Journal of Microbiology

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Expression and purification of intracrine human FGF 11 and study of its FGFR-dependent biological activity: Kyeong Won Lee , Young Jun An , Janet Lee , Ye-Eun Jung , In Young Ko , Jonghwa Jin , Ji Hoon Park , Won Kyu Lee , Kiweon Cha , Sun-Shin Cha , Jung-Hyun Lee , Hyung-Soon Yim; J. Microbiol. 2022;60(11):1086-1094. Published online November 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2406-3

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Fibroblast growth factor 11 (FGF11) is one of intracrine FGFs (iFGFs), which function within cells. Unlike canonical FGFs, FGF11 remains intracellularly and plays biological roles in FGF receptor (FGFR)-independent manner. Here, we established an expression system of recombinant FGF11 proteins in E. coli and investigated whether the extracellular administration of FGF11 can activate cellular signaling. Human FGF11 has two isoforms, FGF11a and FGF11b, depending on the presence of nuclear localization sequences (NLSs) in the N-terminus. Because these two isoforms are unstable, we prepared an FGF11a-Mut by substituting three cysteine residues in the NLS with serine and FGF11b-ΔC with C-terminal truncation. The introduction of mutation in the NLS improved the solubility of FGF11 prepared from E. coli. Exogenous addition of FGF11b and FGF11b-ΔC to BALB3T3 increased cell proliferation, while FGF11a-Mut exerted no effect. FGF11b-ΔC showed higher cell proliferation activity and FGFR signaling than FGF11b. The cell-proliferating activities of FGF11b and FGF11b-ΔC were blocked by an FGFR1 inhibitor or a recombinant FGFR1, confirming the FGFR1- dependent extracellular activity of FGF11b. The analysis of circular dichroism suggested that the C-terminus of FGF11 has an α-helical structure, which may affect its interaction with FGFR1. These results suggest that the N-and C-terminus of recombinant FGF11 are involved in the activation of FGFR1. The above results provide novel insights into the function and mechanism of FGF11 that may aid the development of useful ligands for FGFR regulation.

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Glycosylation of FGF/FGFR: An underrated sweet code regulating cellular signaling programs
Aleksandra Gędaj, Paulina Gregorczyk, Dominika Żukowska, Aleksandra Chorążewska, Krzysztof Ciura, Marta Kalka, Natalia Porębska, Łukasz Opaliński
Cytokine & Growth Factor Reviews.2024; 77: 39. CrossRef
FGF homologous factors are secreted from cells to induce FGFR‐mediated anti‐apoptotic response
Martyna Biadun, Martyna Sochacka, Radoslaw Karelus, Karolina Baran, Aleksandra Czyrek, Jacek Otlewski, Daniel Krowarsch, Lukasz Opalinski, Malgorzata Zakrzewska
The FASEB Journal.2023;[Epub] CrossRef
FGF/FGFR1 system in paired breast tumor-adjacent and tumor tissues, associations with mammographic breast density and tumor characteristics
Öykü Boraka, Marie Klintman, Johan Vallon-Christersson, Sophia Zackrisson, Per Hall, Signe Borgquist, Ann H. Rosendahl
Frontiers in Oncology.2023;[Epub] CrossRef

Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons): Qian Liu , Guoying Fan , Kui Wu , Xiangning Bai , Xi Yang , Wentao Song , Shengen Chen , Yanwen Xiong , Haiying Chen; J. Microbiol. 2022;60(7):668-677. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2089-9

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Abstract

Two novel Gram-positive, non-spore-forming, facultatively anaerobic, non-motile, and short rods to coccoid strains were isolated from the feces of the greater white-fronted geese (Anser albifrons) at Poyang Lake. The 16S rRNA gene sequences of strains 4H37-19T and 3HC-13 shared highest identity to that of Corynebacterium uropygiale Iso10T (97.8%). Phylogenetic and phylogenomic analyses indicated that strains 4H37-19T and 3HC-13 formed an independent clade within genus Corynebacterium and clustered with Corynebacterium uropygiale Iso10T. The average nucleotide identity and digital DNA-DNA hybridization value between strains 4H37-19T and 3HC-13 and members within genus Corynebacterium were all below 95% and 70%, respectively. The genomic G + C content of strains 4H37-19T and 3HC-13 was 52.5%. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylcholine, and phosphatidyl inositol mannosides (PIM) were the major polar lipids, with C18:1ω9c, C16:0, and C18:0 as the major fatty acids, and MK-8 (H4), MK-8(H2), and MK-9(H2) as the predominant respiratory quinones. The major whole cell sugar was arabinose, and the cell wall included mycolic acids. The cell wall peptidoglycan contained meso-diaminopimelic acid (meso-DAP). The polyphasic taxonomic data shows that these two strains represent a novel species of the genus Corynebacterium, for which the name Corynebacterium poyangense sp. nov. is proposed. The type strain of Corynebacterium poyangense is 4H37-19T (=GDMCC 1.1738T = KACC 21671T).

