Journal of Microbiology

Journal Articles

Repeated Exposure of Vancomycin to Vancomycin-Susceptible Staphylococcus aureus (VSSA) Parent Emerged VISA and VRSA Strains with Enhanced Virulence Potentials: An Nguyen, J Jean Sophy Roy, Ji-Hoon Kim, Kyung-Hee Yun, Wonsik Lee, Kyeong Kyu Kim, Truc Kim, Akhilesh Kumar Chaurasia; J. Microbiol. 2024;62(7):535-553. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00139-8

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The emergence of resistance against the last-resort antibiotic vancomycin in staphylococcal infections is a serious concern for human health. Although various drug-resistant pathogens of diverse genetic backgrounds show higher virulence potential, the underlying mechanism behind this is not yet clear due to variability in their genetic dispositions. In this study, we investigated the correlation between resistance and virulence in adaptively evolved isogenic strains. The vancomycin-susceptible Staphylococcus aureus USA300 was exposed to various concentrations of vancomycin repeatedly as a mimic of the clinical regimen to obtain mutation(s)-accrued-clonally-selected (MACS) strains. The phenotypic analyses followed by expression of the representative genes responsible for virulence and resistance of MACS strains were investigated. MACS strains obtained under 2 and 8 µg/ml vancomycin, named Van2 and Van8, respectively; showed enhanced vancomycin minimal inhibitory concentrations (MIC) to 4 and 16 µg/ml, respectively. The cell adhesion and invasion of MACS strains increased in proportion to their MICs. The correlation between resistance and virulence potential was partially explained by the differential expression of genes known to be involved in both virulence and resistance in MACS strains compared to parent S. aureus USA300. Repeated treatment of vancomycin against vancomycin-susceptible S. aureus (VSSA) leads to the emergence of vancomycin-resistant strains with variable levels of enhanced virulence potentials.

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Targeting the G-quadruplex as a novel strategy for developing antibiotics against hypervirulent drug-resistant Staphylococcus aureus
Maria Sultan, Maria Razzaq, Joohyun Lee, Shreyasi Das, Shrute Kannappan, Vinod Kumar Subramani, Wanki Yoo, Truc Kim, Hye-Ra Lee, Akhilesh K. Chaurasia, Kyeong Kyu Kim
Journal of Biomedical Science.2025;[Epub] CrossRef

The Revision of Lichen Flora Around Maxwell Bay, King George Island, Maritime Antarctic: Jae Eun So , Josef P. Halda , Soon Gyu Hong , Jae&# , Ji Hee Kim; J. Microbiol. 2023;61(2):159-173. Published online February 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00015-x

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Abstract

Since the floristic study of lichens at the Barton and Weaver Peninsulas of King George Island in 2006, there have been intense investigations of the lichen flora of the two peninsulas as well as that of Fildes Peninsula and Ardley Island in Maxwell Bay, King George Island, South Shetland Islands, maritime Antarctic. In this study, a total of 104 species belonging to 53 genera, are identified from investigations of lichens that were collected in austral summer seasons from 2008 to 2016. Phenotypic and molecular analyses were incorporated for taxonomic identification. In particular, 31 species are found to be endemic to the Antarctic and 22 species are newly recorded to the Maxwell Bay region. Lepra dactylina, Stereocaulon caespitosum, and Wahlenbergiella striatula are newly recorded in the Antarctic, and the previously reported taxon Cladonia furcata is excluded from the formerly recorded list due to misidentification. We also provide ecological and geographical information about lichen associations and habitat preferences.

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Lichens of Larsemann Hills and adjacent oases in the area of Prydz Bay (Princess Elizabeth Land and MacRobertson Land, Antarctica)
Mikhail Andreev (Mихаил АНДРЕЕВ)
Polar Science.2023; 38: 101009. CrossRef

Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyung Park , Shin Nam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(2):189-197. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00017-9

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Abstract

Indoor fungi obtain carbon sources from natural sources and even recalcitrant biodegradable materials, such as plastics and synthetic dye. Their vigorous activity may have negative consequences, such as structural damage to building materials or the destruction of precious cultural materials. The animal specimen room of the Seoul National University stocked 36,000 animal resources that had been well-maintained for over 80 years. Due to abandonment without the management of temperature and humidity during the rainy summer season, many stuffed animal specimens had been heavily colonized by fungi. To investigate the fungal species responsible for the destruction of the historical specimens, we isolated fungi from the stuffed animal specimens and identified them at the species level based on morphology and molecular analysis of the β-tubulin (BenA) gene. A total of 365 strains were isolated and identified as 26 species in Aspergillus (10 spp.), Penicillium (14 spp.), and Talaromyces (2 spp.). Penicillium brocae and Aspergillus sydowii were isolated from most sections of the animal specimens and have damaged the feathers and beaks of valuable specimens. Our findings indicate that within a week of mismanagement, it takes only a few fungal species to wipe out the decades of history of animal diversity. The important lesson here is to prevent this catastrophe from occurring again through a continued interest, not to put all previous efforts to waste.

