Journal of Microbiology

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Integrated proteomic and metabolomic analyses reveal significant changes in chloroplasts and mitochondria of pepper (Capsicum annuum L.) during Sclerotium rolfsii infection: Hongdong Liao , Xiangyu Wen , Xuelei Deng , Yonghong Wu , Jianping Xu , Xin Li , Shudong Zhou , Xuefeng Li , Chunhui Zhu , Feng Luo , Yanqing Ma , Jingyuan Zheng; J. Microbiol. 2022;60(5):511-525. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1603-4

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Infection by Sclerotium rolfsii will cause serious disease and lead to significant economic losses in chili pepper. In this study, the response of pepper during S. rolfsii infection was explored by electron microscopy, physiological determination and integrated proteome and metabolome analyses. Our results showed that the stomata of pepper stems were important portals for S. rolfsii infection. The plant cell morphology was significantly changed at the time of the fungal hyphae just contacting (T1) or surrounding (T2) the pepper. The chlorophyll, carotenoid, and MDA contents and the activities of POD, SOD, and CAT were markedly upregulated at T1 and T2. Approximately 4129 proteins and 823 metabolites were clearly identified in proteome and metabolome analyses, respectively. A change in 396 proteins and 54 metabolites in pepper stem tissues was observed at T1 compared with 438 proteins and 53 metabolites at T2. The proteins and metabolites related to photosynthesis and antioxidant systems in chloroplasts and mitochondria were disproportionally affected by S. rolfsii infection, impacting carbohydrate and amino acid metabolism. This study provided new insights into the response mechanism in pepper stems during S. rolfsii infection, which can guide future work on fungal disease resistance breeding in pepper.

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Multifaceted chemical and bioactive features of Ag@TiO2 and Ag@SeO2 core/shell nanoparticles biosynthesized using Beta vulgaris L. extract
Khaled M. Elattar, Fatimah O. Al-Otibi, Mohammed S. El-Hersh, Attia A. Attia, Noha M. Eldadamony, Ashraf Elsayed, Farid Menaa, WesamEldin I.A. Saber
Heliyon.2024; 10(7): e28359. CrossRef
Fighting for Survival at the Stomatal Gate
Maeli Melotto, Brianna Fochs, Zachariah Jaramillo, Olivier Rodrigues
Annual Review of Plant Biology .2024; 75(1): 551. CrossRef
Zinc and Boron Soil Applications Affect Athelia rolfsii Stress Response in Sugar Beet (Beta vulgaris L.) Plants
Tamalika Bhadra, Chandan Kumar Mahapatra, Md. Hosenuzzaman, Dipali Rani Gupta, Abeer Hashem, Graciela Dolores Avila-Quezada, Elsayed Fathi Abd_Allah, Md. Anamul Hoque, Swapan Kumar Paul
Plants.2023; 12(19): 3509. CrossRef
Genetic Regulation, Environmental Cues, and Extraction Methods for Higher Yield of Secondary Metabolites in Capsicum
Khushbu Islam, Abdul Rawoof, Ajay Kumar, John Momo, Ilyas Ahmed, Meenakshi Dubey, Nirala Ramchiary
Journal of Agricultural and Food Chemistry.2023; 71(24): 9213. CrossRef
Integrated pathological, proteomic and metabolomic analyses reveal significant changes of Eriocheir sinensis hepatopancreatic in response to the microsporidian Hepatospora eriocheir infection
Libo Hou, Mengdi Wang, Hao Li, Lei Zhu, Xianghui Kong, Wei Gu, Keran Bi, Jie Du, Qingguo Meng
Aquaculture.2023; 577: 739994. CrossRef

Mucilaginibacter limnophilus sp. nov., isolated from a lake: Shih-Yi Sheu , Yi-Ru Xie , Wen-Ming Chen; J. Microbiol. 2019;57(11):967-975. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9146-z

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Abstract

A polyphasic taxonomy approach was used to characterize strain YBJ-36T, isolated from a freshwater lake in Taiwan. Phylogenetic analyses, based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters), indicated that strain YBJ-36T formed a phylogenetic lineage in the genus Mucilaginibacter. 16S rRNA gene sequence similarity indicated that strain YBJ-36T is closely related to species within the genus Mucilaginibacter (93.8–97.8% sequence similarity) and is most similar to Mucilaginibacter fluminis TTM-2T (97.8%), followed by Mucilaginibacter roseus TTM-1T (97.2%). Microbiological analyses demonstrated that strain YBJ-36T is Gram-negative, aerobic, non-motile, rod-shaped, surrounded by a thick capsule, and forms pink-colored colonies. Strain YBJ-36T grew between 20–40°C (optimal range, 35–37°C), pH 5.5–7.0 (optimal pH of 6) and 0–2% NaCl (optimal concentration, 0.5%). The predominant fatty acids of strain YBJ-36T are iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), the major polar lipid is phosphatidylethanolamine, the major polyamine is homospermidine, and the major isoprenoid quinone is MK-7. The draft genome is approximately 4.63 Mb in size with a G+C content of 42.8 mol%. Strain YBJ-36T exhibited less than 35% DNA-DNA relatedness with Mucilaginibacter fluminis TTM-2T and Mucilaginibacter roseus TTM-1T. Based on phenotypic and genotypic properties and phylogenetic inference, strain YBJ-36T should be classified in a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter limnophilus sp. nov. is proposed. The type strain is YBJ-36T (= BCRC 81056T = KCTC 52811T = LMG 30058T).

