacteriostatic effect occurred only when it was coexpressed with the antitoxin DR75_1672. DR75_1948–DR75_1949 and DR75_ 160–DR75_2161 could maintain the stable inheritance of the unstable plasmid pLMO12102 in E. coli. Moreover, the transcription levels of these TAs showed significant differences when cultivated under normal conditions and with different temperatures, antibiotics, anaerobic agents and H2O2. When DR75_2161 was knocked out, the growth of the mutant strain at high temperature and oxidative stress was limited. The experimental characterization of these TAs loci might be helpful to investigate the key roles of type II TA systems in the physiology and environmental stress responses of Enterococcus.

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Reviews

[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.

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Yeast polyubiquitin unit regulates synaptonemal complex formation and recombination during meiosis
Min-Kyung Jo, Kiwon Rhee, Keun Pil Kim, Soogil Hong
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Histone variant H2A.Z promotes meiotic chromosome axis organization in Saccharomyces cerevisiae
Lorencia Chigweshe, Amy J MacQueen, Scott G Holmes, J Berman
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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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Maintenance of genome integrity and active homologous recombination in embryonic stem cells
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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
Soogil Hong, Jeong H Joo, Hyeseon Yun, Nancy Kleckner, Keun P Kim
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Meiotic prophase-like pathway for cleavage-independent removal of cohesin for chromosome morphogenesis
Kiran Challa, Miki Shinohara, Akira Shinohara
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MINIREVIEW] To Peep into Pif1 Helicase: Multifaceted All the Way from Genome Stability to Repair-Associated DNA Synthesis: Woo-Hyun Chung; J. Microbiol. 2014;52(2):89-98. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3524-3

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Abstract

Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.

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Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family
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Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in Saccharomyces cerevisiae
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Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases
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Nature Communications.2019;[Epub] CrossRef
The nature of meiotic chromosome dynamics and recombination in budding yeast
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Journal of Microbiology.2019; 57(4): 221. CrossRef
The Drosophila melanogaster PIF1 Helicase Promotes Survival During Replication Stress and Processive DNA Synthesis During Double-Strand Gap Repair
Ece Kocak, Sarah Dykstra, Alexandra Nemeth, Catherine G Coughlin, Kasey Rodgers, Mitch McVey
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The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity
Carly L Geronimo, Saurabh P Singh, Roberto Galletto, Virginia A Zakian
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DNA-unwinding activity of Saccharomyces cerevisiae Pif1 is modulated by thermal stability, folding conformation, and loop lengths of G-quadruplex DNA
Lei Wang, Qing-Man Wang, Yi-Ran Wang, Xu-Guang Xi, Xi-Miao Hou
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Olga Buzovetsky, Youngho Kwon, Nhung Tuyet Pham, Claire Kim, Grzegorz Ira, Patrick Sung, Yong Xiong
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Research Support, Non-U.S. Gov'ts

Hrq1 Functions Independently of Sgs1 to Preserve Genome Integrity in Saccharomyces cerevisiae: Do-Hee Choi , Rina Lee , Sung-Hun Kwon , Sung-Ho Bae; J. Microbiol. 2013;51(1):105-112. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-3048-2

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Abstract: Maintenance of genome stability in eukaryotes involves a number of conserved proteins, including RecQ helicases, which play multiple roles at various steps in homologous recombination and DNA repair pathways. Sgs1 has been described as the only RecQ helicase in lower eukaryotes. However, recent studies revealed the presence of a second RecQ helicase, Hrq1, which is most homologous to human RECQL4. Here we show that hrq1Δ mutation resulted in increased mitotic recombination and spontaneous mutation in Saccharomyces cerevisiae, and sgs1Δ mutation had additive effects on the phenotypes of hrq1Δ. We also observed that the hrq1Δ mutant was sensitive to 4-nitroquinoline 1-oxide and cisplatin, which was not complemented by overexpression of Sgs1. In addition, the hrq1Δ sgs1Δ double mutant displayed synthetic growth defect as well as a shortened chronological life span compared with the respective single mutants. Analysis of the type of age-dependent Canr mutations revealed that only point mutations were found in hrq1Δ, whereas significant numbers of gross deletion mutations were found in sgs1Δ. Our results suggest that Hrq1 is involved in recombination and DNA repair pathways in S. cerevisiae independent of Sgs1.

Biochemical Properties and Physiological Roles of NADP-Dependent Malic Enzyme in Escherichia coli: Baojuan Wang , Peng Wang , Enxia Zheng , Xiangxian Chen , Hanjun Zhao , Ping Song , Ruirui Su , Xiaoning Li , Guoping Zhu; J. Microbiol. 2011;49(5):797-802. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0487-5

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Abstract

Malic enzymes catalyze the reversible oxidative decarboxylation of L-malate using NAD(P)+ as a cofactor. NADP-dependent malic enzyme (MaeB) from Escherichia coli MG1655 was expressed and purified as a fusion protein. The molecular weight of MaeB was about 83 kDa, as determined by SDS-PAGE. The recombinant MaeB showed a maximum activity at pH 7.8 and 46°C. MaeB activity was dependent on the presence of Mn2+ but was strongly inhibited by Zn2+. In order to understand the physiological roles, recombinant E. coli strains (icdNADP/ΔmaeB and icdNAD/ΔmaeB) containing NADP-dependent isocitrate dehydrogenase (IDH), or engineered NAD-dependent IDH with the deletion of the maeB gene, were constructed using homologous recombination. During growth on acetate, icdNAD/ΔmaeB grew poorly, having a growth rate only 60% that of the wild-type strain (icdNADP). Furthermore, icdNADP/ΔmaeB exhibited a 2-fold greater adaptability to acetate than icdNAD/ΔmaeB, which may be explained by more NADPH production for biosynthesis in icdNADP/ΔmaeB due to its NADP-dependent IDH. These results indicated that MaeB was important for NADPH production for bacterial growth on acetate. We also observed that MaeB activity was significantly enhanced (7.83-fold) in icdNAD, which was about 3-fold higher than that in icdNADP, when switching from glucose to acetate. The marked increase of MaeB activity was probably induced by the shortage of NADPH in icdNAD. Evidently, MaeB contributed to the NADPH generation needed for bacterial growth on two carbon compounds.

