Journal of Microbiology

Review

Prokaryotic DNA methylation and its functional roles: Hoon Je Seong , Sang-Wook Han , Woo Jun Sul; J. Microbiol. 2021;59(3):242-248. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0674-y

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DNA methylation is known as a universal mechanism of epigenetic regulation in all kingdoms of life. Particularly, given that prokaryotes lack key elements such as histones and nucleosomes that can structurally modify DNA, DNA methylation is considered a major epigenetic regulator in these organisms. However, because DNA methylation studies have focused primarily on eukaryotes, the mechanism of prokaryotic DNA methylation has been less studied than in eukaryotes. DNA methylation in prokaryotes plays an important role in regulating not only the host defense system, but also the cell cycle, gene expression, and virulence that can respond directly to the environment. Recent advances in sequencing techniques capable of detecting methylation signals have allowed for the characterization of prokaryotic genome-wide epigenetic regulation. In this review, we describe representative examples of cellular events regulated by DNA methylation in prokaryotes, from early studies to current applications.

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Journal Article

A comprehensive in silico analysis of sortase superfamily: Adeel Malik , Seung Bum Kim; J. Microbiol. 2019;57(6):431-443. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8545-5

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Abstract

Sortases are cysteine transpeptidases that assemble surface proteins and pili in their cell envelope. Encoded by all Grampositive bacteria, few Gram-negative bacteria and archaea, sortases are currently divided into six classes (A-F). Due to the steep increase in bacterial genome data in recent years, the number of sortase homologues have also escalated rapidly. In this study, we used protein sequence similarity networks to explore the taxonomic diversity of sortases and also to evaluate the current classification of these enzymes. The resultant data suggest that sortase classes A, B, and D predominate in Firmicutes and classes E and F are enriched in Actinobacteria, whereas class C is distributed in both Firmicutes and Actinobacteria except Streptomyces family. Sortases were also observed in various Gram-negatives and euryarchaeota, which should be recognized as novel classes of sortases. Motif analysis around the catalytic cysteine was also performed and suggested that the residue at 2nd position from cysteine may help distinguish various sortase classes. Moreover, the sequence analysis indicated that the catalytic arginine is highly conserved in almost all classes except sortase F in which arginine is replaced by asparagine in Actinobacteria. Additionally, class A sortases showed higher structural variation as compared to other sortases, whereas inter-class comparisons suggested structures of class C and D2 exhibited best similarities. A better understanding of the residues highlighted in this study should be helpful in elucidating their roles in substrate binding and the sortase function, and successively could help in the development of strong sortase inhibitors.

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Review

[MINIREVIEW] Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea: Chi Nam Seong , Joo Won Kang , Ji Hee Lee , So Yeon Seo , Jung Jae Woo , Chul Park , Kyung Sook Bae , Mi Sun Kim; J. Microbiol. 2018;56(1):1-10. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7318-x

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Abstract

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

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

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk: Jyotiranjan Bal , Suk-Hyun Yun , Myoung-Suk Choi , Soo-Hwan Yeo , Jung-Mi Kim , Dae-Hyuk Kim; J. Microbiol. 2015;53(12):812-819. Published online December 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5516-3

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Abstract

The emerging global importance of Korea’s alcoholic beverages emphasizes the need for quality enhancement of nuruk, a traditional Korean cereal starter that is used extensively in traditional brewing. Apart from fungi and yeasts, bacteria known to be ubiquitously present are also a part of the nuruk ecosystem and are known to influence fermentation activity by influencing fermentation favorable factors. In the current study, bacterial diversity and temporal variations in the traditional wheat-based nuruk, fermented at two representative temperature conditions for 30 days, along with two commercial wheat-based nuruk samples for comparison analysis were evaluated using libraries of PCR amplicons and 454 pyrosequencing targeting of the hypervariable regions V1 to V3 of the 16S rRNA gene. A total of 90,836 16S reads were analyzed and assigned to a total of 314, 321, and 141 Operational Taxonomic Units (OTUs) for nuruk A, B, and C, respectively. Diversity parameters clearly indicated nuruk B to be more diverse in terms of bacterial composition than nuruk A. Taxonomic assignments indicated that nuruk A was dominated by phylum Cyanobacteria, whereas nuruk B was dominated by phylum Actinobacteria. For both nuruk A and B, members of the phylum Firmicutes mostly converged into the family Bacillaceae; these microorganisms might be present in negligible numbers at the beginning but became significant as the fermentation progressed. The commercial samples were predominated by phylum Firmicutes, which is composed of Lactobacillaceae and Leoconostocaceae. The findings of this study provide new insights into understanding the changes in bacterial community structure during traditional nuruk starter production.

