Journal of Microbiology

Journal Articles

Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses: Xiaowei Gong , Huajun Luo , Liu Hong , Jun Wu , Heng Wu , Chunxia Song , Wei Zhao , Yi Han , Ya Dao , Xia Zhang , Donglai Zhu , Yiyong Luo; J. Microbiol. 2022;60(8):832-842. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2059-2

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Tryptophol (TOL) is a metabolic derivative of tryptophan (Trp) and shows pleiotropic effects in humans, plants and microbes. In this study, the effect of Trp and phenylalanine (Phe) on TOL production in Saccharomyces cerevisiae was determined, and a systematic interpretation of TOL accumulation was offered by transcriptomic and metabolomic analyses. Trp significantly promoted TOL production, but the output plateaued (231.02−266.31 mg/L) at Trp concentrations ≥ 0.6 g/L. In contrast, Phe reduced the stimulatory effect of Trp, which was strongly dependent on the Phe concentration. An integrated genomic, transcriptomic, and metabolomic analysis revealed that the effect of Trp and Phe on TOL production was mainly related to the transamination and decarboxylation of the Ehrlich pathway. Additionally, other genes, including thiamine regulon genes (this), the allantoin catabolic genes dal1, dal2, dal4, and the transcriptional activator gene aro80, may play important roles. These findings were partly supported by the fact that the thi4 gene was involved in TOL production, as shown by heterologous expression analysis. To the best of our knowledge, this novel biological function of thi4 in S. cerevisiae is reported here for the first time. Overall, our findings provide insights into the mechanism of TOL production, which will contribute to TOL production using metabolic engineering strategies.

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The effect and mechanism of acetic acid -(1H-indole-3-ethyl) ester in controlling postharvest blue mold disease in apples
Xiangfeng Zheng, Qinghua Gong, Zhirong Wang, Peiwen Huang, Zihan Zhang, Lu Gao, Shengqi Rao, Zhenquan Yang
Postharvest Biology and Technology.2025; 227: 113618. CrossRef
Engineering the L-tryptophan metabolism for efficient de novo biosynthesis of tryptophol in Saccharomyces cerevisiae
Ye Li, Jingzhen Sun, Zhenhao Fu, Yubing He, Xiaorui Chen, Shijie Wang, Lele Zhang, Jiansheng Jian, Weihua Yang, Chunli Liu, Xiuxia Liu, Yankun Yang, Zhonghu Bai
Biotechnology for Biofuels and Bioproducts.2024;[Epub] CrossRef
Evaluating the Atypical Aging Potential Development in Sparkling Wines Can Be Achieved by Assessing the Base Wines at the End of the Alcoholic Fermentation
Simone Delaiti, Tiziana Nardin, Tomas Roman, Stefano Pedò, Roberto Larcher
Journal of Agricultural and Food Chemistry.2024; 72(9): 4918. CrossRef
Tryptophol Improves the Biocontrol Efficacy of Scheffersomyces spartinae against the Gray Mold of Strawberries by Quorum Sensing
Zichang Zhao, Yingying Wei, Xiurong Zou, Shu Jiang, Yi Chen, Jianfen Ye, Feng Xu, Hongfei Wang, Xingfeng Shao
Journal of Agricultural and Food Chemistry.2023; 71(49): 19739. CrossRef
A comprehensive review and comparison of L-tryptophan biosynthesis in Saccharomyces cerevisiae and Escherichia coli
Xinru Ren, Yue Wei, Honglu Zhao, Juanjuan Shao, Fanli Zeng, Zhen Wang, Li Li
Frontiers in Bioengineering and Biotechnology.2023;[Epub] CrossRef

Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil: Jiyoun Kim , Geeta Chhetri , Inhyup Kim , Hyungdong Kim , Myung Kyum Kim , Taegun Seo; J. Microbiol. 2019;57(11):959-966. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9007-9

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Abstract

A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28T was phylogenetically related to Methylobacterium currus PR1016AT (96.8%), Methylobacterium platani PMB02T (96.2%), Methylobacterium aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae N4211T (96.4%), Methylobacterium frigidaeris IER25-16T (95.8%), and Methylobacterium organophilum JCM 2833T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7–90.4% and 22–39.6%, respectively. The major fatty acids of strain 17Sr1- 28T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28T and its close phylogenetic relatives, strain 17Sr1-28T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904T = NBRC 112873T) is proposed.

