Journal of Microbiology

Volume 61(2); February 2023

Review

The “Cins” of Our Fathers: Rejuvenated Interest in Colicins to Combat Drug Resistance: Sumudu Upatissa , Robert J. Mitchell; J. Microbiol. 2023;61(2):145-158. Published online February 8, 2023; DOI: https://doi.org/10.1007/s12275-023-00023-x

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Abstract: With the growing threat of antibiotic resistance, researchers around the globe are seeking alternatives to stem bacterial pathogenesis. One such alternative is bacteriocins, proteins produced by bacterial species to inhibit the growth and viability of related bacterial species. With their diverse mechanisms, which include pore formation and nuclease activities, and narrow spectrum of activities, which limit their impact to only certain bacterial species, unlike many chemical antibiotics, bacteriocins offer intriguing possibilities to selectively control individual bacterial populations. Within this review, therefore, we highlight current research exploring the application of colicins and microcins, a subset of bacteriocins, with an emphasis on their activities against drug-resistant pathogens, both in in vitro and in vivo settings.

Journal Articles

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.

Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus: Sung&# , Mi&# , Hyun&# , Kae Kyoung Kwon; J. Microbiol. 2023;61(2):175-187. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00022-y

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Abstract: Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5–9 (optimum, pH 7–7.5), and in 0–8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5–56.1 °C) and 44 °C (20.7–50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5–94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. ( MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. ( MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.

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.

Transcriptome‑based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae: Kobkul Laoteng , Jutamas Anantayanon , Chanikul Chutrakul , Sarocha Panchanawaporn , Sukanya Jeennor; J. Microbiol. 2023;61(2):199-210. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00020-0

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Abstract: Transcriptional regulation has been adopted for developing metabolic engineering tools. The regulatory promoter is a crucial genetic element for strain optimization. In this study, a gene set of Aspergillus oryzae with highly constitutive expression across different growth stages was identified through transcriptome data analysis. The candidate promoters were functionally characterized in A. oryzae by transcriptional control of β-glucuronidase (GUS) as a reporter. The results showed that the glyceraldehyde triphosphate dehydrogenase promoter (PgpdA1) of A. oryzae with a unique structure displayed the most robust strength in constitutively controlling the expression compared to the PgpdA2 and other putative promoters tested. In addition, the ubiquitin promoter (Pubi) of A. oryzae exhibited a moderate expression strength. The deletion analysis revealed that the 5' untranslated regions of gpdA1 and ubi with the length of 1028 and 811 nucleotides, counted from the putative translation start site (ATG), respectively, could efficiently drive the GUS expression. Interestingly, both promoters could function on various carbon sources for cell growth. Glucose was the best fermentable carbon source for allocating high constitutive expressions during cell growth, and the high concentrations (6–8% glucose, w/v) did not repress their functions. It was also demonstrated that the secondary metabolite gene coding for indigoidine could express under the control of PgpdA1 or Pubi promoter. These strong and moderate promoters of A. oryzae provided beneficial options in tuning the transcriptional expression for leveraging the metabolic control towards the targeted products.

Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I: Dayeong Bae , Hana Hyeon , Eunkyoung Shin , Ji&# , Kangseok Lee; J. Microbiol. 2023;61(2):211-220. Published online February 22, 2023; DOI: https://doi.org/10.1007/s12275-023-00013-z

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Abstract: RNase E is an essential enzyme in Escherichia coli. The cleavage site of this single-stranded specific endoribonuclease is well-characterized in many RNA substrates. Here, we report that the upregulation of RNase E cleavage activity by a mutation that affects either RNA binding (Q36R) or enzyme multimerization (E429G) was accompanied by relaxed cleavage specificity. Both mutations led to enhanced RNase E cleavage in RNA I, an antisense RNA of ColE1-type plasmid replication, at a major site and other cryptic sites. Expression of a truncated RNA I with a major RNase E cleavage site deletion at the 5′-end (RNA I- 5) resulted in an approximately twofold increase in the steady-state levels of RNA I- 5 and the copy number of ColE1-type plasmid in E. coli cells expressing wild-type or variant RNase E compared to those expressing RNA I. These
results
indicate that RNA I- 5 does not efficiently function as an antisense RNA despite having a triphosphate group at the 5′-end, which protects the RNA from ribonuclease attack. Our study suggests that increased cleavage rates of RNase E lead to relaxed cleavage specificity on RNA I and the inability of the cleavage product of RNA I as an antisense regulator in vivo does not stem from its instability by having 5′-monophosphorylated end.