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Ana L. S. Vasconcelos, Fernando Dini Andreote, Thaiane Defalco, Endrews Delbaje, Leticia Barrientos, Armando C. F. Dias, Fabricio Angelo Gabriel, Angelo F. Bernardino, Kattia Núñez-Montero
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Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1443. CrossRef
Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses
Lingmin Jiang, Dexin Wang, Ji-Sun Kim, Ju Huck Lee, Dae-Hyuk Kim, Suk Weon Kim, Jiyoung Lee
International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3541. CrossRef

Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles: Federica De Lise , Francesca Mensitieri , Giulia Rusciano , Fabrizio Dal Piaz , Giovanni Forte , Flaviana Di Lorenzo , Antonio Molinaro , Armando Zarrelli , Valeria Romanucci , Valeria Cafaro , Antonio Sasso , Amelia Filippelli , Alberto Di Donato , Viviana Izzo; J. Microbiol. 2019;57(6):498-508. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8483-2

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Abstract

Outer membrane vesicles (OMVs) are nanostructures of 20– 200 nm diameter deriving from the surface of several Gramnegative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical “fingerprint”, suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.

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Fangfang Fan, Guangzhang Chen, Siqian Deng, Li Wei, Mariola J. Ferraro
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LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes
Ana Segura, Lázaro Molina
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Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid
Aline Belmok, Felipe Marques de Almeida, Rodrigo Theodoro Rocha, Carla Simone Vizzotto, Marcos Rogério Tótola, Marcelo Henrique Soller Ramada, Ricardo Henrique Krüger, Cynthia Maria Kyaw, Georgios J. Pappas
Brazilian Journal of Microbiology.2023; 54(1): 239. CrossRef
Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer
Federica Dell’Annunziata, Carmela Dell’Aversana, Nunzianna Doti, Giuliana Donadio, Fabrizio Dal Piaz, Viviana Izzo, Anna De Filippis, Marilena Galdiero, Lucia Altucci, Giovanni Boccia, Massimiliano Galdiero, Veronica Folliero, Gianluigi Franci
International Journal of Molecular Sciences.2021; 22(16): 8732. CrossRef

Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1: Sung Ho Yun , Sang-Yeop Lee , Chi-Won Choi , Hayoung Lee , Hyun-Joo Ro , Sangmi Jun , Yong Min Kwon , Kae Kyoung Kwon , Sang-Jin Kim , Gun-Hwa Kim , Seung Il Kim; J. Microbiol. 2017;55(1):56-62. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6581-6

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Abstract

Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25–70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.

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Xinke Nie, Qiqiong Li, Xinyang Chen, Stanley Onyango, Junhua Xie, Shaoping Nie
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Huimin Song, Yilong Ruan, Ya Li, Huirong Yang, Weiwei Zhang
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Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1
Jiaqing Liang, Jiantao Xu, Weijun Zhao, Jiaofeng Wang, Kai Chen, Yuqian Li, Yun Tian
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NOTE] Complete Sequence and Organization of the Sphingobium chungbukense DJ77 pSY2 Plasmid: Sun-Mi Yeon , Young-Chang Kim; J. Microbiol. 2011;49(4):684-688. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-1262-3

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Abstract

Sphingobium chungbukense DJ77 is capable of metabolizing priority chemicals of human health concern such as polycyclic aromatic hydrocarbons (PAHs), extracellular polysaccharide (EPS), and antibiotics. Here, we report the complete DNA and genetic organization of the plasmid pSY2 from strain DJ77. A DNA sequence analysis revealed that pSY2 comprises 18,779 bp encoding 22 open reading frames (ORFs) with 59.5% G+C content. The ORFs on pSY2 were classified into DNA replication, conjugative function, transposition, plasmid stability/partition, and other functional groups (transport, fatty acid biosynthesis, stress, and growth rate regulation). Three ORFs on pSY2 were hypothetical proteins.

