Journal of Microbiology

Journal Article

Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6: Younkyung Choi , Minju Joo , Wooseok Song , Minho Lee , Hana Hyeon , Hyun-Lee Kim , Ji-Hyun Yeom , Kangseok Lee , Eunkyoung Shin; J. Microbiol. 2022;60(12):1162-1167. Published online November 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2437-9

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Ribosomes composed of genome-encoded heterogeneous rRNAs are implicated in the rapid adaptation of bacterial cells to environmental changes. A previous study showed that ribosomes bearing the most heterogeneous rRNAs expressed from the rrnI operon (I-ribosomes) are implicated in the preferential translation of a subset of mRNAs, including hspA and tpiA, in Vibrio vulnificus CMCP6. In this study, we show that HspA nascent peptides were predominantly bound to I-ribosomes. Specifically, I-ribosomes were enriched more than two-fold in ribosomes that were pulled down by immunoprecipitation of HspA peptides compared with the proportion of I-ribosomes in crude ribosomes and ribosomes pulled down by immunoprecipitation of RNA polymerase subunit ß peptides in the wild-type (WT) and rrnI-completed strains. Other methods that utilized the incorporation of an affinity tag in 23S rRNA or chimeric rRNA tethering 16S and 23S rRNAs, which generated specialized functional ribosomes in Escherichia coli, did not result in functional I-ribosomes in V. vulnificus CMCP6. This study provides direct evidence of the preferential translation of hspA mRNA by I-ribosomes.

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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
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
Journal of Microbiology.2023; 61(2): 211. CrossRef

Review

Protective and pathogenic role of humoral responses in COVID-19: Uni Park , Nam-Hyuk Cho; J. Microbiol. 2022;60(3):268-275. Published online March 2, 2022; DOI: https://doi.org/10.1007/s12275-022-2037-8

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Abstract

Since the advent of SARS-CoV-2 in Dec. 2019, the global endeavor to identify the pathogenic mechanism of COVID-19 has been ongoing. Although humoral immunity including neutralizing activity play an important role in protection from the viral pathogen, dysregulated antibody responses may be associated with the pathogenic progression of COVID-19, especially in high-risk individuals. In addition, SARS-CoV-2 spike-specific antibodies acquired by prior infection or vaccination act as immune pressure, driving continuous population turnover by selecting for antibody-escaping mutations. Here, we review accumulating knowledge on the potential role of humoral immune responses in COVID-19, primarily focusing on their beneficial and pathogenic properties. Understanding the multifaceted regulatory mechanisms of humoral responses during SARS-CoV-2 infection can help us to develop more effective therapeutics, as well as protective measures against the ongoing pandemic.

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Rise in broadly cross-reactive adaptive immunity against human β-coronaviruses in MERS-recovered patients during the COVID-19 pandemic
So-Hee Kim, Yuri Kim, Sangeun Jeon, Uni Park, Ju-Il Kang, Kyeongseok Jeon, Hye-Ran Kim, Songhyeok Oh, Ji-Young Rhee, Jae-Phil Choi, Wan Beom Park, Sang Won Park, Jeong-Sun Yang, Joo-Yeon Lee, Jihye Kang, Hyoung-Shik Shin, Yeonjae Kim, Seungtaek Kim, Yeon-
Science Advances.2024;[Epub] CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef

Journal Article

Distribution characteristics of fungal communities with depth in paddy fields of three soil types in China: Xu Li , Huanhuan Wang , Xiang Li , Xinyu Li , Huiwen Zhang; J. Microbiol. 2020;58(4):279-287. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9409-8

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Abstract

Little is known about the distribution of fungal communities with soil depth on relatively large scales. In this study, typical paddy soils in three regions (Hailun, Changshu, and Yingtan) from north to south China were selected to investigate the vertical distribution (0-100 cm) of the fungal community by Illumina MiSeq sequencing, and to identify the main factors influencing the fungal community distribution. The results indicated that the structure of the soil fungal community changed significantly with region and soil depth. Soil fungal taxa such as Zygomycota, Glomeromycota, Saccharomycete, Kazachstania, Mortierella, Massariosphaeria, Hypholoma, and Zopfiella were enriched at depths of 0–20 cm, whereas Dothideomycetes, Microbotryomycetes, Tremellomycetes, Sporobolomyces, Cryptococcus, Rhodotorula, Fusarium, and Pyrenochaetopsis had high relative abundances at 80–100 cm. Variance partitioning analysis indicated that the geographic distance contributed more to the fungal community variation than environmental variables on a large scale. In addition, soil total carbon and nitrogen contents were the main environmental factors driving the vertical distribution of the fungal community in paddy soils.