Secretions from Serratia marcescens Inhibit the Growth and Biofilm Formation of Candida spp. and Cryptococcus neoformans: Caiyan Xin , Fen Wang , Jinping Zhang , Quan Zhou , Fangyan Liu , Chunling Zhao , Zhangyong Song; J. Microbiol. 2023;61(2):221-232. Published online February 21, 2023; DOI: https://doi.org/10.1007/s12275-022-00007-3

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Abstract: Candida spp. and Cryptococcus are conditional pathogenic fungi that commonly infect immunocompromised patients. Over the past few decades, the increase in antifungal resistance has prompted the development of new antifungal agents. In this study, we explored the potential antifungal effects of secretions from Serratia marcescens on Candida spp. and Cryptococcus neoformans. We confirmed that the supernatant of S. marcescens inhibited fungal growth, suppressed hyphal and biofilm formation, and downregulated the expression of hyphae-specific genes and virulence-related genes in Candida spp. and C. neoformans. Furthermore, the S. marcescens supernatant retained biological stability after heat, pH, and protease K treatment. The chemical profile of the S. marcescens supernatant was characterized by ultra-high-performance liquid chromatography–linear ion trap/orbitrap high resolution mass spectrometry analysis and a total of 61 compounds with an mzCloud best match of greater than 70 were identified. In vivo, treatment with the S. marcescens supernatant reduced the mortality of fungi-infected Galleria mellonella. Taken together, our results revealed that the stable antifungal substances in the supernatant of S. marcescens have promising potential applications in the development of new antifungal agents.

Alpha‑Hemolysin from Staphylococcus aureus Obstructs Yeast‑Hyphae Switching and Diminishes Pathogenicity in Candida albicans: Xiaoyu Yu , Yinhe Mao , Guangbo Li , Xianwei Wu , Qiankun Xuan , Simin Yang , Xiaoqing Chen , Qi Cao , Jian Guo , Jinhu Guo , Wenjuan Wu; J. Microbiol. 2023;61(2):233-243. Published online February 9, 2023; DOI: https://doi.org/10.1007/s12275-022-00006-4

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Abstract: The use of antibiotics can disrupt the body’s natural balance and increase the susteptibility of patients towards fungal infections. Candida albicans is a dimorphic opportunistic fungal pathogen with niches similar to those of bacteria. Our aim was to study the interaction between this pathogen and bacteria to facilitate the control of C. albicans infection. Alpha-hemolysin (Hla), a protein secreted from Staphylococcus aureus, causes cell wall damage and impedes the yeast–hyphae transition in C. albicans. Mechanistically, Hla stimulation triggered the formation of reactive oxygen species that damaged the cell wall and mitochondria of C. albicans. The cell cycle was arrested in the G0/G1 phase, CDC42 was downregulated, and Ywp1 was upregulated, disrupting yeast hyphae switching. Subsequently, hyphae development was inhibited. In mouse models, C. albicans pretreated with Hla reduced the C. albicans burden in skin and vaginal mucosal infections, suggesting that S. aureus Hla can inhibit hyphal development and reduce the pathogenicity of candidiasis in vivo.

