Journal of Microbiology

Volume 60(11); November 2022

Review

[Minireview]Cytoplasmic molecular chaperones in Pseudomonas species: Hyunhee Kim , Seongjoon Moon , Soojeong Ham , Kihyun Lee , Ute Römling , Changhan Lee; J. Microbiol. 2022;60(11):1049-1060. Published online November 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2425-0

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Pseudomonas is widespread in various environmental and host niches. To promote rejuvenation, cellular protein homeostasis must be finely tuned in response to diverse stresses, such as extremely high and low temperatures, oxidative stress, and desiccation, which can result in protein homeostasis imbalance. Molecular chaperones function as key components that aid protein folding and prevent protein denaturation. Pseudomonas, an ecologically important bacterial genus, includes human and plant pathogens as well as growth-promoting symbionts and species useful for bioremediation. In this review, we focus on protein quality control systems, particularly molecular chaperones, in ecologically diverse species of Pseudomonas, including the opportunistic human pathogen Pseudomonas aeruginosa, the plant pathogen Pseudomonas syringae, the soil species Pseudomonas putida, and the psychrophilic Pseudomonas antarctica.

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An innovative utilization approach for by-products of biogas desulfurization：Co-hydrothermal treatment of sulfur with biogas slurry to prepare sulfur-enriched liquid fertilizer
Zhijie Xie, Fang Deng, Yuqin Wan, Yiping Luo, Qin Cao, Yichao Chen, Dong Li
Process Biochemistry.2024; 147: 522. CrossRef
Isolation of Pseudomonas oleovorans Carrying Multidrug Resistance Proteins MdtA and MdtB from Wastewater
Haifeng Wang, Chenyang Sun, Xing Chen, Kai Yan, Hongxuan He
Molecules.2023; 28(14): 5403. CrossRef
Development of heat-shock resistance in Legionella pneumophila modeled by experimental evolution
Jeffrey Liang, Gillian Cameron, Sébastien P. Faucher, Christopher A. Elkins
Applied and Environmental Microbiology.2023;[Epub] CrossRef

Journal Articles

Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish: Do-Hun Gim , So-Yeon Lee , Jeong Eun Han , Jae-Yun Lee , Seo Min Kang , Jin-Woo Bae; J. Microbiol. 2022;60(11):1061-1069. Published online September 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2250-5

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Abstract

Three novel strains, (D17T, D13, and D25T) isolated from the gut of the Korean dark sleeper (Odontobutis platycephala), Kumgang fat minnow (Rhynchocypris kumgangensis), and the Korean oily bitterling (Tanakia koreensis) were identified as two novel species. Strains D17T and D13 showed the highest similarities in 16S rRNA gene and complete genome sequences to Deefgea rivuli WB 3.4-79T (98.0% and 97.9%, respectively, of 16S rRNA gene sequence similarity, 77.8% and 77.7%, respectively, of orthologous average nucleotide identity, Ortho- ANI, and 21.9% and 21.9%, respectively, of digital DNA-DNA hybridization, dDDH). Strain D17T showed the highest similarities in 16S rRNA gene and complete genome sequences to D13 (99.9% of 16S rRNA gene sequence similarity, 91.8% of OrthoANI, and 45.1% of dDDH); therefore, strains D17T and D13 were assigned as the same species. Strain D25T showed the highest similarities in 16S rRNA gene and complete genome sequences to D. chitinilytica Nsw-4T (98.2% of 16S rRNA gene sequence similarity, 82.4% of OrthoANI, and 25.1% of dDDH). Strains D17T and D13 were Gram-stain-negative, facultative anaerobes, rod-shaped, non-motile, and non-flagellated. Strain D25T was Gram-stain-negative, facultative anaerobe, rodshaped, and motile by a single polar flagellum. These strains had C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as the major cellular fatty acids and possessed Q-8 as a major respiratory ubiquinone. All three strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. Based on polyphasic taxonomic data, strains D17T, D13, and D25T represent two novel species of the genus Deefgea. We propose the name Deefgea piscis sp. nov. for strains D17T (= KCTC 82958T = JCM 34941T) and D13 (= KCTC 92368), and Deefgea tanakiae sp. nov. for strain D25T (= KCTC 82959T = JCM 34942T).