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Region and Crop Type Influenced Fungal Diversity and Community Structure in Agricultural Areas in Qinghai Province
Lianyu Zhou, Xuelan Ma, Longrui Wang, Wenjuan Sun, Yu Liu, Yun Ma, Huichun Xie, Feng Qiao
Agriculture.2023; 14(1): 6. CrossRef
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Kelly C. Shannon, Natasha R. Christman, Byron C. Crump, Michael P. Carey, Joshua Koch, Laura L. Lapham, Jonathan O’Donnell, Brett A. Poulin, Ken D. Tape, Jason A. Clark, Frederick S. Colwell
Journal of Geophysical Research: Biogeosciences.2023;[Epub] CrossRef
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Alexa K. Byers, Loretta G. Garrett, Charlotte Armstrong, Fiona Dean, Steve A. Wakelin
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Microbial communities in the diagnostic horizons of agricultural Isohumosols in northeast China reflect their soil classification
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Jing Chen, Hui Zeng
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Soil texture is a stronger driver of the maize rhizosphere microbiome and extracellular enzyme activities than soil depth or the presence of root hairs
Bunlong Yim, Zeeshan Ibrahim, Lioba Rüger, Minh Ganther, Lorrie Maccario, Søren J. Sørensen, Anna Heintz-Buschart, Mika T. Tarkka, Doris Vetterlein, Michael Bonkowski, Evgenia Blagodatskaya, Kornelia Smalla
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The Effects of Drainage on the Soil Fungal Community in Freshwater Wetlands
Qingqing Zhao, Junhong Bai, Jia Jia, Guangliang Zhang, Jianing Wang, Yongchao Gao
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Diversity and structure of soil fungal communities unveil the building history of a burial mound of ancient Japan (Tobiotsuka Kofun, Okayama Prefecture)
Samuele Voyron, Chiara Tonon, Laura Guglielmone, Luisella Celi, Cesare Comina, Hajime Ikeda, Naoko Matsumoto, Daniele Petrella, Joseph Ryan, Kazuhiro Sato, Akira Seike, Ivan Varriale, Jun Yamashita, Sergio E. Favero-Longo, Eleonora Bonifacio
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Straw retention efficiently improves fungal communities and functions in the fallow ecosystem
Caifang Zhang, Zhaoli Lin, Youxiong Que, Nyumah Fallah, Muhammad Tayyab, Shiyan Li, Jun Luo, Zichu Zhang, Ahmad Yusuf Abubakar, Hua Zhang
BMC Microbiology.2021;[Epub] CrossRef

Research Support, Non-U.S. Gov't

Fungal Community Associated with Genetically Modified Poplar During Metal Phytoremediation: Moonsuk Hur , Young Woon Lim , Jae Jeong Yu , Se Uk Cheon , Young Im Choi , Seok-Hwan Yoon , Sang-Cheol Park , Dong-Il Kim , Hana Yi; J. Microbiol. 2012;50(6):910-915. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2491-9

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Abstract

Due to the increasing demand for phytoremediation, many transgenic poplars have been developed to enhance the bioremediation of heavy metals. However, structural changes to indigenous fungal communities by genetically modified organisms (GMO) presents a major ecological issue, due to the important role of fungi for plant growth in natural environments. To evaluate the effect of GM plant use on environmental fungal soil communities, extensive sequencing-based community analysis was conducted, while controlling the influence of plant clonality, plant age, soil condition, and harvesting season. The rhizosphere soils of GM and wild type (WT) poplars at a range of growth stages were sampled together with unplanted, contaminated soil, and the fungal community structures were investigated by pyrosequencing the D1/D2 region of the 28S rRNA gene. The results show that the overall structure of the rhizosphere fungal community was not significantly influenced by GM poplars. However, the presence of GM specific taxa, and faster rate of community change during poplar growth, appeared to be characteristic of the GM plant-induced effects on soil-born fungal communities. The results of this study provide additional information about the potential effects of GM poplar trees aged 1.5–3 years, on the soil fungal community.

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