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Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids
Dongjin Choi , Yoonsoo Hahn
J. Microbiol. 2023;61(10):917-927.   Published online October 16, 2023
DOI: https://doi.org/10.1007/s12275-023-00083-z
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AbstractAbstract
Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage at a conserved GAA AAA A ( GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA polymerase slippage rates at the GA6 motif. Our analysis revealed that the frequency of the A insertion variant ranges from 0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6 slippage site, and contribute to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.

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  • Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
    Dongjin Choi, Hyerin Park, Seungwoo Baek, Myeung Seok Choi, Sylvain Legay, Gea Guerriero, Jean-François Hausman, Yoonsoo Hahn
    Acta Virologica.2025;[Epub]     CrossRef
  • Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins
    Veronika Hýsková, Kateřina Bělonožníková, Josef Chmelík, Hana Hoffmeisterová, Noemi Čeřovská, Tomáš Moravec, Helena Ryšlavá
    Plants.2024; 13(9): 1236.     CrossRef
  • Reconceptualizing transcriptional slippage in plant RNA viruses
    Adrian A. Valli, María Luisa Domingo-Calap, Alfonso González de Prádena, Juan Antonio García, Hongguang Cui, Cécile Desbiez, Juan José López-Moya, Shou-Wei Ding, Andrew Firth
    mBio.2024;[Epub]     CrossRef
Comparative genomics analysis of Pediococcus acidilactici species
Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao
J. Microbiol. 2021;59(6):573-583.   Published online May 15, 2021
DOI: https://doi.org/10.1007/s12275-021-0618-6
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  • 18 Web of Science
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AbstractAbstract
Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.

