Journal of Microbiology

Review

Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration‑Inhibitory Conditions: Yuna Oh , Ha-Na Lee , Eon-Min Ko , Ji-A Jeong , Sae Woong Park , Jeong-Il Oh; J. Microbiol. 2023;61(3):297-315. Published online February 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00026-8

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Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.

Citations

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Host Immune Pathways to Mycobacterium tuberculosis Infection
Eun-Jin Park, Insoo Kim, Eun-Kyeong Jo
Journal of Bacteriology and Virology.2024; 54(3): 167. CrossRef
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Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef

Journal Articles

Propionate, together with triple antibiotics, inhibits the growth of Enterococci: Soyoung Jeong , Yunjae Lee , Cheol-Heui Yun , Ok-Jin Park , Seung Hyun Han; J. Microbiol. 2019;57(11):1019-1024. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9434-7

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Abstract

Enterococci are Gram-positive facultative anaerobic bacteria that colonize the oral cavity and gastrointestinal tract. Enterococcal infections, mainly caused by Enterococcus faecalis and Enterococcus faecium, include apical periodontitis, endocarditis, and bloodstream infections. Recently, vancomycinresistant Enterococci are considered major pathogens that are common but difficult to treat, especially in nosocomial settings. Moreover, E. faecalis is closely associated with recurrent endodontic infections and failed endodontic treatment. In this study, we investigated the effects of short-chain fatty acids (SCFAs), acetate, propionate, and butyrate, which are metabolites fermented by gut microbiota, on the growth of Enterococci. Enterococci were cultured in the presence or absence of acetate, propionate, or butyrate, and the optical density at 600 nm was measured to determine bacterial growth. The minimum inhibitory concentration/minimum bactericidal concentration test was conducted. Bacteria were treated with a SCFA, together with clinically used endodontic treatment methods such as triple antibiotics (metronidazole, minocycline, and ciprofloxacin) and chlorhexidine gluconate (CHX) to determine the effects of combination treatment. Of the SCFAs, propionate had a bacteriostatic effect, inhibiting the growth of E. faecalis in a dose-dependent manner and also that of clinical strains of E. faecalis isolated from dental plaques. Meanwhile, acetate and butyrate had minimal effects on E. faecalis growth. Moreover, propionate inhibited the growth of other Enterococci including E. faecium. In addition, combination treatment of propionate and triple antibiotics led to further growth inhibition, whereas no cooperative effect was observed at propionate plus CHX. These results indicate that propionate attenuates the growth of Enterococci, suggesting propionate as a potential agent to control Enterococcal infections, especially when combined with triple antibiotics.

Citations

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Serotype-Dependent Inhibition of Streptococcus pneumoniae Growth by Short-Chain Fatty Acids
Suwon Lim, Dongwook Lee, Sungho Jeong, Jeong Woo Park, Jintaek Im, Bokeum Choi, Donghyun Gwak, Cheol-Heui Yun, Ho Seong Seo, Seung Hyun Han
Journal of Microbiology and Biotechnology.2024; 34(1): 47. CrossRef
Microbiota signatures associated with invasive Candida albicans infection in the gastrointestinal tract of immunodeficient mice
Jia-Ying Yan, Tsung-Han Lin, Yu-Tang Jong, Jun-Wei Hsueh, Sze-Hsien Wu, Hsiu-Jung Lo, Yee-Chun Chen, Chien-Hsiung Pan
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium
Paul B. Stege, Dirkjan Schokker, Frank Harders, Soumya K. Kar, Norbert Stockhofe, Vera Perricone, Johanna M. J. Rebel, Ingrid C. de Jong, Alex Bossers
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Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics
Yahan Wei, Dennise Palacios Araya, Kelli L. Palmer
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Jiajia Zhu, Yunsheng Chen, Kálmán Imre, Damla Arslan-Acaroz, Fatih Ramazan Istanbullugil, Yuwen Fang, Gaspar Ros, Kui Zhu, Ulas Acaroz
One Health Advances.2023;[Epub] CrossRef
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Fangfang Yue, Jiaxin Xu, Sitan Zhang, Xinyu Hu, Xin Wang, Xin Lü
International Journal of Biological Macromolecules.2022; 209: 825. CrossRef
Dual role of microbiota-derived short-chain fatty acids on host and pathogen
Rasoul Mirzaei, Elahe Dehkhodaie, Behnaz Bouzari, Mandana Rahimi, Abolfazl Gholestani, Seyed Reza Hosseini-Fard, Hossein Keyvani, Ali Teimoori, Sajad Karampoor
Biomedicine & Pharmacotherapy.2022; 145: 112352. CrossRef
RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus growth inhibition by propionate
Jintaek Im, Dongwook Lee, Ok-Jin Park, Sathishkumar Natarajan, Junhyung Park, Cheol-Heui Yun, Seung Hyun Han
Frontiers in Microbiology.2022;[Epub] CrossRef
Propionate Attenuates Growth of Oral Streptococci through Enhancing Methionine Biosynthesis
Taehwan Park, Jintaek Im, A Reum Kim, Dongwook Lee, Sungho Jeong, Cheol-Heui Yun, Seung Hyun Han
Journal of Microbiology and Biotechnology.2022; 32(10): 1234. CrossRef
Bacterial-Induced Blood Pressure Reduction: Mechanisms for the Treatment of Hypertension via the Gut
Tyler Alexander Cookson
Frontiers in Cardiovascular Medicine.2021;[Epub] CrossRef
Influence of operating conditions on the persistence of E. coli, enterococci, Clostridium perfringens and Clostridioides difficile in semi-continuous mesophilic anaerobic reactors
Derongs Lorine, Druilhe Céline, Le Maréchal Caroline, Barbut Frédéric, Heurtevent Lorette, Buffet Julie, Martin Laure, Ziebal Christine, Poezevara Typhaine, Rouxel Sandra, Houard Emmanuelle, Syed Zaidi Rabab, Couturier Jeanne, Pourcher Anne-Marie
Waste Management.2021; 134: 32. CrossRef
Short-Chain Fatty Acids as a Potential Treatment for Infections: a Closer Look at the Lungs
Marina Gomes Machado, Valentin Sencio, François Trottein, Andreas J. Bäumler
Infection and Immunity.2021;[Epub] CrossRef
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Valentin Sencio, Marina Gomes Machado, François Trottein
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Enhanced biofilm formation of Streptococcus gordonii with lipoprotein deficiency
Ok‐Jin Park, Solmin Jung, Taehwan Park, A Reum Kim, Dongwook Lee, Hyun Jung Ji, Ho Seong Seo, Cheol‐Heui Yun, Seung Hyun Han
Molecular Oral Microbiology.2020; 35(6): 271. CrossRef

