Journal of Microbiology

Journal Articles

Pat- and Pta-mediated protein acetylation is required for horizontallyacquired virulence gene expression in Salmonella Typhimurium: Hyojeong Koo , Eunna Choi , Shinae Park , Eun-Jin Lee , Jung-Shin Lee; J. Microbiol. 2022;60(8):823-831. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2095-y

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Abstract: Salmonella Typhimurium is a Gram-negative facultative pathogen that causes a range of diseases, from mild gastroenteritis to severe systemic infection in a variety of animal hosts. S. Typhimurium regulates virulence gene expression by a silencing mechanism using nucleoid-associated proteins such as Histone-like Nucleoid Structuring protein (H-NS) silencing. We hypothesize that the posttranslational modification, specifically protein acetylation, of proteins in gene silencing systems could affect the pathogenic gene expression of S. Typhimurium. Therefore, we created acetylation-deficient mutant by deleting two genes, pat and pta, which are involved in the protein acetylation pathway. We observed that the pat and pta deletion attenuates mouse virulence and also decreases Salmonella’s replication within macrophages. In addition, the Δpat Δpta strain showed a decreased expression of the horizontally-acquired virulence genes, mgtC, pagC, and ugtL, which are highly expressed in low Mg2+. The decreased virulence gene expression is possibly due to higher H-NS occupancy to those promoters because the pat and pta deletion increases H-NS occupancy whereas the same mutation decreases occupancy of RNA polymerase. Our results suggest that Pat- and Pta-mediated protein acetylation system promotes the expression of virulence genes by regulating the binding affinity of H-NS in S. Typhimurium.

CagL polymorphisms between East Asian and Western Helicobacter pylori are associated with different abilities to induce IL-8 secretion: Yun Hui Choi , Jing Lai , Myeong-A Kim , Aeryun Kim , Jinmoon Kim , Hanfu Su , Linhu Ge , Jeong-Heon Cha; J. Microbiol. 2021;59(8):763-770. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1136-2

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Abstract: Helicobacter pylori colonizes human gastric mucosa. Its infection is associated with gastric diseases including gastric cancer. CagA is one of the most important toxins produced by H. pylori. It is related to gastric cancer which can be injected into host cells via a type IV secretion system (T4SS). CagL is a structural component of T4SS apparatus, which triggers host cell signaling pathway. It has been reported that CagL polymorphisms may influence the severity of disease development. To explore the contribution of CagL polymorphisms between East Asian and Western H. pylori in pathogenesis, cagL gene in G27 H. pylori was swapped by K74 cagL which is identical to East Asian CagL consensus sequence and by Western 26695 H. pylori, resulting in G27ΔcagL/cagLK74 and G27ΔcagL/cagL26695, respectively. Intriguingly, G27ΔcagL/ cagLK74 showed significantly less ability of IL-8 induction than G27ΔcagL/cagL26695 while displayed similar abilities of CagA phosphorylation, and cell elongation. Taken together, this study suggests that the CagL polymorphism may influence IL-8 induction, and K74 CagL has less ability to induce IL-8 secretion than G27 or 26695 CagL. Further research should address how the different capabilities of IL-8 induction between intraspecies-CagL are associated with the large differences of the incidence of gastric cancer between East Asian and Western countries.

Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae: Jeeeun Park , Young-Sam Kim , Seong-Jin Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Min-Ju Yu , Young Jae Jeon , Kyoung-Ho Kim; J. Microbiol. 2021;59(6):546-551. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-0678-7

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Abstract: A novel bacterium, designated strain RR4-56T, was isolated from a biofilter of a seawater recirculating aquaculture system. The 16S rRNA gene sequence analysis showed that the isolate was closely related to Halovulum dunhuangense YYQ- 30T (92.6%), Albimonas donghaensis DS2T (91.3%), Pontivivens insulae GYSW-23T (91.3%), and Monaibacterium marinum C7T (90.9%), belonging to the family Rhodobacteraceae. The strain was aerobic, Gram-negative, rod-shaped, oxidasepositive, and catalase-negative. Its optimum temperature, pH, and salinity for growth were 25–30°C, pH 8.5, and 2–3% NaCl (w/v), respectively. Its growth occurred at 15–35°C, pH 5.0–9.5, and 0–7% NaCl (w/v). It contained ubiquinone-10 (Q-10), a respiratory quinone, and the major cellular fatty acids were 11-methyl C18:1 ω7c (31.9%), C18:1 ω6c (30.4%), and C19:0 cyclo ω8c (16.1%). The polar lipids present in the strain were phosphatidylglycerol, an unidentified phospholipid, and an unidentified aminolipid. The strain had one 4,373,045 bp circular chromosome with G + C contents of 65.9 mol% including 4,169 genes, 4,118 coding sequences (CDSs), 3 rRNAs, and 45 tRNAs. Genome annotation predicted some gene clusters related to the degradation of several types of organic matter such as protocatechuate, catechol, and phthalate. Based on the polyphasic characteristics, RR4-56T represents a novel genus and species in the family Rhodobacteraceae, for which the name Pikeienuella piscinae gen. nov., sp. nov. was proposed. The type strain is RR4-56T (= KCTC 52648T = DSM 107918T).

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides: Seong-Yun Jeong , Hong-Joo Son; J. Microbiol. 2021;59(4):389-400. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1086-8

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11 Citations

Abstract: The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β- amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

Reviews

Metaviromics coupled with phage-host identification to open the viral ‘black box’: Kira Moon , Jang-Cheon Cho; J. Microbiol. 2021;59(3):311-323. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1016-9

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10 Citations

Abstract: Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium- based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture- independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.

The functional study of human proteins using humanized yeast: Seho Kim , Juhee Park , Taekyung Kim , Jung-Shin Lee; J. Microbiol. 2020;58(5):343-349. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0136-y

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Abstract: The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the mechanisms required for the functional and optimal expression of human genes. The yeast Saccharomyces cerevisiae has evolved independently of humans for billions of years. Nevertheless, S. cerevisiae has many conserved genes and expression mechanisms that are similar to those in humans. Yeast is the most commonly used model organism for studying the function and expression mechanisms of human genes because it has a relatively simple genome structure, which is easy to manipulate. Many previous studies have focused on understanding the functions and mechanisms of human proteins using orthologous genes and biological systems of yeast. In this review, we mainly introduce two recent studies that replaced human genes and nucleosomes with those of yeast. Here, we suggest that, although yeast is a relatively small eukaryotic cell, its humanization is useful for the direct study of human proteins. In addition, yeast can be used as a model organism in a broader range of studies, including drug screening.

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