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Investigating the Role of Microclimate and Microorganisms in the Deterioration of Stone Heritage: The Case of Rupestrian Church from Jac, Romania
Dorina Camelia Ilieș, Andrei-Ionuț Apopei, Cristina Mircea, Alexandru Ilieș, Tudor Caciora, Berdenov Zharas, Lucian Barbu-Tudoran, Nicolaie Hodor, Alexandru Turza, Ana Cornelia Pereș, Thowayeb H. Hassan, Bahodirhon Safarov, Ioan-Cristian Noje
Applied Sciences.2024; 14(18): 8136. CrossRef
Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation
Geoffrey Michael Gadd, Marina Fomina, Flavia Pinzari, Mark D. Rose
Microbiology and Molecular Biology Reviews.2024;[Epub] CrossRef

Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(12):1048-1055. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9260-y

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Abstract

A Gram-stain-negative, strictly aerobic, marine bacterium, designated GH2-2T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) in Gangwha Island, the Republic of Korea. The cells of the organism were oxidase- positive, catalase-positive, flagellated, short rods that grew at 10–40°C, pH 4–10, and 0–13% (w/v) NaCl. The predominant ubiquinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acid is C18:1. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed an independent lineage at the base of the radiation encompassing members of the genus Thioclava, except for Thioclava arenosa. The closest relatives were T. nitratireducens (96.03% sequence similarity) and T. dalianensis (95.97%). The genome size and DNA G+C content were 3.77 Mbp and 59.6 mol%, respectively. Phylogenomic analysis supported phylogenetic distinctness based on 16S rRNA gene sequences. Average nucleotide identity values were 73.6–74.0% between the novel strain and members of the genus Thioclava. On the basis of data obtained from a polyphasic approach, the strain GH2-2T (= KCTC 62124T = DSM 105743T) represents a novel species of a new genus for which the name Hahyoungchilella caricis gen. nov., sp. nov. is proposed. Moreover, the transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava gen. nov. as Pseudothioclava arenosa comb. nov. is also proposed. Finally, Thioclava electrotropha Chang et al. 2018 is proposed to be a later heterosynonym of Thioclava sediminum Liu et al. 2017.

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Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat
Zhaobin Huang, Meiqin Li, Aharon Oren, Qiliang Lai
Frontiers in Microbiology.2024;[Epub] CrossRef
Sustainable agricultural management of saline soils in arid and semi-arid Mediterranean regions through halophytes, microbial and soil-based technologies
Salvadora Navarro-Torre, Pedro Garcia-Caparrós, Amaia Nogales, Maria Manuela Abreu, Erika Santos, Ana Lúcia Cortinhas, Ana Delaunay Caperta
Environmental and Experimental Botany.2023; 212: 105397. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4061. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef

Metabolism-mediated induction of zinc tolerance in Brassica rapa by Burkholderia cepacia CS2-1: Sang-Mo Kang , Raheem Shahzad , Saqib Bilal , Abdul Latif Khan , Young-Hyun You , Won-Hee Lee , Hee-La Ryu , Ko-Eun Lee , In-Jung Lee; J. Microbiol. 2017;55(12):955-965. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7305-7

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Abstract

Brassica rapa (Chinese cabbage) is an essential component of traditional Korean food. However, the crop is often subject to zinc (Zn+) toxicity from contaminated irrigation water, which, as a result, compromises plant growth and production, as well as the health of human consumers. The present study investigated the bioaccumulation of Zn+ by Burkholderia cepacia CS2-1 and its effect on the heavy metal tolerance of Chinese cabbage. Strain CS2-1 was identified and characterized on the basis of 16S rRNA sequences and phylogenetic analysis. The strain actively produced indole-3-acetic acid (3.08 ± 0.21 μg/ml) and was also able to produce siderophore, solubilize minerals, and tolerate various concentrations of Zn+. The heavy metal tolerance of B. rapa plants was enhanced by CS2-1 inoculation, as indicated by growth attributes, Zn+ uptake, amino acid synthesis, antioxidant levels, and endogenous hormone (ABA and SA) synthesis. Without inoculation, the application of Zn+ negatively affected the growth and physiology of B. rapa plants. However, CS2-1 inoculation improved plant growth, lowered Zn+ uptake, altered both amino acid regulation and levels of flavonoids and phenolics, and significantly decreased levels of superoxide dismutase, endogenous abscisic acid, and salicylic acid. These findings indicate that B. cepacia CS2-1 is suitable for bioremediation against Zn+-induced oxidative stress.

