Journal of Microbiology

Journal Articles

Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota: Dao-Feng Zhang , Yu-Fang Yao , Hua-Peng Xue , Zi-Yue Fu , Xiao-Mei Zhang , Zongze Shao; J. Microbiol. 2022;60(9):905-915. Published online August 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2102-3

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Abstract: A novel bacterium, designated YYF0007T, was isolated from an agar-degrading co-culture. The strain was found harboring four CRISPR-Cas systems of two classes in the chromosome and subsequently subjected to a study on polyphasic taxonomy. Pairwise analyses of the 16S rRNA gene sequences indicated that strain YYF0007T had highest 16S rRNA gene sequence similarity (92.2%) to Jiulongibacter sediminis JN- 14-9T. The phylogenomic trees based on the 16S rRNA gene and 269 single-copy orthologous gene clusters (OCs) indicated that strain YYF0007T should be recognized as a novel genus of the family Spirosomaceae. The cells were Gramstain- negative, nonmotile, strictly aerobic, and straight long rods with no flagellum. Optimum growth occurred at 28°C and pH 7.0 with the presence of NaCl concentration 1.0–3.0% (w/v). The strain showed oxidase and catalase activities. The major fatty acids were C16:1ω5c, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant isoprenoid quinone was MK-7. The complete genome size was 4.64 Mb with a DNA G + C content of 44.4%. Further typing of CRISPR-Cas systems in the family Spirosomaceae and the phylum Bacteroidota indicated that it was remarkable for strain YYF0007T featured by such a set of CRISPR-Cas systems. This trait highlights the applications of strain YYF- 0007T in studies on the evolutionary dynamics and bacterial autoimmunity of CRISPR-Cas system as a potential model. The name Marinilongibacter aquaticus gen. nov., sp. nov. is proposed, and the type strain is YYF0007T (= MCCC 1K06017T = GDMCC 1.2428T = JCM 34683T).

Characterization of staphylococcal endolysin LysSAP33 possessing untypical domain composition: Jun-Hyeok Yu , Do-Won Park , Jeong-A Lim , Jong-Hyun Park; J. Microbiol. 2021;59(9):840-847. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1242-1

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Abstract: Endolysin, a peptidoglycan hydrolase derived from bacteriophage, has been suggested as an alternative antimicrobial agent. Many endolysins on staphylococcal phages have been identified and applied extensively against Staphylococcus spp. Among them, LysK-like endolysin, a well-studied staphylococcal endolysin, accounts for most of the identified endolysins. However, relatively little interest has been paid to LysKunlike endolysin and a few of them has been characterized. An endolysin LysSAP33 encoded on bacteriophage SAP33 shared low homology with LysK-like endolysin in sequence by 41% and domain composition (CHAP-unknown CBD). A green fluorescence assay using a fusion protein for Lys- SAP33_CBD indicated that the CBD domain (157-251 aa) was bound to the peptidoglycan of S. aureus. The deletion of LysSAP33_CBD at the C-terminal region resulted in a significant decrease in lytic activity and efficacy. Compared to LysK-like endolysin, LysSAP33 retained its lytic activity in a broader range of temperature, pH, and NaCl concentrations. In addition, it showed a higher activity against biofilms than LysK-like endolysin. This study could be a helpful tool to develop our understanding of staphylococcal endolysins not belonging to LysK-like endolysins and a potential biocontrol agent against biofilms.

Analysis of the L-malate biosynthesis pathway involved in poly(β-L-malic acid) production in Aureobasidium melanogenum GXZ-6 by addition of metabolic intermediates and inhibitors: Wei Zeng , Bin Zhang , Qi Liu , Guiguang Chen , Zhiqun Liang; J. Microbiol. 2019;57(4):281-287. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8424-0

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Abstract: Poly(β-L-malic acid) (PMA) is a promising polyester formed from L-malate in microbial cells. Malate biosynthesis is crucial for PMA production. Previous studies have shown that the non-oxidative pathway or oxidative pathway (TCA cycle) is the main biosynthetic pathway of malate in most of PMAproducing strains, while the glyoxylate cycle is only a supplementary pathway. In this study, we investigated the effect of exogenous metabolic intermediates and inhibitors of the malate biosynthetic pathway on PMA production by Aureobasidium melanogenum GXZ-6. The results showed that PMA production was stimulated by maleic acid (a fumarase inhibitor) and sodium malonate (a succinate dehydrogenase inhibitor) but inhibited by succinic acid and fumaric acid. This indicated that the TCA cycle might not be the only biosynthetic pathway of malate. In addition, the PMA titer increased by 18.1% upon the addition of glyoxylic acid after 72 h of fermentation, but the PMA titer decreased by 7.5% when itaconic acid (an isocitrate lyase inhibitor) was added, which indicated that malate for PMA production was synthesized significantly via the glyoxylate cycle rather than the TCA cycle. Furthermore, in vitro enzyme activities of the TCA and glyoxylate cycles suggested that the glyoxylate cycle significantly contributed to the PMA production, which is contradictory to what has been reported previously in other PMA-producing A. pullulans.