Gut Lactobacillus and Probiotics Lactobacillus lactis/rhamnosis Ameliorate Liver Fibrosis in Prevention and Treatment: Sung Min Won , Na Young Lee , Ki&# , Haripriya Gupta , Satya Priya Sharma , Kyung Hwan Kim , Byoung Kook Kim , Hyun Chae Joung , Jin Ju Jeong , Raja Ganesan , Sang Hak Han , Sang Jun Yoon , Dong Joon Kim , Ki Tae Suk; J. Microbiol. 2023;61(2):245-257. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00014-y

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Abstract: The progression and exacerbation of liver fibrosis are closely related to the gut microbiome. It is hypothesized that some probiotics may slow the progression of liver fibrosis. In human stool analysis [healthy group (n = 44) and cirrhosis group (n = 18)], difference in Lactobacillus genus between healthy group and cirrhosis group was observed. Based on human data, preventive and therapeutic effect of probiotics Lactobacillus lactis and L. rhamnosus was evaluated by using four mice fibrosis models. L. lactis and L. rhamnosus were supplied to 3,5-diethoxycarbonyl-1,4-dihydrocollidine or carbon tetrachloride-induced liver fibrosis C57BL/6 mouse model. Serum biochemical measurements, tissue staining, and mRNA expression in the liver were evaluated. The microbiome was analyzed in mouse cecal contents. In the mouse model, the effects of Lactobacillus in preventing and treating liver fibrosis were different for each microbe species. In case of L. lactis, all models showed preventive and therapeutic effects against liver fibrosis. In microbiome analysis in mouse models administered Lactobacillus, migration and changes in the ratio and composition of the gut microbial community were confirmed. L. lactis and L. rhamnosus showed preventive and therapeutic effects on the progression of liver fibrosis, suggesting that Lactobacillus intake may be a useful strategy for prevention and treatment.

Varicella‑Zoster Virus ORF39 Transmembrane Protein Suppresses Interferon‑Beta Promoter Activation by Interacting with STING: Gwang Myeong Lee , Shuang Gong , Seong&# , Hyemin Ko , Woo&# , Jihyun Lee , Ok Sarah Shin , Jin&#; J. Microbiol. 2023;61(2):259-270. Published online February 20, 2023; DOI: https://doi.org/10.1007/s12275-023-00019-7

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Abstract: Varicella-Zoster virus (VZV) causes varicella in primary infection of children and zoster during reactivation in adults. Type I interferon (IFN) signaling suppresses VZV growth, and stimulator of interferon genes (STING) plays an important role in anti-VZV responses by regulating type I IFN signaling. VZV-encoded proteins are shown to inhibit STING-mediated activation of the IFN-β promoter. However, the mechanisms by which VZV regulates STING-mediated signaling pathways are largely unknown. In this study, we demonstrate that the transmembrane protein encoded by VZV open reading frame (ORF) 39 suppresses STING-mediated IFN-β production by interacting with STING. In IFN-β promoter reporter assays, ORF39 protein (ORF39p) inhibited STING-mediated activation of the IFN-β promoter. ORF39p interacted with STING in co-transfection assays, and this interaction was comparable to that of STING dimerization. The cytoplasmic N-terminal 73 amino acids region of ORF39P was not necessary for ORF39 binding and suppression of STING-mediated IFN-β activation. ORF39p also formed a complex containing both STING and TBK1. A recombinant VZV expressing HA-tagged ORF39 was produced using bacmid mutagenesis and showed similar growth to its parent virus. During HA-ORF39 virus infection, the expression level of STING was markedly reduced, and HA-ORF39 interacted with STING. Moreover, HA-ORF39 also colocalized with glycoprotein K (encoded by ORF5) and STING at the Golgi during virus infection. Our results demonstrate that the transmembrane protein ORF39p of VZV plays a role in evading the type I IFN responses by suppressing STINGmediated activation of the IFN-β promoter.

Published Erratum

Erratum to: Physiological roles of catalases Cat1 and Cat2 in Myxococcus xanthus: Yoshio Kimura , Yuri Yoshioka , Kie Toshikuni; J. Microbiol. 2023;61(2):271-271.; DOI: https://doi.org/10.1007/s12275-023-00025-9

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