Isolation, cultivation, and genome analysis of proteorhodopsincontaining SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322: Junhak Lee , Kae Kyoung Kwon , Seung-Il Lim , Jaeho Song , Ah Reum Choi , Sung-Hyun Yang , Kwang-Hwan Jung , Jung-Hyun Lee , Sung Gyun Kang , Hyun-Myung Oh , Jang-Cheon Cho; J. Microbiol. 2019;57(8):676-687. Published online June 14, 2019; DOI: https://doi.org/10.1007/s12275-019-9001-2

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Abstract

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmicphase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.

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Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322
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Stephen C. Hardies, Byung Cheol Cho, Gwang Il Jang, Zhiqing Wang, Chung Yeon Hwang
Viruses.2023; 15(7): 1475. CrossRef
Seasonal niche differentiation among closely related marine bacteria
Adrià Auladell, Albert Barberán, Ramiro Logares, Esther Garcés, Josep M Gasol, Isabel Ferrera
The ISME Journal.2022; 16(1): 178. CrossRef
Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef
Towards culturing the microbe of your choice
J. Cameron Thrash
Environmental Microbiology Reports.2021; 13(1): 36. CrossRef
Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics
Atsushi Kobiyama, Jonaira Rashid, Md. Shaheed Reza, Yuri Ikeda, Yuichiro Yamada, Toshiaki Kudo, Nanami Mizusawa, Saki Yanagisawa, Daisuke Ikeda, Shigeru Sato, Takehiko Ogata, Kazuho Ikeo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Sat
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Shan-Hui Li, Jaeho Song, Ilnam Kang, Juchan Hwang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(6): 463. CrossRef
Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea
Paul A. Steiner, Javier Geijo, Eduard Fadeev, Aleix Obiol, Eva Sintes, Thomas Rattei, Gerhard J. Herndl
Frontiers in Microbiology.2020;[Epub] CrossRef
High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(11): 893. CrossRef
Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy
Konstantinos T. Konstantinidis, Ramon Rosselló‐Móra, Rudolf Amann
Environmental Microbiology.2020; 22(3): 819. CrossRef
Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation
Michael W. Henson, V. Celeste Lanclos, David M. Pitre, Jessica Lee Weckhorst, Anna M. Lucchesi, Chuankai Cheng, Ben Temperton, J. Cameron Thrash, Robert M. Kelly
Applied and Environmental Microbiology.2020;[Epub] CrossRef

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

Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii: Hackwon Do , Chang Woo Lee , Sung Gu Lee , Hara Kang , Chul Min Park , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee; J. Microbiol. 2016;54(2):114-121. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5549-2

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Abstract

The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NADdependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.

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Journal of Molecular Biology.2019; 431(3): 524. CrossRef
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M. G. Khrenova, E. D. Kots, A. M. Kulakova, A. V. Nemukhin
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NAD+ promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1
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NOTE] Biosynthetic Pathway for Poly(3-Hydroxypropionate) in Recombinant Escherichia coli: Qi Wang , Changshui Liu , Mo Xian , Yongguang Zhang , Guang Zhao; J. Microbiol. 2012;50(4):693-697. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2234-y

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Abstract: Poly(3-hydroxypropionate) (P3HP) is a biodegradable and biocompatible thermoplastic. In this study, we engineered a P3HP biosynthetic pathway in recombinant Escherichia coli. The genes for malonyl-CoA reductase (mcr, from Chloroflexus aurantiacus), propionyl-CoA synthetase (prpE, from E. coli), and polyhydroxyalkanoate synthase (phaC1, from Ralstonia eutropha) were cloned and expressed in E. coli. The E. coli genes accABCD encoding acetyl-CoA carboxylase were used to channel the carbon into the P3HP pathway. Using glucose as a sole carbon source, the cell yield and P3HP content were 1.32 g/L and 0.98% (wt/wt [cell dry weight]), respectively. Although the yield is relatively low, our study shows the feasibility of engineering a P3HP biosynthetic pathway using a structurally unrelated carbon source in bacteria.

Published Erratum

Erratum] The transcription factor Cas5 suppresses hyphal morphogenesis during yeast-form growth in Candida albicans: Jong-Myeong Kim , Hye Yun Moon , Dong Wook Lee , Hyun Ah Kang , Jeong-Yoon Kim; J. Microbiol. 2021;59(11):1063-1063.; DOI: https://doi.org/10.1007/s12275-021-0326-2

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