Citations

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  • Pediococcus acidilactici Y01 reduces HFD-induced obesity via altering gut microbiota and metabolomic profiles and modulating adipose tissue macrophage M1/M2 polarization
    Yujing Wang, Yu Xue, Huan Xu, Qian Zhu, Kaili Qin, Zhonglei He, Aixiang Huang, Min Mu, Xinrong Tao
    Food & Function.2025;[Epub]     CrossRef
  • Draft genome sequence of Pediococcus acidilactici 3G3 isolated from Philippine fermented pork
    Zachary B. Lara, Mia Beatriz C. Amoranto, Francisco B. Elegado, Leslie Michelle M. Dalmacio, Marilen Parungao Balolong, Catherine Putonti
    Microbiology Resource Announcements.2024;[Epub]     CrossRef
  • The Potential of Pediococcus acidilactici Cell-Free Supernatant as a Preservative in Food Packaging Materials
    Katherine Kho, Adinda Darwanti Kadar, Mario Donald Bani, Ihsan Tria Pramanda, Leon Martin, Matthew Chrisdianto, Ferren Pratama, Putu Virgina Partha Devanthi
    Foods.2024; 13(5): 644.     CrossRef
  • The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers
    Wagiha S. Elkalla, Yasser M. Ragab, Mohamed A. Ramadan, Nahla M. Mansour
    Egyptian Pharmaceutical Journal.2024; 23(4): 702.     CrossRef
  • Effects of Pediococcus acidilactici and Rhizopus Oryzae on protein degradation and flavor formation in fermented mutton sausages
    Zihan Li, Wei Su, Yingchun Mu, Qi Qi, Li Jiang
    LWT.2024; 213: 117075.     CrossRef
  • Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs
    Shaoqi Tian, Yinhong Jiang, Qiannan Han, Chuang Meng, Feng Ji, Bin Zhou, Manhong Ye
    Probiotics and Antimicrobial Proteins.2024;[Epub]     CrossRef
  • Effect of ginsenoside fermented by Pediococcus acidilactici XM-06 on preventing diarrhea in mice via regulating intestinal barrier function and gut microbiota
    Wen-Man Xu, Qi Liu, Si-Yao Fan, Zi-Xin Wang, Shi-Rui Lu, Jie Liu, Hong-Jie Piao, Wenxiu Ji, Wei-Wei Dong
    Journal of Functional Foods.2024; 123: 106594.     CrossRef
  • Population and functional genomics of lactic acid bacteria, an important group of food microorganism: Current knowledge, challenges, and perspectives
    Weicheng Li, Qiong Wu, Lai‐yu Kwok, Heping Zhang, Renyou Gan, Zhihong Sun
    Food Frontiers.2024; 5(1): 3.     CrossRef
  • CRISPR-Cas systems of lactic acid bacteria and applications in food science
    Yanhua Cui, Xiaojun Qu
    Biotechnology Advances.2024; 71: 108323.     CrossRef
  • Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
    Ismail Gumustop, Fatih Ortakci
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods
    Ruhong Wang, Junrui Wu, Nan Jiang, Hao Lin, Feiyu An, Chen Wu, Xiqing Yue, Haisu Shi, Rina Wu
    Critical Reviews in Food Science and Nutrition.2023; 63(5): 569.     CrossRef
  • Changes in Lacto-Fermented Agaricus bisporus (White and Brown Varieties) Mushroom Characteristics, including Biogenic Amine and Volatile Compound Formation
    Elena Bartkiene, Paulina Zarovaite, Vytaute Starkute, Ernestas Mockus, Egle Zokaityte, Gintare Zokaityte, João Miguel Rocha, Romas Ruibys, Dovile Klupsaite
    Foods.2023; 12(13): 2441.     CrossRef
  • Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages
    José García-López, Claudia Teso-Pérez, Antonio Martín-Platero, Juan Peralta-Sánchez, Juristo Fonollá-Joya, Manuel Martínez-Bueno, Alberto Baños
    Foods.2023; 12(13): 2445.     CrossRef
  • Exploring the impact of initial moisture content on microbial community and flavor generation in Xiaoqu baijiu fermentation
    Huan Wang, Chunhong Sun, Shengzhi Yang, Yulei Ruan, Linjie Lyu, Xuewu Guo, Xiaole Wu, Yefu Chen
    Food Chemistry: X.2023; 20: 100981.     CrossRef
  • Screening and Constructing a Library of Promoter-5′-UTR Complexes with Gradient Strength in Pediococcus acidilactici
    Yize Jia, Chao Huang, Yin Mao, Shenghu Zhou, Yu Deng
    ACS Synthetic Biology.2023; 12(6): 1794.     CrossRef
  • Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods
    Basista Rabina Sharma, Prakash M. Halami, Jyoti Prakash Tamang
    Food Science and Biotechnology.2022; 31(1): 1.     CrossRef
  • Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections
    Hassan M. Al-Emran, Jannatul Ferdouse Moon, Md. Liton Miah, Nigar Sultana Meghla, Rine Christopher Reuben, Mohammad Jashim Uddin, Habiba Ibnat, Shovon Lal Sarkar, Pravas Chandra Roy, M. Shaminur Rahman, A. S. M. Rubayet Ul Alam, Ovinu Kibria Islam, Iqbal
    Scientific Reports.2022;[Epub]     CrossRef
  • Production of Antibacterial Agents and Genomic Characteristics of Probiotics Strains for the Foodborne Pathogen Control
    Su Jin Kim, Jin Song Shin, Han Sol Park, Ji Seop Song, Ki Won Lee, Woo-Suk Bang, Tae Jin Cho
    Current Topic in Lactic Acid Bacteria and Probiotics.2022; 8(1): 1.     CrossRef
The effects of cigarettes and alcohol on intestinal microbiota in healthy men
Renbin Lin , Yawen Zhang , Luyi Chen , Yadong Qi , Jiamin He , Mengjia Hu , Ying Zhang , Lina Fan , Tao Yang , Lan Wang , Misi Si , Shujie Chen
J. Microbiol. 2020;58(11):926-937.   Published online October 30, 2020
DOI: https://doi.org/10.1007/s12275-020-0006-7
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AbstractAbstract
Human intestinal microbiota is affected by the exogenous microenvironment. This study aimed to determine the effects of cigarettes and alcohol on the gut microbiota of healthy men. In total, 116 healthy male subjects were enrolled and divided into four groups: non-smoking and non-drinking (Group A), smoking only (Group B), drinking only (Group C), and smoking and drinking combined (Group D). Fecal samples were collected and sequenced using 16S rRNA to analyze the microbial composition. Short-chain fatty acid (SCFAs) levels in feces were determined by gas chromatography. We found that cigarette and alcohol consumptions can alter overall composition of gut microbiota in healthy men. The relative abundances of phylum Bacteroidetes and Firmicutes and more than 40 genera were changed with cigarette and alcohol consumptions. SCFAs decreased with smoking and alcohol consumption. Multivariate analysis indicated that when compared with group A, group B/C/D had higher Bacteroides, and lower Phascolarctobacterium, Ruminococcaceae_ UCG-002, Ruminococcaceae_UCG-003, and Ruminiclostridium_ 9 regardless of BMI and age. Additionally, the abundance of Bacteroides was positively correlated with the smoking pack-year (r = 0.207, p < 0.05), the abundance of predicted pathway of bacterial toxins (r = 0.3672, p < 0.001) and the level of carcinoembryonic antigen in host (r = 0.318, p < 0.01). Group D shared similar microbial construction with group B, but exerted differences far from group C with lower abundance of Haemophilus. These results demonstrated that cigarette and alcohol consumption separately affected the intestinal microbiota and function in healthy men; furthermore, the co-occurrence of cigarette and alcohol didn’t exacerbate the dysbiosis and cigarette played the predominated role on the alteration.