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Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023
Erik Munson, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Keratokonjunktivitisli bir tavuktan Corynebacterium spp. ve Arcanobacterium spp. izolasyonu
Hüban GÖÇMEN, Banur BOYNUKARA
Veteriner Hekimler Derneği Dergisi.2023; 94(2): 161. CrossRef

Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase: Jisub Hwang , Chang-Sook Jeong , Chang Woo Lee , Seung Chul Shin , Han-Woo Kim , Sung Gu Lee , Ui Joung Youn , Chang Sup Lee , Tae-Jin Oh , Hak Jun Kim , Hyun Park , Hyun Ho Park , Jun Hyuck Lee; J. Microbiol. 2020;58(7):606-613. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-0089-1

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Abstract

Crystal structures of enoyl-coenzyme A (CoA) isomerase from Bosea sp. PAMC 26642 (BoECI) and enoyl-CoA hydratase from Hymenobacter sp. PAMC 26628 (HyECH) were determined at 2.35 and 2.70 Å resolution, respectively. BoECI and HyECH are members of the crotonase superfamily and are enzymes known to be involved in fatty acid degradation. Structurally, these enzymes are highly similar except for the orientation of their C-terminal helix domain. Analytical ultracentrifugation was performed to determine the oligomerization states of BoECI and HyECH revealing they exist as trimers in solution. However, their putative ligand-binding sites and active site residue compositions are dissimilar. Comparative sequence and structural analysis revealed that the active site of BoECI had one glutamate residue (Glu135), this site is occupied by an aspartate in some ECIs, and the active sites of HyECH had two highly conserved glutamate residues (Glu118 and Glu138). Moreover, HyECH possesses a salt bridge interaction between Glu98 and Arg152 near the active site. This interaction may allow the catalytic Glu118 residue to have a specific conformation for the ECH enzyme reaction. This salt bridge interaction is highly conserved in known bacterial ECH structures and ECI enzymes do not have this type of interaction. Collectively, our comparative sequential and structural studies have provided useful information to distinguish and classify two similar bacterial crotonase superfamily enzymes.

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ECHDC2 inhibits the proliferation of gastric cancer cells by binding with NEDD4 to degrade MCCC2 and reduce aerobic glycolysis
Jiancheng He, Jianfeng Yi, Li Ji, Lingchen Dai, Yu Chen, Wanjiang Xue
Molecular Medicine.2024;[Epub] CrossRef
Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite
Zhenhong Chen, Bo Song, Hongyu Guo, Dapin Xia, Yidong Cai, Yongjun Wang, Weizhong Zhao
Environmental Research.2023; 227: 115777. CrossRef
Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex
Hyeoncheol Francis Son, Jae-Woo Ahn, Jiyeon Hong, Jihye Seok, Kyeong Sik Jin, Kyung-Jin Kim
Archives of Biochemistry and Biophysics.2022; 730: 109391. CrossRef
Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8
Sivaraman Padavattan, Sneha Jos, Hemanga Gogoi, Bagautdin Bagautdinov
Acta Crystallographica Section F Structural Biology Communications.2021; 77(5): 148. CrossRef

Crystal structure of the inactive state of the receiver domain of Spo0A from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier: Chang Woo Lee , Sun-Ha Park , Sung Gu Lee , Seung Chul Shin , Se Jong Han , Han-Woo Kim , Hyun Ho Park , Sunghwan Kim , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee; J. Microbiol. 2017;55(6):464-474. Published online March 9, 2017; DOI: https://doi.org/10.1007/s12275-017-6599-9