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Assessing the health of climate-sensitive trees in a subalpine ecosystem through microbial community dynamics
Bo Ram Kang, Soo Bin Kim, Jin-Kyung Hong, Seok Hyun Ahn, Jinwon Kim, Nayeon Lee, Tae Kwon Lee
Science of The Total Environment.2024; 957: 177724. CrossRef
Exploring the Phosphate Solubilising Rhizobacteria isolated from Wild Musa Rhizosphere and their Efficacy on Growth Promotion of Phaseolus vulgaris
Mum Tatung, Chitta Ranjan Deb
Journal of Experimental Biology and Agricultural Sciences.2024; 12(5): 742. CrossRef
Remediation of benzo[a]pyrene contaminated soils by moderate chemical oxidation coupled with microbial degradation
Bin Chen, Jiang Xu, Huijie Lu, Lizhong Zhu
Science of The Total Environment.2023; 871: 161801. CrossRef
Assessing the Involvement of Selected Phenotypes of Pseudomonas simiae PICF7 in Olive Root Colonization and Biological Control of Verticillium dahliae
Nuria Montes-Osuna, Carmen Gómez-Lama Cabanás, Antonio Valverde-Corredor, Roeland L. Berendsen, Pilar Prieto, Jesús Mercado-Blanco
Plants.2021; 10(2): 412. CrossRef
Ameliorative effect of indole-3-acetic acid- and siderophore-producing Leclercia adecarboxylata MO1 on cucumber plants under zinc stress
Sang-Mo Kang, Raheem Shahzad, Muhammad Aaqil Khan, Zuhair Hasnain, Ko-Eun Lee, Hee-Soon Park, Lee-Rang Kim, In-Jung Lee
Journal of Plant Interactions.2021; 16(1): 30. CrossRef
Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2–6
Xin Cheng, Bowen Yang, Jinfang Zheng, Hongyu Wei, Xuehuan Feng, Yanbin Yin
Computational and Structural Biotechnology Journal.2021; 19: 5678. CrossRef
Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions
Sang-Mo Kang, Sajjad Asaf, Abdul Latif Khan, Lubna, Adil Khan, Bong-Gyu Mun, Muhammad Aaqil Khan, Humaira Gul, In-Jung Lee
Microorganisms.2020; 8(3): 382. CrossRef
The plant-growth promoting bacteria promote cadmium uptake by inducing a hormonal crosstalk and lateral root formation in a hyperaccumulator plant Sedum alfredii
Yingjie Wu, Luyao Ma, Qizhen Liu, Mette Vestergård, Olivera Topalovic, Qiong Wang, Qiyao Zhou, Lukuan Huang, Xiaoe Yang, Ying Feng
Journal of Hazardous Materials.2020; 395: 122661. CrossRef
Effect of Ammonia and Indole-3-acetic Acid Producing Endophytic Klebsiella pneumoniae YNA12 as a Bio-Herbicide for Weed Inhibition: Special Reference with Evening Primroses
Sang-Mo Kang, Saqib Bilal, Raheem Shahzad, Yu-Na Kim, Chang-Wook Park, Ko-Eun Lee, Jeong-Ran Lee, In-Jung Lee
Plants.2020; 9(6): 761. CrossRef
Potential role of plant growth-promoting bacteria in Miscanthus x giganteus phytotechnology applied to the trace elements contaminated soils
Valentina Pidlisnyuk, Aigerim Mamirova, Kumar Pranaw, Pavlo Y. Shapoval, Josef Trögl, Asil Nurzhanova
International Biodeterioration & Biodegradation.2020; 155: 105103. CrossRef
Phytohormones enabled endophytic Penicillium funiculosum LHL06 protects Glycine max L. from synergistic toxicity of heavy metals by hormonal and stress-responsive proteins modulation
Saqib Bilal, Raheem Shahzad, Abdul Latif Khan, Ahmed Al-Harrasi, Chang Kil Kim, In-Jung Lee
Journal of Hazardous Materials.2019; 379: 120824. CrossRef
Amelioration of heavy metal stress by endophytic Bacillus amyloliquefaciens RWL-1 in rice by regulating metabolic changes: potential for bacterial bioremediation
Raheem Shahzad, Saqib Bilal, Muhammad Imran, Abdul Latif Khan, Areej Ahmed Alosaimi, Hussah Abdullah Al-Shwyeh, Hanan Almahasheer, Suriya Rehman, In-Jung Lee
Biochemical Journal.2019; 476(21): 3385. CrossRef