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Fecal metagenomic and metabolomic analyses reveal non-invasive biomarkers of Flavobacterium psychrophilum infection in ayu ( Plecoglossus altivelis )
Mio Takeuchi, Erina Fujiwara-Nagata, Kyohei Kuroda, Kenji Sakata, Takashi Narihiro, Jun Kikuchi, Katherine McMahon
mSphere.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef

Rasiella rasia gen. nov. sp. nov. within the family Flavobacteriaceae isolated from seawater recirculating aquaculture system: Seong-Jin Kim , Young-Sam Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Jeeeun Park , Min-Ju Yu , Kyoung-Ho Kim; J. Microbiol. 2022;60(11):1070-1076. Published online October 17, 2022; DOI: https://doi.org/10.1007/s12275-022-2099-7

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Abstract

A novel bacterium designated RR4-40T was isolated from a biofilter of seawater recirculating aquaculture system in Busan, South Korea. Cells are strictly aerobic, Gram-negative, irregular short rod, non-motile, and oxidase- and catalase-negative. Growth was observed at 15–30°C, 0.5–6% NaCl (w/v), and pH 5.0–9.5. The strain grew optimally at 28°C, 3% salinity (w/v), and pH 8.5. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain RR4-40T was most closely related to Marinirhabdus gelatinilytica NH83T (94.16% of 16S rRNA gene similarity) and formed a cluster with genera within the family Flavobacteriaceae. The values of the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) between genomes of strain RR4-40T and M. gelatinilytica NH83T were 72.91, 18.2, and 76.84%, respectively, and the values against the strains in the other genera were lower than those. The major fatty acids were iso-C15:0 (31.34%), iso-C17:0 3-OH (13.65%), iso-C16:0 3-OH (10.61%), and iso-C15:1 G (10.38%). The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, aminolipid, glycolipid, and sphingolipid. The major respiratory quinone was menaquinone-6 (MK-6) and the DNA G + C content of strain RR4-40T was 37.4 mol%. According to the polyphasic analysis, strain RR4-40T is considered to represent a novel genus within the family Flavobacteriaceae, for which the name Rasiella rasia gen. nov, sp. nov. is proposed. The type strain is RR4-40T (= KCTC 52650T = MCCC 1K04210T).

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Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef
Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Correlation between fat accumulation and fecal microbiota in crossbred pigs: Xin Li , Mengyu Li , Jinyi Han , Chuang Liu , Xuelei Han , Kejun Wang , Ruimin Qiao , Xiu-Ling Li , Xin-Jian Li; J. Microbiol. 2022;60(11):1077-1085. Published online September 9, 2022; DOI: https://doi.org/10.1007/s12275-022-2218-5

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Abstract

Backfat thickness (BF) is an important indicator of fat deposition capacity and lean meat rate in pigs and is very important in porcine genetics and breeding. Intestinal microbiota plays a key role in nutrient digestion and utilization with a profound impact on fat deposition of livestock animals. To investigate the relationship between the pig gut microbiome and BF, 20 low-BF (L-BF) and 20 high-BF (H-BF) pigs were selected as two groups from Yunong Black pigs in the present study. Fecal samples from pigs were analyzed for microbial diversity, composition, and predicted functionality using 16S rRNA gene sequencing. The results showed that there were significant differences in microbial β diversity between the two groups. LEfSe analysis revealed a number of bacterial features being differentially enriched in either L-BF or H-BF pigs. Spearman correlation analysis identified the abundance of Oscillospira, Peptococcus, and Bulleidia were significantly positive correlations with BF (P < 0.05), while Sutterella and Bifidobacterium were significantly negatively correlated with BF (P < 0.05). Importantly, the bacteria significantly positively correlated with BF mainly belong to Clostridium, which can ferment host-indigestible plant polysaccharides into shortchain fatty acid (SCFA) and promote fat synthesis and deposition. Predictive functional analysis indicated that the pathway abundance of cell motility and glycan biosynthesis were significantly widespread in the microbiota of the H-BF group. The results of this study will be useful for the development of microbial biomarkers for predicting and improving porcine BF, as well as for the investigation of targets for dietary strategies.