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Abstract

The two-component phosphorelay system is the most pre-valent mechanism for sensing and transducing environ-mental signals in bacteria. Spore formation, which relies on the two-component phosphorelay system, enables the long- term survival of the glacial bacterium Paenisporosarcina sp. TG-14 in the extreme cold environment. Spo0A is a key re-sponse regulator of the phosphorelay system in the early stage of spore formation. The protein is composed of a regu-latory N-terminal phospho-receiver domain and a DNA- binding C-terminal activator domain. We solved the three- dimensional structure of the unphosphorylated (inactive) form of the receiver domain of Spo0A (PaSpo0A-R) from Paenisporosarcina sp. TG-14. A structural comparison with phosphorylated (active form) Spo0A from Bacillus stearo-thermophilus (BsSpo0A) showed minor notable differences. A molecular dynamics study of a model of the active form and the crystal structures revealed significant differences in the α4 helix and the preceding loop region where phosphorylation occurs. Although an oligomerization study of PaSpo0A-R by analytical ultracentrifugation (AUC) has shown that the protein is in a monomeric state in solution, both crosslinking and crystal-packing analyses indicate the possibility of weak dimer formation by a previously undocumented mechanism. Collectively, these observations provide insight into the me-chanism of phosphorylation-dependent activation unique to Spo0A.

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Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile
Michael A. DiCandia, Adrianne N. Edwards, Joshua B. Jones, Grace L. Swaim, Brooke D. Mills, Shonna M. McBride
Journal of Molecular Biology.2022; 434(13): 167641. CrossRef

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

Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii: Hackwon Do , Chang Woo Lee , Sung Gu Lee , Hara Kang , Chul Min Park , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee; J. Microbiol. 2016;54(2):114-121. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5549-2

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Abstract

The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NADdependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.

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Where do the electrons go? How numerous redox processes drive phytochemical diversity
Patrick J. Horn
Phytochemistry Reviews.2021; 20(2): 367. CrossRef
Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer
Li-Kai Liu, John J. Tanner
Journal of Molecular Biology.2019; 431(3): 524. CrossRef
Reconstructing the Electron Density of Intermediates of the Hydrolysis of N-Acetylaspartate by Aspartoacylase
M. G. Khrenova, E. D. Kots, A. M. Kulakova, A. V. Nemukhin
Russian Journal of Physical Chemistry A.2019; 93(10): 1873. CrossRef
NAD+ promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1
David A. Korasick, Tommi A. White, Srinivas Chakravarthy, John J. Tanner
FEBS Letters.2018; 592(19): 3229. CrossRef
Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde
Lourdes Gómez-Gómez, Luis F. Pacios, Araceli Diaz-Perales, María Garrido-Arandia, Javier Argandoña, Ángela Rubio-Moraga, Oussama Ahrazem
International Journal of Molecular Sciences.2018; 19(5): 1409. CrossRef
X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC
Matthew Wilding, Colin Scott, Thomas S. Peat, Janet Newman
Acta Crystallographica Section F Structural Biology Communications.2017; 73(1): 24. CrossRef

The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding: Kim-Hung Huynh , Myoung-ki Hong , Clarice Lee , Huyen-Thi Tran , Sang Hee Lee , Yeh-Jin Ahn , Sun-Shin Cha , Lin-Woo Kang; J. Microbiol. 2015;53(11):776-782. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5475-8

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Abstract

Acinetobacter baumannii, which is emerging as a multidrugresistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.

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In Silico Design and In Vitro Assessment of Bicyclic Trifluoromethylated Pyrroles as New Antibacterial and Antifungal Agents
Diana Hodyna, Anton Klipkov, Maryna Kachaeva, Yurii Shulha, Igor Gerus, Larysa Metelytsia, Vasyl Kovalishyn
Chemistry & Biodiversity.2024;[Epub] CrossRef
Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Jinxin Zhao, Yan Zhu, Jiru Han, Yu-Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
Microorganisms.2020; 8(11): 1793. CrossRef
Identification of natural inhibitors against Acinetobacter baumannii d-alanine-d-alanine ligase enzyme: A multi-spectrum in silico approach
Sajjad Ahmad, Saad Raza, Sumra Wajid Abbasi, Syed Sikander Azam
Journal of Molecular Liquids.2018; 262: 460. CrossRef
Molecular characterization of SCO0765 as a cellotriose releasing endo-β-1,4-cellulase from Streptomyces coelicolor A(3)
Joo-Bin Hong, Vijayalakshmi Dhakshnamoorthy, Chang-Ro Lee
Journal of Microbiology.2016; 54(9): 626. CrossRef