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Exploring the diversity and potential functional characteristics of microbiota associated with different compartments of Schisandra chinensis
Wenjuan Hou, Yanping Xing, Hefei Xue, Yanchang Huang, Yutong Huang, Wenxiao Men, Yanyun Yang, Tingguo Kang, Deqiang Dou, Han Zheng, Liang Xu
Frontiers in Microbiology.2024;[Epub] CrossRef
Detoxification pathways of multiple metals from intensive copper production by indigenous ureolytic microbes coupled with soil nitrogen transformation
Juan Zhang, Shuo Wang, Xin Wang, Minghua Zhang, Shukai Fan
Journal of Cleaner Production.2023; 384: 135643. CrossRef
Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter
Geeta Chhetri, Inhyup Kim, Taegun Seo
Antonie van Leeuwenhoek.2023; 116(3): 231. CrossRef
Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter
Jiyoun Kim, Byungjo Lee, Geeta Chhetri, Inhyup Kim, Yoonseop So, Wonhee Jang, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants
Geeta Chhetri, Inhyup Kim, Minchung Kang, Jiyoun Kim, Yoonseop So, Taegun Seo
Journal of Microbiology.2022; 60(1): 1. CrossRef
Cohnella terricola sp. nov., isolated from soil
Jiyoun Kim, Geeta Chhetri, Inhyup Kim, Minchung Kang, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Metataxonomic analysis of tissue-associated microbiota in grooved carpet-shell (Ruditapes decussatus) and Manila (Ruditapes philippinarum) clams
Diego Gerpe, Aide Lasa, Alberto Lema, Jesús L. Romalde
International Microbiology.2021; 24(4): 607. CrossRef
Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species
Ola Alessa, Yoshitoshi Ogura, Yoshiko Fujitani, Hideto Takami, Tetsuya Hayashi, Nurettin Sahin, Akio Tani
Frontiers in Microbiology.2021;[Epub] CrossRef
Fuscibacter oryzae gen. nov., sp. nov., a phosphate-solubilizing bacterium isolated from the rhizosphere of rice plant
Geeta Chhetri, Minchung Kang, Jiyoun Kim, Inhyup Kim, Yoonseop So, Taegun Seo
Antonie van Leeuwenhoek.2021; 114(9): 1453. CrossRef
The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community
Fangying Lei, Xueduan Liu, Haonan Huang, Shaodong Fu, Kai Zou, Shuangfei Zhang, Li Zhou, Jianguo Zeng, Hongwei Liu, Luhua Jiang, Bo Miao, Yili Liang
Frontiers in Microbiology.2021;[Epub] CrossRef
International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020
Philippe de Lajudie, Seyed Abdollah Mousavi, J. Peter W. Young
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula
Geeta Chhetri, Inhyup Kim, Minchung Kang, Jiyoun Kim, Yoonseop So, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants
Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Minchung Kang, Yoonseop So, Taegun Seo
Antonie van Leeuwenhoek.2021; 114(11): 1925. CrossRef
Methylobacterium ajmalii sp. nov., Isolated From the International Space Station
Swati Bijlani, Nitin K. Singh, V. V. Ramprasad Eedara, Appa Rao Podile, Christopher E. Mason, Clay C. C. Wang, Kasthuri Venkateswaran
Frontiers in Microbiology.2021;[Epub] CrossRef
Reinekea thalattae sp. nov., a New Species of the Genus Reinekea Isolated from Surface Seawater in Sehwa Beach
Inhyup Kim, Geeta Chhetri, Jiyoun Kim, Minchung Kang, Taegun Seo
Current Microbiology.2020; 77(12): 4174. CrossRef
Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil
Jiyoun Kim, Geeta Chhetri, Inhyup Kim, Myung Kyum Kim, Taegun Seo
Antonie van Leeuwenhoek.2020; 113(2): 211. CrossRef
International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019
Philippe de Lajudie, J. Peter W. Young
International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3563. CrossRef
Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil
Jiyoun Kim, Geeta Chhetri, Inhyup Kim, Byungjo Lee, Wonhee Jang, Myung Kyum Kim, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2449. CrossRef
Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater
Inhyup Kim, Geeta Chhetri, Jiyoun Kim, Minchung Kang, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2020; 70(12): 6180. CrossRef
Flavobacterium baculatum sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field
Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Minchung Kang, Byungjo Lee, Wonhee Jang, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

