Journal of Microbiology

Journal Article

Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish): Dong-Wook Hyun , Yun-Seok Jeong , Jae-Yun Lee , Hojun Sung , So-Yeon Lee , Jee-Won Choi , Hyun Sik Kim , Pil Soo Kim , Jin-Woo Bae; J. Microbiol. 2021;59(6):552-562. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1036-5

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A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW- 15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).

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Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis: Thinh-Phat Cao , Joong-Su Kim , Mi-Hee Woo , Jin Myung Choi , Youngsoo Jun , Kun Ho Lee , Sung Haeng Lee; J. Microbiol. 2016;54(4):311-321. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-6029-4

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Abstract

2-deoxyribose-5-phosphate aldolase (DERA) is a class I aldolase that catalyzes aldol condensation of two aldehydes in the active site, which is particularly germane in drug manufacture. Structural and biochemical studies have shown that the active site of DERA is typically loosely packed and displays broader substrate specificity despite sharing conserved folding architecture with other aldolases. The most distinctive structural feature of DERA compared to other aldolases is short and flexible C-terminal region. This region is also responsible for substrate recognition. Therefore, substrate tolerance may be related to the C-terminal structural features of DERA. Here, we determined the crystal structures of full length and C-terminal truncated DERA from Streptococcus suis (SsDERA). In common, both contained the typical (α/β)8 TIM-barrel fold of class I aldolases. Surprisingly, C-terminal truncation
result
ing in missing the last α9 and β8 secondary elements, allowed DERA to maintain activity comparable to the fulllength enzyme. Specifically, Arg186 and Ser205 residues at the C-terminus appeared mutually supplemental or less indispensible for substrate phosphate moiety recognition. Our results suggest that DERA might adopt a shorter C-terminal region than conventional aldolases during evolution pathway, resulting in a broader range of substrate tolerance through active site flexibility.

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Synthetic Activity of Recombinant Whole Cell Biocatalysts Containing 2‐Deoxy‐D‐ribose‐5‐phosphate Aldolase from Pectobacterium atrosepticum
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ChemBioChem.2022;[Epub] CrossRef
Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol
Taeho Kim, Peter J. Stogios, Anna N. Khusnutdinova, Kayla Nemr, Tatiana Skarina, Robert Flick, Jeong Chan Joo, Radhakrishnan Mahadevan, Alexei Savchenko, Alexander F. Yakunin
Journal of Biological Chemistry.2020; 295(2): 597. CrossRef
Sensitization of colorectal cancer to irinotecan therapy by PARP inhibitor rucaparib
Titto Augustine, Radhashree Maitra, Jinghang Zhang, Jay Nayak, Sanjay Goel
Investigational New Drugs.2019; 37(5): 948. CrossRef
Conformational Sampling of the Intrinsically Disordered C-Terminal Tail of DERA Is Important for Enzyme Catalysis
Marianne Schulte, Dušan Petrović, Philipp Neudecker, Rudolf Hartmann, Jörg Pietruszka, Sabine Willbold, Dieter Willbold, Vineet Panwalkar
ACS Catalysis.2018; 8(5): 3971. CrossRef
1H, 13C, and 15N backbone and sidechain resonance assignments of a monomeric variant of E. coli deoxyribose-5-phosphate aldolase
Marianne Schulte, Matthias Stoldt, Philipp Neudecker, Jӧrg Pietruszka, Dieter Willbold, Vineet Panwalkar
Biomolecular NMR Assignments.2017; 11(2): 197. CrossRef

Comparative Proteome Analysis of Bacillus anthracis with pXO1 Plasmid Content: Sudipto Shahid , Ji Hyun Park , Hyung Tae Lee , Seong-Joo Kim , Ji Cheon Kim , Sang Hoon Kim , Dal Mu Ri Han , Dong In Jeon , Kyoung Hwa Jung , Young Gyu Chai; J. Microbiol. 2010;48(6):771-777. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0136-4

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Abstract: Bacillus anthracis the causative agent of anthrax, is an important pathogen among the Bacillus cereus group of species because of its physiological characteristics and its importance as a biological warfare agent. Tripartite anthrax toxin proteins and a poly-D-glutamic acid capsule are produced by B. anthracis vegetative cells during mammalian hosts infection and when cultured in conditions that are thought to mimic the host environment. To identify the factors regulating virulence in B. anthracis the whole cell proteins were extracted from two B. anthracis strains and separated by narrow range immobilized pH gradient (IPG) strips (pH 4-7), followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins that were differentially expressed were identified by the peptide fingerprinting using matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). A total of 23 proteins were identified as being either upregulated or downregulated in the presence or absence of the virulence plasmid pXO1. Two plasmid encoded proteins and 12 cellular proteins were identified and documented as potential virulence factors.

Cyanobacterial Hybrid Kinase Sll0043 Regulates Phototaxis by Suppressing Pilin and Twitching Motility Protein: Bong-Jeong Shin , Jeehyun Oh , Sungsoo Kang , Young-Ho Chung , Young Mok Park , Young Hwan Kim , Seungil Kim , Jong Bhak , Jong-Soon Choi; J. Microbiol. 2008;46(3):300-308. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-007-0212-6

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Abstract: The unicellular cyanobacterium Synechocystis sp. PCC 6803 glides toward a light source through the interplay of positive phototaxis genes and proteins. In genetic analysis, the complete disruption of the hybrid sensory kinase sll0043 produced negative phototaxis. Furthermore, Sll0043 was found to be a hub protein by in silico prediction of protein-protein interaction, in which Sll0043 was predominantly linked to seven two-component proteins with high confidence. To understand the regulation and networking of positive phototaxis proteins, the proteomic profile of the sll0043 mutant was compared to that of wild-type. In the sll0043 mutant, 18 spots corresponding to 15 unique proteins were altered by 1.3 to 59 fold; the spots were identified by 2-DE/MALDI-MS analysis. Down-regulated proteins in the sll0043 null-mutant included chaperonins, superoxide dismutase, and phycocyanin β-subunit. In contrast, nine proteins involved in photosynthesis, translation, regulatory function, and other functions were up-regulated. In particular, a twitching motility protein (PilT1) was induced over 2-fold in sll0043 mutant. Moreover, semiquantitative and quantitative RT-PCR analysis revealed that pilin (pilA1), pili motor (pilT1), and pili switch gene (pilT2) were significantly increased in sll0043 mutant. These results suggest that the hybrid kinase Sll0043 regulates positive phototaxis by suppressing the expression of pili biosynthesis and regulatory genes and through the interplay with positive phototaxis/motility two-component proteins.

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