Crystal structure of the bacterial type VI secretion system component TssL from Vibrio cholerae: Jeong Ho Chang , Yeon-Gil Kim; J. Microbiol. 2015;53(1):32-37. Published online December 4, 2014; DOI: https://doi.org/10.1007/s12275-015-4539-0

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Abstract

The type VI secretion system (T6SS), commonly found in Gram-negative bacteria, is responsible for exporting effector proteins. The T6SS has been reported to be cytotoxic to host cells. While the components and assembly of the T6SS complex have been largely assessed, structural data on T6SS components from virulent bacteria is remarkably insufficient. Here, we report the crystal structure of Vibrio cholerae TssL (VcTssL), a core component of T6SS. In spite of a relatively low sequence identity, the overall structure of VcTssL is largely similar to those from other bacterial homologs except for several differences found in local structural elements. A unique feature attributed to the C-terminal fragment of Vc- TssL is a crystallographic artifact. This incidental feature of VcTssL may provide insights into screening of molecular partners for the cytoplasmic domain of TssL. Additionally, our results may help in the design of molecular probes for a detailed understanding of the functional relationship between TssL and other T6SS components.

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Structural Characterization of TssL from Acinetobacter baumannii: a Key Component of the Type VI Secretion System
Federico M. Ruiz, Juvenal Lopez, C. Gastón Ferrara, Elena Santillana, Yanis R. Espinosa, Mario F. Feldman, Antonio Romero, Ann M. Stock
Journal of Bacteriology.2020;[Epub] CrossRef
In situ and high‐resolution cryo‐ EM structure of a bacterial type VI secretion system membrane complex
Chiara Rapisarda, Yassine Cherrak, Romain Kooger, Victoria Schmidt, Riccardo Pellarin, Laureen Logger, Eric Cascales, Martin Pilhofer, Eric Durand, Rémi Fronzes
The EMBO Journal.2019;[Epub] CrossRef
Crystal Structure of the Type VI Secretion System Accessory Protein TagF from Pseudomonas Aeruginosa
Chang-Kyu Ok, Jeong Ho Chang
Protein & Peptide Letters.2019; 26(3): 204. CrossRef
Structure and Activity of the Type VI Secretion System
Yassine Cherrak, Nicolas Flaugnatti, Eric Durand, Laure Journet, Eric Cascales, Maria Sandkvist, Peter J. Christie
Microbiology Spectrum.2019;[Epub] CrossRef
Crystal structure of the periplasmic domain of TssL, a key membrane component of Type VI secretion system
Xiangbei Wang, Bo Sun, Mengxue Xu, Shenshen Qiu, Dongqing Xu, Tingting Ran, Jianhua He, Weiwu Wang
International Journal of Biological Macromolecules.2018; 120: 1474. CrossRef
Tryptophan-mediated Dimerization of the TssL Transmembrane Anchor Is Required for Type VI Secretion System Activity
Abdelrahim Zoued, Jean-Pierre Duneau, Eric Durand, Alexandre P. España, Laure Journet, Françoise Guerlesquin, Eric Cascales
Journal of Molecular Biology.2018; 430(7): 987. CrossRef
Structure–Function Analysis of the TssL Cytoplasmic Domain Reveals a New Interaction between the Type VI Secretion Baseplate and Membrane Complexes
Abdelrahim Zoued, Chloé J. Cassaro, Eric Durand, Badreddine Douzi, Alexandre P. España, Christian Cambillau, Laure Journet, Eric Cascales
Journal of Molecular Biology.2016; 428(22): 4413. CrossRef
Aim, Load, Fire: The Type VI Secretion System, a Bacterial Nanoweapon
Francesca R. Cianfanelli, Laura Monlezun, Sarah J. Coulthurst
Trends in Microbiology.2016; 24(1): 51. CrossRef
Biogenesis and structure of a type VI secretion membrane core complex
Eric Durand, Van Son Nguyen, Abdelrahim Zoued, Laureen Logger, Gérard Péhau-Arnaudet, Marie-Stéphanie Aschtgen, Silvia Spinelli, Aline Desmyter, Benjamin Bardiaux, Annick Dujeancourt, Alain Roussel, Christian Cambillau, Eric Cascales, Rémi Fronzes
Nature.2015; 523(7562): 555. CrossRef
Type VI secretion system: secretion by a contractile nanomachine
Marek Basler
Philosophical Transactions of the Royal Society B: Biological Sciences.2015; 370(1679): 20150021. CrossRef

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