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

Methylobacterium dankookense sp. nov., Isolated from Drinking Water: Si-Won Lee , Hyun-Woo Oh , Kang-Hyun Lee , Tae-Young Ahn; J. Microbiol. 2009;47(6):716-720. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0126-6

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Abstract

A pink-pigmented bacterium, designated SW08-7T was isolated from the drinking water of a water purifier. Cells were Gram-negative, rod-shaped, strictly aerobic, and non-spore-forming. It grew optimally at 25°C, pH 6~7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SW08-7T belongs to the genus Methylobacterium. The highest 16S rRNA gene sequence similarities were found to Methylobacterium mesophilicum JCM 2829T (96.9%), Methylobacterium brachiatum B0021T (96.9%), Methylobacterium phyllosphaerae CBMB27T (96.6%), Methylobacterium radiotolerans JCM 2831T (96.6%), and Methylobacterium hispanicum GP34T (96.5%). DNA-DNA hybridization experiment revealed low-level (28.5%) of DNA- DNA relatedness between strain SW08-7T and Methylobacterium hispanicum. The genomic DNA G+C content was 68.9 mol% and the major isoprenoid quinone was Q-10. The major cellular fatty acid of strain SW08-7T was C18:1 ω7c (79.8±2.1%). Results of phylogenetic, phenotypic, and biochemical analyses revealed that strain SW08-7T could be classified as representing a novel species of genus Methylobacterium, for which the name Methylobacterium dankookense sp. nov. is proposed. The type strain is SW08-7T (=KCTC 22512T =DSM 22415T).

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Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.
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Transmission of Methylobacterium mesophilicum by Bucephalogonia xanthophis for Paratransgenic Control Strategy of Citrus Variegated Chlorosis: Cláudia Santos Gai , Paulo Teixeira Lacava , Maria Carolina Quecine , Marie-Christine Auriac , João Roberto Spotti Lopes , Welington Luiz Araújo , Thomas Albert Miller , João Lúcio Azevedo; J. Microbiol. 2009;47(4):448-454. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-008-0303-z

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Abstract

Methylobacterium mesophilicum, originally isolated as an endophytic bacterium from citrus plants, was genetically transformed to express green fluorescent protein (GFP). The GFP-labeled strain of M. mesophilicum was inoculated into Catharanthus roseus (model plant) seedlings and further observed colonizing its xylem vessels. The transmission of this endophyte by Bucephalogonia xanthophis, one of the insect vectors that transmit Xylella fastidiosa subsp. pauca, was verified by insects feeding from fluids containing the GFP bacterium followed by transmission to plants and isolating the endophyte from C. roseus plants. Forty-five days after inoculation, the plants exhibited endophytic colonization by M. mesophilicum, confirming this bacterium as a nonpathogenic, xylem-associated endophyte. Our data demonstrate that M. mesophilicum not only occupy the same niche of X. fastidiosa subsp. pauca inside plants but also may be transmitted by B. xanthophis. The transmission, colonization, and genetic manipulation of M. mesophilicum is a prerequisite to examining the potential use of symbiotic control to interrupt the transmission of X. fastidiosa subsp. pauca, the bacterial pathogen causing Citrus variegated chlorosis by insect vectors.

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