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Carboxymethyl chitosan-dialdehyde glucan/polydopamine carrier targeted delivery Bacillus subtilis on enhancing oral utilization and intestinal colonization in mice
Lulu Chu, Luyu Xie, Bingzhi Chen, Yuji Jiang, Wenjie Wang
International Journal of Biological Macromolecules.2024; 280: 135574. CrossRef
Impact of Early Weaning on Development of the Swine Gut Microbiome
Benoit St-Pierre, Jorge Yair Perez Palencia, Ryan S. Samuel
Microorganisms.2023; 11(7): 1753. CrossRef
Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes
Kang Xiao, Zhengyu Chen, Qin Long
Journal of Microbiology.2023; 61(5): 571. CrossRef

Expression and purification of intracrine human FGF 11 and study of its FGFR-dependent biological activity: Kyeong Won Lee , Young Jun An , Janet Lee , Ye-Eun Jung , In Young Ko , Jonghwa Jin , Ji Hoon Park , Won Kyu Lee , Kiweon Cha , Sun-Shin Cha , Jung-Hyun Lee , Hyung-Soon Yim; J. Microbiol. 2022;60(11):1086-1094. Published online November 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2406-3

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Abstract

Fibroblast growth factor 11 (FGF11) is one of intracrine FGFs (iFGFs), which function within cells. Unlike canonical FGFs, FGF11 remains intracellularly and plays biological roles in FGF receptor (FGFR)-independent manner. Here, we established an expression system of recombinant FGF11 proteins in E. coli and investigated whether the extracellular administration of FGF11 can activate cellular signaling. Human FGF11 has two isoforms, FGF11a and FGF11b, depending on the presence of nuclear localization sequences (NLSs) in the N-terminus. Because these two isoforms are unstable, we prepared an FGF11a-Mut by substituting three cysteine residues in the NLS with serine and FGF11b-ΔC with C-terminal truncation. The introduction of mutation in the NLS improved the solubility of FGF11 prepared from E. coli. Exogenous addition of FGF11b and FGF11b-ΔC to BALB3T3 increased cell proliferation, while FGF11a-Mut exerted no effect. FGF11b-ΔC showed higher cell proliferation activity and FGFR signaling than FGF11b. The cell-proliferating activities of FGF11b and FGF11b-ΔC were blocked by an FGFR1 inhibitor or a recombinant FGFR1, confirming the FGFR1- dependent extracellular activity of FGF11b. The analysis of circular dichroism suggested that the C-terminus of FGF11 has an α-helical structure, which may affect its interaction with FGFR1. These results suggest that the N-and C-terminus of recombinant FGF11 are involved in the activation of FGFR1. The above results provide novel insights into the function and mechanism of FGF11 that may aid the development of useful ligands for FGFR regulation.

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Glycosylation of FGF/FGFR: An underrated sweet code regulating cellular signaling programs
Aleksandra Gędaj, Paulina Gregorczyk, Dominika Żukowska, Aleksandra Chorążewska, Krzysztof Ciura, Marta Kalka, Natalia Porębska, Łukasz Opaliński
Cytokine & Growth Factor Reviews.2024; 77: 39. CrossRef
FGF homologous factors are secreted from cells to induce FGFR‐mediated anti‐apoptotic response
Martyna Biadun, Martyna Sochacka, Radoslaw Karelus, Karolina Baran, Aleksandra Czyrek, Jacek Otlewski, Daniel Krowarsch, Lukasz Opalinski, Malgorzata Zakrzewska
The FASEB Journal.2023;[Epub] CrossRef
FGF/FGFR1 system in paired breast tumor-adjacent and tumor tissues, associations with mammographic breast density and tumor characteristics
Öykü Boraka, Marie Klintman, Johan Vallon-Christersson, Sophia Zackrisson, Per Hall, Signe Borgquist, Ann H. Rosendahl
Frontiers in Oncology.2023;[Epub] CrossRef

Sulforaphane kills Mycobacterium tuberculosis H37Ra and Mycobacterium smegmatis mc2155 through a reactive oxygen species dependent mechanism: Yongjie Zhao , Shengwen Shang , Ya Song , Tianyue Li , Mingliang Han , Yuexuan Qin , Meili Wei , Jun Xi , Bikui Tang; J. Microbiol. 2022;60(11):1095-1105. Published online September 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2284-8