Achromobacter panacis sp. nov., isolated from rhizosphere of Panax ginseng: Priyanka Singh , Yeon Ju Kim , Hina Singh , Mohamed El-Agamy Farh , Deok-Chun Yang; J. Microbiol. 2017;55(6):428-434. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-6612-3

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Abstract

A novel strain DCY105T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Re-public of Korea. Strain DCY105T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5–7.0 and in the absence of NaCl. Phylogenetically, strain DCY105T is most closely related to Achromobacter marplatensis LMG 26219T (96.81%). The DNA G+C content of strain DCY105T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and dipho-sphatidylglycerol were amongst the major polar lipids. C16:00, C8:03OH and iso-C17:03OH were identified as the major fatty acids present in DCY105T. The results of physiological and biochemical tests allowed strain DCY105T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105T (=CCTCCAB 2015193T =KCTC 42751T).

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Zwartia vadi sp. nov., a Novel Species of the GKS98 Cluster Isolated from a Stream, and the Reclassification of ‘Achromobacter Panacis’ as Zwartia panacis comb. nov
Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Microorganisms.2023; 11(9): 2150. CrossRef
Achromobacter spp. prevalence and adaptation in cystic fibrosis lung infection
Laura Veschetti, Marzia Boaretti, Giulia Maria Saitta, Rebeca Passarelli Mantovani, Maria M. Lleò, Angela Sandri, Giovanni Malerba
Microbiological Research.2022; 263: 127140. CrossRef
Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster
Martin W. Hahn, Alexandra Pitt, Johanna Schmidt, Ulrike Koll, Jacqueline Wolf, William B. Whitman, Paul L. E. Bodelier, Meina Neumann-Schaal
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Strong Antimicrobial Activity of Silver Nanoparticles Obtained by the Green Synthesis in Viridibacillus sp. Extracts
Priyanka Singh, Ivan Mijakovic
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Silver nanoparticles produced from Cedecea sp. exhibit antibiofilm activity and remarkable stability
Priyanka Singh, Santosh Pandit, Carsten Jers, Abhayraj S. Joshi, Jørgen Garnæs, Ivan Mijakovic
Scientific Reports.2021;[Epub] CrossRef
A Sustainable Approach for the Green Synthesis of Silver Nanoparticles from Solibacillus isronensis sp. and Their Application in Biofilm Inhibition
Priyanka Singh, Santosh Pandit, VRSS Mokkapati, Jørgen Garnæs, Ivan Mijakovic
Molecules.2020; 25(12): 2783. CrossRef
Emerging Gram-negative bacteria
Heather Green, Andrew M. Jones
Current Opinion in Pulmonary Medicine.2018; 24(6): 592. CrossRef

Latent Kaposi’s sarcoma-associated herpesvirus infection in bladder cancer cells promotes drug resistance by reducing reactive oxygen species: Suhyuk Lee , Jaehyuk Jang , Hyungtaek Jeon , Jisu Lee , Seung-Min Yoo , Jinsung Park , Myung-Shin Lee; J. Microbiol. 2016;54(11):782-788. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6388-x

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Abstract

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the major etiologic agent of Kaposi’s sarcoma, primary effusion lymphoma, and multicentric Castleman’s disease. Recent studies have indicated that KSHV can be detected at high frequency in patient-derived bladder cancer tissue and might be associated with the pathogenesis of bladder cancer. Bladder cancer is the second most common cancer of the genitourinary tract, and it has a high rate of recurrence. Because drug resistance is closely related to chemotherapy failure and cancer recurrence, we investigated whether KSHV infection is associated with drug resistance of bladder cancer cells. Some KSHV-infected bladder cancer cell lines showed resistance to an anti-cancer drug, cisplatin, possibly as a result of downregulation of reactive oxygen species. Additionally, drug resistance acquired from KSHV infection could partly be overcome by HDAC1 inhibitors. Taken together, the data suggest the possible role of KSHV in chemo-resistant bladder cancer, and indicate the therapeutic potential of HDAC1 inhibitors in drug-resistant bladder cancers associated with KSHV infection.