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Biochemical characterization and molecular docking analysis of novel esterases from Sphingobium chungbukense DJ77
Woo-Ri Shin, Hyun-Ju Um, Young-Chang Kim, Sun Chang Kim, Byung-Kwan Cho, Ji-Young Ahn, Jiho Min, Yang-Hoon Kim
International Journal of Biological Macromolecules.2021; 168: 403. CrossRef
Molecular Docking Analysis and Biochemical Evaluation of Levansucrase from Sphingobium chungbukense DJ77
Soo Youn Lee, Woo-Ri Shin, Simranjeet Singh Sekhon, Jin-Pyo Lee, Young-Chang Kim, Ji-Young Ahn, Yang-Hoon Kim
ACS Combinatorial Science.2018; 20(7): 414. CrossRef
Degradative plasmids from sphingomonads
Andreas Stolz
FEMS Microbiology Letters.2014; 350(1): 9. CrossRef

Genetic Diversity of Chromosomal Metallo-β-Lactamase Genes in Clinical Isolates of Elizabethkingia meningoseptica from Korea: Jong Hwa Yum , Eun Young Lee , Sung-Ho Hur , Seok Hoon Jeong , Hyukmin Lee , Dongeun Yong , Yunsop Chong , Eun-Woo Lee , Patrice Nordmann , Kyungwon Lee; J. Microbiol. 2010;48(3):358-364. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9308-5

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Abstract: This study was performed to characterize the chromosomal metallo-β-lactamases (MBLs) of Elizabethkingia meningoseptica isolated from Korea and to propose a clustering method of BlaB and GOB MBLs based on their amino acid similarities. Chromosomal MBL genes were amplified by PCR from 31 clinical isolates of E. meningoseptica. These PCR products were then cloned into a vector and electrotransformed into E. coli DH5α. Nucleotide sequencing was performed by the dideoxy chain termination method using PCR products or cloned DNA fragments. Antimicrobial susceptibilities were determined by the agar dilution method. PCR experiments showed that all 31 E. meningoseptica isolates contained both the blaB and the blaGOB genes. DNA sequence analysis revealed that E. meningoseptica isolates possessed seven types of blaB gene, including five novel variants (blaB-9 to blaB-13) and 11 types of blaGOB gene, including 10 novel variants (blaGOB-8 to blaGOB-17). The most common combination of MBL was BlaB-12 plus GOB-17 (n=19). Minimum inhibitory concentrations of imipenem and meropenem for the electrotransformants harboring novel BlaB and GOB MBLs were two- or four-fold higher than those for the recipient E. coli DH5α. BlaB and GOB MBLs were grouped in three and six clusters including fifteen novel variants, respectively, based on amino acid similarities.

Characterization of Plasmid pSY3 in Sphingobium chungbukense DJ77: Sun-Mi Yeon , Young-Chang Kim; J. Microbiol. 2009;47(6):796-800. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0329-x

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Abstract: This study determined the complete nucleotide sequence of the plasmid pSY3 from Sphingobium chungbukense DJ77. It was 35,735 bp long with a G+C content of 61.9%. Forty open reading frames (ORFs) were found. We predicted these ORFs would encode proteins associated with plasmid replication, conjugative transfer, transposition of genes, plasmid stability/partition, hypothetical protein, and some other functions. Genes for biodegradation were not found. No other plasmid homologous to pSY3 in the overall nucleotide sequence or gene organization could be found in the NCBI database.

Sphingobacterium bambusae sp. nov., Isolated from Soil of Bamboo Plantation: Shengwen Duan , Zhengchu Liu , Xiangyuan Feng , Ke Zheng , Lifeng Cheng; J. Microbiol. 2009;47(6):693-698. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0296-2

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Abstract

A Gram-negative, non-motile, non-spore-forming bacterial strain designated IBFC2009T was isolated from soil of a bamboo plantation. The strain could grow at 11°C~39°C, pH 6.0~9.0, and in the presence of 0~5% NaCl. Based on 16S rRNA gene sequence analysis, Strain IBFC2009T belonged to the genus Sphingobacterium and showed the highest sequence similarity of 94.6% (S. composti T5-12T) with the type strains within the genus. The major fatty acids were summed feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c, 34.4%), iso-C15:0 (22.4%), C16:0 3-OH (15.2%), and iso-C17:0 3-OH (12.8%). The G+C content of the genomic DNA was 41.0 mol%. According to the phenotypic and genotypic characteristics, Strain IBFC2009T should represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium bambusae sp. nov. is proposed. The type strain is IBFC2009T (=CCTCC AB 209162T =KCTC 22814T).