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Abstract

Mycobacterium tuberculosis (M. tuberculosis) is a highly pathogenic intracellular pathogen that causes tuberculosis (TB), the leading cause of mortality from single infections. Redox homeostasis plays a very important role in the resistance of M. tuberculosis to antibiotic damage and various environmental stresses. The antioxidant sulforaphane (SFN) has been reported to exhibit anticancer activity and inhibit the growth of a variety of bacteria and fungi. Nonetheless, it remains unclear whether SFN exhibits anti-mycobacterial activity. Our
results
showed that the SFN against M. tuberculosis H37Ra exhibited bactericidal activity in a time and dose-dependent manner. The anti-tubercular activity of SFN was significantly correlated with bacterial reactive oxygen species (ROS) levels. In addition, SFN promoted the bactericidal effect of macrophages on intracellular bacteria in a dose-dependent manner, mediated by increasing intracellular mitochondrial ROS levels and decreasing cytoplasmic ROS levels. Taken together, our data revealed the previously unrecognized antimicrobial functions of SFN. Future studies focusing on the mechanism of SFN in macrophages against M. tuberculosis are essential for developing new host-directed therapeutic approaches against TB.

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NK-derived exosome miR-1249-3p inhibits Mycobacterium tuberculosis survival in macrophages by targeting SKOR1
Fengqian Ma, Xuan Wang, Zhanghua Qiu, Shoupeng Ding, Wenya Du, Yumei Dai, Tao Ma, Linzhi Yue, Guofu Wang, Tao Wang, Ling Geng, Lixian Wu
Cytokine.2024; 175: 156481. CrossRef
Lactobacillus plantarum increase the sulforaphane formation efficiency via microbial-targeted delivery system in vivo
Yunping Wang, Yiteng Zhang, Xiude Li, Liping Luo, Fangjian Ning, Tao Liu, Jinwang Li
Food Bioscience.2024; 62: 105544. CrossRef
Identifying autophagy-related genes as potential targets for immunotherapy in tuberculosis
Sifang Xiao, Ting Zhou, Jianhua Pan, Xiaohua Ma, Guomin Shi, Binyuan Jiang, Yan-gen Xiang
International Immunopharmacology.2023; 118: 109956. CrossRef

Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV’s oncogenic role: Chunpeng Yu , Jian Li , Qun Li , Shuai Chang , Yufeng Cao , Hui Jiang , Lingling Xie , Gang Fan , Song Wang; J. Microbiol. 2022;60(11):1106-1112. Published online October 17, 2022; DOI: https://doi.org/10.1007/s12275-022-2371-x

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Abstract

Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.

Citations

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Conserved spatiotemporal expression landscape of dominant tRNA genes in human and mouse
Evan Y. Wu, Laura Landry
Biochemical and Biophysical Research Communications.2023; 681: 173. CrossRef
Evolution and diversity of nucleotide and dinucleotide composition in poxviruses
Cristian Molteni, Diego Forni, Rachele Cagliani, Ignacio G. Bravo, Manuela Sironi
Journal of General Virology .2023;[Epub] CrossRef
Krüppel-like factor 15 in liver diseases: Insights into metabolic reprogramming
Hao Chen, Lan-Lan Li, Yan Du
Frontiers in Pharmacology.2023;[Epub] CrossRef

Inhibition of KIF20A suppresses the replication of influenza A virus by inhibiting viral entry: Hoyeon Jeon , Younghyun Lim , In-Gu Lee , Dong-In Kim , Keun Pil Kim , So-Hee Hong , Jeongkyu Kim , Youn-Sang Jung , Young-Jin Seo; J. Microbiol. 2022;60(11):1113-1121. Published online November 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2436-x

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Abstract

The influenza A virus (IAV) has caused several pandemics, and therefore there are many ongoing efforts to identify novel antiviral therapeutic strategies including vaccines and antiviral drugs. However, influenza viruses continuously undergo antigenic drift and shift, resulting in the emergence of mutated viruses. In turn, this decreases the efficiency of existing vaccines and antiviral drugs to control IAV infection. Therefore, this study sought to identify alternative therapeutic strategies targeting host cell factors rather than viruses to avoid infection by mutated viruses. Particularly, we investigated the role of KIF20A that is one of kinesin superfamily proteins in the replication of IAV. The KIF20A increased viral protein levels in IAV-infected cells by regulating the initial entry stage during viral infection. Furthermore, the KIF20A inhibitor significantly suppressed viral replication, which protected mice from morbidity and mortality. Therefore, our findings demonstrated that KIF20A is highly involved in the viral replication process and viral propagation both in vitro and in vivo, and could thus be used as a target for the development of novel antiviral drugs.

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Emerging roles of cytoskeletal transport and scaffold systems in human viral propagation
Younghyun Lim, Yong-Bin Cho, Young-Jin Seo
Animal Cells and Systems.2024; 28(1): 506. CrossRef

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