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Development of KSHV vaccine platforms and chimeric MHV68-K-K8.1 glycoprotein for evaluating the in vivo immunogenicity and efficacy of KSHV vaccine candidates
Wan-Shan Yang, Dokyun Kim, Soowon Kang, Chih-Jen Lai, Inho Cha, Pei-Ching Chang, Jae U. Jung, Satya Dandekar
mBio.2024;[Epub] CrossRef
Genomic analysis of schistosomiasis-associated colorectal cancer reveals a unique mutational landscape and therapeutic implications
Dong Yu, Anqi Wang, Jing Zhang, Xinxing Li, Caifeng Jiang, Haiyang Zhou
Genes & Diseases.2023; 10(3): 657. CrossRef
Revisiting Histone Deacetylases in Human Tumorigenesis: The Paradigm of Urothelial Bladder Cancer
Aikaterini F. Giannopoulou, Athanassios D. Velentzas, Eumorphia G. Konstantakou, Margaritis Avgeris, Stamatia A. Katarachia, Nikos C. Papandreou, Nikolas I. Kalavros, Vassiliki E. Mpakou, Vassiliki Iconomidou, Ema Anastasiadou, Ioannis K. Kostakis, Issido
International Journal of Molecular Sciences.2019; 20(6): 1291. CrossRef
Hepatitis C Virus-Induced FUT8 Causes 5-FU Drug Resistance in Human Hepatoma Huh7.5.1 Cells
Shu Li, Xiao-Yu Liu, Qiu Pan, Jian Wu, Zhi-Hao Liu, Yong Wang, Min Liu, Xiao-Lian Zhang
Viruses.2019; 11(4): 378. CrossRef
Mechanistic Insights into Chemoresistance Mediated by Oncogenic Viruses in Lymphomas
Jungang Chen, Samantha Kendrick, Zhiqiang Qin
Viruses.2019; 11(12): 1161. CrossRef
Primary lymphocyte infection models for KSHV and its putative tumorigenesis mechanisms in B cell lymphomas
Sangmin Kang, Jinjong Myoung
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Chitin Oligosaccharide (COS) Reduces Antibiotics Dose and Prevents Antibiotics-Caused Side Effects in Adolescent Idiopathic Scoliosis (AIS) Patients with Spinal Fusion Surgery
Yang Qu, Jinyu Xu, Haohan Zhou, Rongpeng Dong, Mingyang Kang, Jianwu Zhao
Marine Drugs.2017; 15(3): 70. CrossRef

Research Support, Non-U.S. Gov'ts

Hrq1 Facilitates Nucleotide Excision Repair of DNA Damage Induced by 4-Nitroquinoline-1-Oxide and Cisplatin in Saccharomyces cerevisiae: Do-Hee Choi , Moon-Hee Min , Min-Ji Kim , Rina Lee , Sung-Hun Kwon , Sung-Ho Bae; J. Microbiol. 2014;52(4):292-298. Published online March 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4018-z

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Abstract

Hrq1 helicase is a novel member of the RecQ family. Among the five human RecQ helicases, Hrq1 is most homologous to RECQL4 and is conserved in fungal genomes. Recent genetic and biochemical studies have shown that it is a functional gene, involved in the maintenance of genome stability. To better define the roles of Hrq1 in yeast cells, we investigated genetic interactions between HRQ1 and several DNA repair genes. Based on DNA damage sensitivities induced by 4-nitroquinoline- 1-oxide (4-NQO) or cisplatin, RAD4 was found to be epistatic to HRQ1. On the other hand, mutant strains defective in either homologous recombination (HR) or postreplication repair (PRR) became more sensitive by additional deletion of HRQ1, indicating that HRQ1 functions in the RAD4-dependent nucleotide excision repair (NER) pathway independent of HR or PRR. In support of this, yeast twohybrid analysis showed that Hrq1 interacted with Rad4, which was enhanced by DNA damage. Overexpression of Hrq1K318A helicase-deficient protein rendered mutant cells more sensitive to 4-NQO and cisplatin, suggesting that helicase activity is required for the proper function of Hrq1 in NER.