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Peng Zhao, Zhengfu Zhou, Ming Chen, Wenna Lin, Wei Zhang, Gehong Wei
International Journal of Systematic and Evolutionary Microbiology .2014; 64(Pt_12): 3931. CrossRef
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Hao Feng, Yanhua Zeng, Yili Huang
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Shijie Jiang, Ming Chen, Shiyou Su, Mingkun Yang, Aihua Li, Chen Zhang, Min Lin, Wei Zhang, Xuegang Luo
International Journal of Systematic and Evolutionary Microbiology .2014; 64(Pt_1): 248. CrossRef
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Shi Peng, Dong Dan Hong, Yang Bing Xin, Li Ming Jun, Wei Ge Hong
International Journal of Systematic and Evolutionary Microbiology .2014; 64(Pt_11): 3862. CrossRef
Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo
Iftikhar Ahmed, Muhammad Ehsan, Yeseul Sin, Jayoung Paek, Nauman Khalid, Rifat Hayat, Young H. Chang
Antonie van Leeuwenhoek.2014; 105(2): 325. CrossRef
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Young Rae Koh, Shine Young Kim, Chulhun L Chang, Ho-Jin Shin, Kye-Hyung Kim, Jongyoun Yi
Annals of Laboratory Medicine.2013; 33(4): 283. CrossRef
Sphingobacterium caeni sp. nov., isolated from activated sludge
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International Journal of Systematic and Evolutionary Microbiology.2013; 63(Pt_6): 2260. CrossRef
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Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense
Dong-Heon Lee, Jae Seoun Hur, Hyung-Yeel Kahng
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_2): 755. CrossRef
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International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_3): 952. CrossRef
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Ana M. Marqués, César Burgos-Díaz, Francisco José Aranda, José Antonio Teruel, Àngels Manresa, Antonio Ortiz, Maribel Farfán
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_12): 3036. CrossRef
Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco
Jie Liu, Ling-Ling Yang, Chuan-Kun Xu, Jia-Qin Xi, Fa-Xiang Yang, Feng Zhou, Yu Zhou, Ming-He Mo, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_8): 1809. CrossRef
Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment
Verena S. J. Schmidt, Mareike Wenning, Siegfried Scherer
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_7): 1506. CrossRef
A rapid process of ramie bio-degumming by Pectobacterium sp. CXJZU-120
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Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge
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International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_3): 683. CrossRef
Sphingomonas rosea sp. nov. and Sphingomonas swuensis sp. nov., rosy colored β-glucosidase-producing bacteria isolated from soil
Sathiyaraj Srinivasan, Jae-Jin Lee, Myung Kyum Kim
The Journal of Microbiology.2011; 49(4): 610. CrossRef
Sphingomonas humi sp. nov., isolated from soil
Tae Hoo Yi, Chang-Kyun Han, Sathiyaraj Srinivasan, Kang Jin Lee, Myung Kyum Kim
The Journal of Microbiology.2010; 48(2): 165. CrossRef
List of new names and new combinations previously effectively, but not validly, published

International Journal of Systematic and Evolutionary Microbiology.2010; 60(7): 1477. CrossRef

Organization of Three rRNA (rrn) Operons from Sphingobium chungbukense DJ77: Sun-Mi Yeon , Beom-Soon Choi , Young-Chang Kim; J. Microbiol. 2008;46(6):697-703. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0193-0

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Abstract: The nucleotide sequences of all three rRNA operons (rrnA, rrnB, and rrnC) of Sphingobium chungbukense DJ77 were determined. The three rrn operons have the same gene order (16S rRNA-tRNAIle-tRNAAla-23S rRNA-5S rRNA-tRNAfMet). The nucleotide sequences were identical over a 5,468 bp region spanning the 16S rRNA gene to the 5S rRNA gene. Variability was observed in the 5S rRNA-tRNAfMet spacer sequence of rrnB. The tRNAfMet gene sequences were identical except for two bases (T5794 and A5871 in rrnB, T5942 and A5956 in rrnA, but C5942 and G5956 in rrnC). Comparative sequence analyses of ribosomal RNA operons from DJ77 with those of the class Alphaproteobacteria, to which the genus Sphingobium belongs, reveal close evolutionary relationships with other members of the order Sphingomonadales.

Nucleotide Sequence and Secondary Structure of 5S rRNA from Sphingobium chungbukense DJ77: Hae-Ryong Kwon , Young-Chang Kim; J. Microbiol. 2007;45(1):79-82.; DOI: https://doi.org/2486 [pii]

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Abstract: The 5S rRNA gene from Sphingobium chungbukense DJ77 was identified. The secondary structure of the 199-base-long RNA was proposed. The two-base-long D loop was the shortest among all of the known 5S rRNAs. The U19-U64 non-canonical pair in the helix II region was uniquely found in strain DJ77 among all of the sphingomonads.

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