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  • Potential roles of cigarette smoking on gut microbiota profile among Chinese men
    Jiayao Fan, Fangfang Zeng, Haili Zhong, Jun Cai, Wentao Shen, Chunxiao Cheng, Chunfeng He, Yuanjiao Liu, Yuan Zhou, Shujie Chen, Yimin Zhu, Tao Liu, Ju-Sheng Zheng, Lan Wang, Yu-Ming Chen, Wenjun Ma, Dan Zhou
    BMC Medicine.2025;[Epub]     CrossRef
  • Gut Microbiota at the Crossroad of Hepatic Oxidative Stress and MASLD
    Fabrizio Termite, Sebastiano Archilei, Francesca D’Ambrosio, Lucrezia Petrucci, Nicholas Viceconti, Roberta Iaccarino, Antonio Liguori, Antonio Gasbarrini, Luca Miele
    Antioxidants.2025; 14(1): 56.     CrossRef
  • A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design
    Sun-Young Kim, So-Youn Woo, Hyung-Lae Kim, Yoosoo Chang, Seungho Ryu, Han-Na Kim
    Journal of Affective Disorders.2025; 376: 26.     CrossRef
  • An Investigation into the Relationship of Circulating Gut Microbiome Molecules and Inflammatory Markers with the Risk of Incident Dementia in Later Life
    Kolade Oluwagbemigun, Andrea Anesi, Urska Vrhovsek, Fulvio Mattivi, Pamela Martino Adami, Michael Pentzek, Martin Scherer, Steffi G. Riedel-Heller, Siegfried Weyerer, Horst Bickel, Birgitt Wiese, Matthias Schmid, John F. Cryan, Alfredo Ramirez, Michael Wa
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  • The role of the gut microbiome in the development of hepatobiliary cancers
    Neil Daniel, Flavia Genua, Mazda Jenab, Ana-Lucia Mayén, Anastasia Chrysovalantou Chatziioannou, Pekka Keski-Rahkonen, David J. Hughes
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  • The interplay between microbiome and host factors in pathogenesis and therapy of head and neck cancer
    Martina Raudenská, Maria Bugajová, David Kalfeřt, Jan Plzák, Adam Šubrt, Petra Tesařová, Michal Masařík
    Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2024; 1879(6): 189216.     CrossRef
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  • The Protective Effects of Ganoderic Acids from Ganoderma lucidum Fruiting Body on Alcoholic Liver Injury and Intestinal Microflora Disturbance in Mice with Excessive Alcohol Intake
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    Foods.2022; 11(7): 949.     CrossRef
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    Anna Olsson, Stefan Gustavsen, Thao Duy Nguyen, Margareta Nyman, Annika R. Langkilde, Tue H. Hansen, Finn Sellebjerg, Annette B. Oturai, Helle Bach Søndergaard
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    Frontiers in Cellular and Infection Microbiology.2021;[Epub]     CrossRef
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Research Support, Non-U.S. Gov'ts
Microbial Community on Healthy and Diseased Leaves of an Invasive Plant Eupatorium adenophorum in Southwest China
Zhen-Xin Zhou , Huan Jiang , Chen Yang , Ming-Zhi Yang , Han-Bo Zhang
J. Microbiol. 2010;48(2):139-145.   Published online May 1, 2010
DOI: https://doi.org/10.1007/s12275-010-9185-y
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AbstractAbstract
Invasive plants have caused great economic losses and environmental problems worldwide. Eupatorium adenophorum is one of the most invasive weeds in China. To better understand its invasive mechanisms, in the present paper, the microbial communities of healthy and diseased leaves of E. adenophorum were obtained using both culture-independent and -dependent methods and their diversities were compared. The bacteria obtained from culture-independent method belong to Proteobacteria (95.8%), Actinobacteria (2.1%), and Firmicutes (2.1%) and fungi belong to Ascomycota (65.2%) and Basidiomycota (34.8%). Very few overlapped microbial species were found by culture-dependent and -independent methods. Healthy leaves display higher bacterial diversity than diseased leaves. Phylogenetic structures are very different between healthy and diseased phyllosphere microbial communities. Bacteria close to Acinetobacter and Pseudomonas were dominant on healthy leaves, whereas those close to Shigella were dominant on diseased leaves. 52.9% of fungal clones from healthy leaves were Ustilaginomycetes, close to Rhodotorula phylloplana and uncultured basidomycete; by contrast, 60% of clones from diseased leaves were Lecanoromycetes, close to Umbilicaria muehlenbergii. No bacteria but four fungal strains phylogenetically close to Myrothecium sp. and Alternaria alternate were pathogenic to seedlings and detached leaves of the invasive plant. Therefore, this plant may be resistant to pathogens from bacteria but not fungi in its introduced range.
Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People
Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae
J. Microbiol. 2008;46(5):491-501.   Published online October 31, 2008
DOI: https://doi.org/10.1007/s12275-008-0199-7
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AbstractAbstract
The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

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