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Metabolomics Combined with Physiology and Transcriptomics Reveal the Response of Samsoniella hepiali to Key Metabolic Pathways and Its Degradation Mechanism during Subculture
Hui He, Zhengfei Cao, Tao Wang, Chuyu Tang, Yuling Li, Xiuzhang Li
Antioxidants.2024; 13(7): 780. CrossRef
Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO
Daria S. Spasskaya, Kirill A. Kulagin, Evgenia N. Grineva, Pamila J. Osipova, Svetlana V. Poddubko, Julia A. Bubis, Elizaveta M. Kazakova, Tomiris T. Kusainova, Vladimir A. Gorshkov, Frank Kjeldsen, Vadim L. Karpov, Irina A. Tarasova, Dmitry S. Karpov
Journal of Fungi.2023; 9(3): 351. CrossRef
Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer
Thong T. Luong, Zheqi Li, Nolan Priedigkeit, Phoebe S. Parker, Stefanie Böhm, Kyle Rapchak, Adrian V. Lee, Kara A. Bernstein, Dmitry A. Gordenin
PLOS Genetics.2022; 18(9): e1010122. CrossRef
A skipping rope translocation mechanism in a widespread family of DNA repair helicases
Johann J Roske, Sunbin Liu, Bernhard Loll, Ursula Neu, Markus C Wahl
Nucleic Acids Research.2021; 49(1): 504. CrossRef
Role and Regulation of the RECQL4 Family during Genomic Integrity Maintenance
Thong T. Luong, Kara A. Bernstein
Genes.2021; 12(12): 1919. CrossRef
Zuo1 supports G4 structure formation and directs repair toward nucleotide excision repair
Alessio De Magis, Silvia Götz, Mona Hajikazemi, Enikő Fekete-Szücs, Marco Caterino, Stefan Juranek, Katrin Paeschke
Nature Communications.2020;[Epub] CrossRef
The Genetic and Physical Interactomes of theSaccharomyces cerevisiaeHrq1 Helicase
Cody M Rogers, Elsbeth Sanders, Phoebe A Nguyen, Whitney Smith-Kinnaman, Amber L Mosley, Matthew L Bochman
G3 Genes|Genomes|Genetics.2020; 10(12): 4347. CrossRef
Maintenance of Yeast Genome Integrity by RecQ Family DNA Helicases
Sonia Vidushi Gupta, Kristina Hildegard Schmidt
Genes.2020; 11(2): 205. CrossRef
Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae
Ju-Hee Choi, Ye-Seul Lim, Min-Ku Kim, Sung-Ho Bae
Journal of Microbiology.2020; 58(11): 957. CrossRef
DNA Helicases as Safekeepers of Genome Stability in Plants
Annika Dorn, Holger Puchta
Genes.2019; 10(12): 1028. CrossRef
The RecQ‐like helicase HRQ1 is involved in DNA crosslink repair in Arabidopsis in a common pathway with the Fanconi anemia‐associated nuclease FAN1 and the postreplicative repair ATPase RAD5A
Sarah Röhrig, Annika Dorn, Janina Enderle, Angelina Schindele, Natalie J. Herrmann, Alexander Knoll, Holger Puchta
New Phytologist.2018; 218(4): 1478. CrossRef
Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase
Cody M. Rogers, Joseph Che-Yen Wang, Hiroki Noguchi, Tsuyoshi Imasaki, Yuichiro Takagi, Matthew L. Bochman
Nucleic Acids Research.2017; 45(9): 5217. CrossRef
Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells
Maciej Kliszczak, Hana Sedlackova, Ganesha P. Pitchai, Werner W. Streicher, Lumir Krejci, Ian D. Hickson
Oncotarget.2015; 6(38): 40464. CrossRef
DNA repair defects ascribed to pby1 are caused by disruption of Holliday junction resolvase Mus81-Mms4
Gizem Ölmezer, Dominique Klein, Ulrich Rass
DNA Repair.2015; 33: 17. CrossRef
Characterization of Hrq1-Rad14 Interaction in Saccharomyces cerevisiae
Moon-Hee Min, Min-Ji Kim, You-Jin Choi, Min-Ju You, Uy-Ra Kim, Hyo-Bin An, Chae-Hyun Kim, Chae-Yeon Kwon, Sung-Ho Bae
The Korean Journal of Microbiology.2014; 50(2): 95. CrossRef

Cyclic Dipeptides from Lactic Acid Bacteria Inhibit the Proliferation of Pathogenic Fungi: Min-Kyu Kwak , Rui Liu , Min-Kyu Kim , Dohyun Moon , Andrew HyoungJin Kim , Sung-Hyun Song , Sa-Ouk Kang; J. Microbiol. 2014;52(1):64-70. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3520-7

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Abstract

Lactobacillus plantarum LBP-K10 was identified to be the most potent antifungal strain from Korean traditional fermented vegetables. The culture filtrate of this strain showed remarkable antifungal activity against Ganoderma boninense. Five fractions from the culture filtrate were observed to have an inhibitory effect against G. boninense. Also, the electron ionization and chemical ionization indicated that these compounds might be cyclic dipeptides. Of the five active fractions, two fractions showed the most significant anti-Ganoderma activity, and one of these fractions inhibited the growth of Candida albicans. These compounds were identified to be cis-cyclo(L-Val-L-Pro) and cis-cyclo(L-Phe-L-Pro), as confirmed by X-ray crystallography.