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The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense
Edileusa C. M. Gerhardt, Erick Parize, Fernanda Gravina, Flávia L. D. Pontes, Adrian R. S. Santos, Gillize A. T. Araújo, Ana C. Goedert, Alysson H. Urbanski, Maria B. R. Steffens, Leda S. Chubatsu, Fabio O. Pedrosa, Emanuel M. Souza, Karl Forchhammer, Ele
mSystems.2020;[Epub] CrossRef
Metabolic changes in peripheral blood lymphocytes from children with recurrent respiratory infections
L. M. Kurtasova, N. A. Shakina, T. V. Lubnina
Russian Journal of Infection and Immunity.2020; 10(3): 515. CrossRef
The NADP-dependent malic enzyme MaeB is a central metabolic hub controlled by the acetyl-CoA to CoASH ratio
Luciano F. Huergo, Gillize A.T. Araújo, Adrian S.R. Santos, Edileusa C.M. Gerhardt, Fabio O. Pedrosa, Emanuel M. Souza, Karl Forchhammer
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.2020; 1868(9): 140462. CrossRef
Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals
Hyun Gyu Lim, Ji Hoon Lee, Myung Hyun Noh, Gyoo Yeol Jung
Journal of Agricultural and Food Chemistry.2018; 66(16): 3998. CrossRef
Enhanced performance of the methylerythritol phosphate pathway by manipulation of redox reactions relevant to IspC, IspG, and IspH
Jia Zhou, Liyang Yang, Chonglong Wang, Eui-Sung Choi, Seon-Won Kim
Journal of Biotechnology.2017; 248: 1. CrossRef
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Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation
Eleni Theodosiou, Oliver Frick, Bruno Bühler, Andreas Schmid
Microbial Cell Factories.2015;[Epub] CrossRef
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Sebastiaan K. Spaans, Ruud A. Weusthuis, John van der Oost, ServÃ© W. M. Kengen
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Development of a toxA Gene Knock-out Mutant of Pasteurella multocida and Evaluation of its Protective Effects: Tae Jung Kim , Jae Il Lee , Bong Joo Lee; J. Microbiol. 2006;44(3):320-326.; DOI: https://doi.org/2380 [pii]

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Abstract: Pasteurella multocida is an important veterinary and opportunistic human pathogen. In particular, strains of P. multocida serogroup D cause progressive atrophic rhinitis, and produce a potent, intracellular, mitogenic toxin known as P. multocida toxin (PMT), which is encoded by the toxA gene. To further investigate the toxigenic and pathogenic effects of PMT, a toxA-deleted mutant was developed by homologous gene recombination. When administrated to mice, the toxigenicity of the toxA mutant P. multocida was drastically reduced, suggesting that the PMT constributes the major part of the toxigenicity of P. multocida. Similar results were obtained in a subsequent experiment, while high mortalities were observed when toxA(+) P. multocida bacterial culture or culture lysate were administrated. Mice immunized with toxA(? P. multocida were not protected (none survived) following challenge with toxA(+) P. multocida or bacterial culture lysate (toxin). These results suggest that the toxigenicity of P. multocida is mainly derived from PMT.

Improvement of 4-chlorobiphenyl degradation bya recombinant strain, pseudomonas sp. DJ12-C: Kim, Ji Young , Kim, Young Chang , Lim, Jai Yun , Lee, Ki Sung , Ka, Jong Ok , Min, Kyung Hee , Kim, Chi Kyung; J. Microbiol. 1997;35(1):53-60.

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Abstract: Pseudomonas sp. P20 and Pseudomonas sp. DJ-12 isolated from the polluted environment are capable of degrading biphenyl and 4-chlorobiphenyl (4CB) to produce benzoic acid and 4-chlorobenzoic acid (4CBA) respectively, by pcbABCD-encoded enzymes. 4CBA can be further degraded by Pseudomonas sp. DJ-12, but not by Pseudomonas sp P20. However, the meta-cleavage activities of 2,3-dihydroxybiphenyl (2, 3-DHBP) and 4-chloro-2,3-DHBP dioxygenases (2, 3-DHBD) encoded by pcbC in Pseudomonas sp. P20 were stronger than Pseudomonas sp. DJ-12. In this study, the pcbC gene encoding 2, 3-DHBD was cloned from the genomic DNA of Pseudomonas sp. P20 by using pKT230. A hybrid plasmid pKK1 was constructed and E. coli KK1 transformant was selected by transforming the pKK1 hybrid plasmid carrying pcbC into E. coli XL1-Blue. By transferring the pKK1 plasmide of E. coli KK1 into Pseudomonas sp. DJ-12 by conjugation, a recombinant strain Pseudomonas sp. P20, Pseudomonas sp. DJ-12, and the recombinant cell assay methods. Pseudomonas sp. DJ12-C readily degraded 4CB and 2, 3-DHBP to produce 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoic acid (HOPDA), and the resulting 4CBA and benzoic acid were continuously catabolized. Pseudomonas sp. DJ12-C degraded 1 mM 4CB completely after incubation for 20 h, but Pseudomonas sp. P20 and Pseudomonas sp. DJ-12 showed only 90% and Pseudomonas sp. DJ-12 had, but its degradation activity to 2, 3-DHBP, 3-methylcatechol, and catechol was improved.

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