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NOTE] Lysinibacillus jejuensis sp. nov., Isolated from Swinery Waste: Ji-Young Kim , So-Hyun Park , Duck-Chul Oh , Young-Ju Kim; J. Microbiol. 2013;51(6):872-876. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-2500-7

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Abstract

A Gram-positive, endospore-forming, rod-shaped bacterium, designated strain N2-5T, was isolated from swinery waste collected in Jeju, Republic of Korea. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain N2-5T formed a phyletic group within the phylum Firmicutes with less than 97.0% similarities to members of the genus Lysinibacillus, its nearest phylogenetic neighbors. The highest levels of sequence similarity to the isolate were observed against Lysinibacillus xylanilyticus XDB9T (96.8%), Lysinibacillus macroides LMG 18474T (95.6%), and Lysinibacillus parviboronicapiens BAM-582 T (95.6%). The organism grew optimally at 30°C and pH 7 and in the presence of 1–3% (w/v) NaCl. Strain N2-5T was chemotaxonomically characterized by possessing menaquinone-7 (MK-7) as the major menaquinone, and iso-C15:0 (54.9%), iso-C17:1ω10c (12.0%), and C16:1ω7c alcohol (11.8%) as the predominant fatty acids. The genomic DNA G+C content of the novel strain was 43.3 mol% and the cell-wall peptidoglycan was type A4α. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Based on its phenotypic properties and phylogenetic data, strain N2-5T (=DSM 28310T =KCTC13837 T) represents a novel species in the genus Lysinibacillus, for which the name Lysinibacillus jejuensis sp. nov. is proposed.

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Bhargavaea indica sp. nov., a Member of the Phylum Firmicutes, Isolated from Arabian Sea Sediment: Pankaj Verma , Chi Nam Seong , Prashant Kumar Pandey , Ramesh Ramchandra Bhonde , Cathrin Spröer , Manfred Rohde , Yogesh Shreepad Shouche; J. Microbiol. 2013;51(1):36-42. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2488-z

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Abstract

A Gram-positive, aerobic, coccoid-rod shaped, non-motile, catalase- and oxidase-positive bacterium, designated strain KJW98T, was isolated from the marine sediment of Karwar jetty, west coast of India. The strain was β-haemolytic, nonendospore-forming and grew with 0–8.5% (w/v) NaCl, at 15–48°C and at pH 6.5–9.0, with optimum growth with 0.5% (w/v) NaCl, at 42°C and at pH 7.0–8.0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences showed that strain KJW98T forms a lineage within the genus Bhargavaea. The G+C content of the genomic DNA was 55 mol%. The DNA–DNA relatedness values of strain KJW98T with B. eijingensis DSM 19037T, B. cecembensis LMG 24411T and B. ginsengi DSM 19038T were 43.2, 39 and 26.5%, respectively. The major fatty acids were anteiso-C15:0 (37.7%), iso-C15:0 (19.7%), anteiso-C17:0 (17.0%) and iso-C16:0 (11.1%). The predominant menaquinone was MK-8 and the cell-wall peptidoglycan was of A4α type with L-lysine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The phenotypic, genotypic and DNA–DNA relatedness data indicate that strain KJW98T should be distinguished from the members of the genus Bhargavaea, for which the name Bhargavaea indica sp. nov. is proposed with the type strain KJW98T (=KCTC 13583T =LMG 25219T).

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