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Purification, structural characterization, and neuroprotective effect of 3,6‐diisobutyl‐2,5‐piperazinedione from Halomonas pacifica CARE‐V15 against okadaic acid‐induced neurotoxicity in zebrafish model
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Cyclic Dipeptides from Lactic Acid Bacteria Inhibit Proliferation of the Influenza A Virus: Min-Kyu Kwak , Rui Liu , Jun-Oh Kwon , Min-Kyu Kim , Andrew HyoungJin Kim , Sa-Ouk Kang; J. Microbiol. 2013;51(6):836-843. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3521-y

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Abstract

We isolated Lactobacillus plantarum LBP-K10 from the traditional Korean fermented food kimchi. When organic acids were removed, the culture filtrate of this isolate showed high antiviral activity (measured using a plaque-forming assay) against the influenza A (H3N2) virus. Two fractions that were active against influenza A virus were purified from the culture filtrate using a C18 column with high-performance liquid chromatography. These active fractions were crystallized and identified to be the cyclic dipeptides cis-cyclo (L-Leu-L-Pro) and cis-cyclo(L-Phe-L-Pro) using gas chromatography-mass spectrometry; this identification was confirmed by X-ray crystallography. These cyclic dipeptides were identified in the culture filtrate of other lactic acid bacteria, including Lactobacillus spp., Leuconostoc spp., Weissella spp., and Lactococcus lactis.

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Tularemia Progression Accompanied with Oxidative Stress and Antioxidant Alteration in Spleen and Liver of BALB/c Mice: Miroslav Pohanka , Oto Pavlis , Branislav Ruttkay-Nedecky , Jiri Sochor , Jakub Sobotka , Jiri Pikula , Vojtech Adam , Rene Kizek; J. Microbiol. 2012;50(3):401-408. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1621-8

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Abstract: Francisella tularensis is the causative agent of tularemia. It is an intracellular pathogen with the ability to survive within phagosomes and induce pyroptotic cell death. In this study, we attempted to prove whether oxidative imbalance plays a significant role in tularemia pathogenesis. In our experimental model, we subcutaneously infected female BALB/c mice (dose 105 CFU of F. tularensis LVS). Liver, spleen, and blood were collected from mice at regular intervals from days 1–15 after infection. The bacterial burden was assessed by a cultivation test. The burden was unchanging from the 2nd to 6th day after infection. The bacterial burden corresponded to the plasmatic level of IFN-γ, IL-6, and liver malondialdehyde. After the phase of acute bacteraemia and the innate immunity reaction, the levels of reduced glutathione and total low molecular weight antioxidants decreased significantly and the activity of caspase-3 increased in the liver. The level of reduced glutathione decreased to 25% of the original level, and the total level of low molecular weight antioxidants was less than 50% of the initial amount. The demonstrated effects of tularemia-induced pathology had a more extensive impact on the liver than on the spleen.

Journal Article

Transcriptional and Biochemical Characterization of Two Azotobacter vinelandii FKBP Family Members: Maria Dimou , Chrysoula Zografou , Anastasia Venieraki , Panagiotis Katinakis; J. Microbiol. 2011;49(4):635-640. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0498-2

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Abstract: Peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), a class of enzymes that catalyse the rate-limiting step of the cis/trans isomerization in protein folding, are divided into three structurally unrelated families: cyclophilins, FK506-binding proteins (FKBPs), and parvulins. Two recombinant FKBPs from the soil nitrogenfixing bacterium Azotobacter vinelandii, designated as AvfkbX and AvfkbB, have been purified and their peptidyl-prolyl cis/trans isomerase activity against Suc-Ala-Xaa-Pro-Phe-pNA synthetic peptides characterised. The substrate specificity of both enzymes is typical for bacterial FKBPs, with Suc-Ala-Phe-Pro-Phe-pNA being the most rapidly catalysed substrate by AvfkbX and Suc-Ala-Leu-Pro-Phe-pNA by AvfkbB. Both FKBPs display chaperone activity as well in the citrate synthase thermal aggregation assay. Furthermore, using real-time RT-qPCR, we demonstrated that both genes were expressed during the exponential growth phase on glucose minimal medium, while their expression declined dramatically during the stationary growth phase as well as when the growth medium was supplied exogenously with ammonium.

Research Support, Non-U.S. Gov'ts

Ruminococcus faecis sp. nov., Isolated from Human Faeces: Min-Soo Kim , Seong Woon Roh , Jin-Woo Bae; J. Microbiol. 2011;49(3):487-491. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0505-7

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Abstract: Bacterial strain Eg2T, an anaerobic, Gram-positive, non-motile, and non-spore-forming coccus, was isolated from human faeces. The optimal temperature for its growth was 37°C. Oxidase activity was negative, but catalase activity was positive. The strain was able to hydrolyze esculin and to produce acids from the fermentation of several substrates, including glucose. Lactic and acetic acids were the main products of glucose fermentation. The major fatty acids present in this strain were C16:0, C14:0, and C18:1 cis11 DMA. The G+C content was 43.4 mol%. Based on the 16S rRNA gene sequence, strain Eg2T was closely related to species of the genus Ruminococcus (96.3% similarity to R. torques and 96.2% similarity to R. lactaris), and its taxonomic position was placed within the Clostridium cluster XIVa. Based on phenotypic, chemotaxonomic, genotypic, and phylogenetic evidence, we propose that this novel strain be assigned to the genus Ruminococcus and be named Ruminococcus faecis sp. nov. The type strain is Eg2T (=KCTC 5757T =JCM 15917T).

Comparative Proteome Analysis of Bacillus anthracis with pXO1 Plasmid Content: Sudipto Shahid , Ji Hyun Park , Hyung Tae Lee , Seong-Joo Kim , Ji Cheon Kim , Sang Hoon Kim , Dal Mu Ri Han , Dong In Jeon , Kyoung Hwa Jung , Young Gyu Chai; J. Microbiol. 2010;48(6):771-777. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0136-4

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Abstract: Bacillus anthracis the causative agent of anthrax, is an important pathogen among the Bacillus cereus group of species because of its physiological characteristics and its importance as a biological warfare agent. Tripartite anthrax toxin proteins and a poly-D-glutamic acid capsule are produced by B. anthracis vegetative cells during mammalian hosts infection and when cultured in conditions that are thought to mimic the host environment. To identify the factors regulating virulence in B. anthracis the whole cell proteins were extracted from two B. anthracis strains and separated by narrow range immobilized pH gradient (IPG) strips (pH 4-7), followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins that were differentially expressed were identified by the peptide fingerprinting using matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). A total of 23 proteins were identified as being either upregulated or downregulated in the presence or absence of the virulence plasmid pXO1. Two plasmid encoded proteins and 12 cellular proteins were identified and documented as potential virulence factors.

Journal Article

Psychroflexus lacisalsi sp. nov., a Moderate Halophilic Bacterium Isolated from a Hypersaline Lake (Hunazoko-Ike) in Antarctica: Hongyan Zhang , Shoko Hosoi-Tanabe , Syuhei Ban , Satoshi Imura; J. Microbiol. 2010;48(2):160-164. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-0018-9

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Abstract: A novel Gram-negative, aerobic, moderate halophilic, and psychrotolerant bacterium, designated as strain H7T, was isolated from a hypersaline lake located in Skarvsnes, Antarctica. Cells were filaments with varying lengths. Coccoid bodies developed in old cultures. Growth occurred with 0.5-15% (w/v) NaCl (optimum, 5.8-7.0%), at pH 6.0-10.0 (optimum, pH 7.0-8.0), and at 10-28°C (optimum, 25°C). The strain had a G+C content of 34.9 mol%, which is within the range of 32-36 mol% reported for the genus Psychroflexus. Chemotaxonomic data (major respiratory quinone: MK-6; major fatty acids: aC15:0, iC16:0 3-OH, and aC15: 1 A) supported the classification of strain H7T within the genus Psychroflexus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H7T should be assigned to the genus Psychroflexus and has a homology with Psychroflexus salinarum (98.2%), P. sediminis (96.1%), P. torquis (95.2%), P. tropicus (95.8%), and P. gondwanense (92.2%). Strain H7 is not identified as P. salinarum because that DNA-DNA hybridization data were 8.5% between strain H7T and P. salinarum. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics, and chemotaxonomic differences supported the view that strain H7T represents a novel species of the genus Psychroflexus. The name Psychroflexus lacisalsi is proposed, and the type strain is H7T (=JCM 16231T =KACC 14089T).

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