Gentic overexpression increases production of hypocrellin A in Shiraia bambusicola S4201: Dan Li , Ning Zhao , Bing-Jing Guo , Xi Lin , Shuang-Lin Chen , Shu-Zhen Yan; J. Microbiol. 2019;57(2):154-162. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8259-8

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Abstract: Hypocrellin A (HA) is a perylenequinone (PQ) isolated from Shiraia bambusicola that shows antiviral and antitumor activities, but its application is limited by the low production from wild fruiting body. A gene overexpressing method was expected to augment the production rate of HA in S. bambusicola. However, the application of this molecular biology technology in S. bambusicola was impeded by a low genetic transformation efficiency and little genomic information. To enhance the plasmid transformant ratio, the Polyethylene Glycol-mediated transformation system was established and optimized. The following green fluorescent protein (GFP) analysis showed that the gene fusion expression system we constructed with a GAPDH promoter Pgpd1 and a rapid 2A peptide was successfully expressed in the S. bambusicola S4201 strain. We successfully obtained the HA high-producing strains by overexpressing O-methyltransferase/FAD-dependent monooxygenase gene (mono) and the hydroxylase gene (hyd), which were the essential genes involved in our putative HA biosynthetic pathway. The overexpression of these two genes increased the production of HA by about 200% and 100%, respectively. In general, this study will provide a basis to identify the genes involved in the hypocrellin A biosynthesis. This improved transformation method can also be used in genetic transformation studies of other fungi.

De novo transcriptome assembly and characterization of the 10-hydroxycamptothecin-producing Xylaria sp. M71 following salicylic acid treatment: Xiaowei Ding , Kaihui Liu , Yonggui Zhang , Feihu Liu; J. Microbiol. 2017;55(11):871-876. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7173-1

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Abstract: In the present study, we identified genes that are putatively involved in the production of fungal 10-hydroxycamptothecin via transcriptome sequencing and characterization of the Xylaria sp. M71 treated with salicylic acid (SA). A total of 60,664,200 raw reads were assembled into 26,044 unigenes. BLAST assigned 8,767 (33.7%) and 10,840 (41.6%) unigenes to 40 Gene Ontology (GO) annotations and 108 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 3,713 unigenes comprising 1,504 upregulated and 2,209 downregulated unigenes were found to be differentially expressed between SA-induced and control fungi. Based on the camptothecin biosynthesis pathway in plants, 13 functional genes of Xylaria sp. M71 were mapped to the mevalonate (MVA) pathway, suggesting that the fungal 10-hydroxycamptothecin is produced via the MVA pathway. In summary, analysis of the Xylaria sp. M71 transcriptome allowed the identification of unigenes that are putatively involved in 10-hydroxycamptothecin biosynthesis in fungi.

Review

MINIREVIEW] Hydroxylation of methane through component interactions in soluble methane monooxygenases: Seung Jae Lee; J. Microbiol. 2016;54(4):277-282. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5642-6

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Abstract: Methane hydroxylation through methane monooxygenases (MMOs) is a key aspect due to their control of the carbon cycle in the ecology system and recent applications of methane gas in the field of bioenergy and bioremediation. Methanotropic bacteria perform a specific microbial conversion from methane, one of the most stable carbon compounds, to methanol through elaborate mechanisms. MMOs express particulate methane monooxygenase (pMMO) in most strains and soluble methane monooxygenase (sMMO) under copper-limited conditions. The mechanisms of MMO have been widely studied from sMMO belonging to the bacterial multicomponent monooxygenase (BMM) superfamily. This enzyme has diiron active sites where different types of hydrocarbons are oxidized through orchestrated hydroxylase, regulatory and reductase components for precise control of hydrocarbons, oxygen, protons, and electrons. Recent advances in biophysical studies, including structural and enzymatic achievements for sMMO, have explained component interactions, substrate pathways, and intermediates of sMMO. In this account, oxidation of methane in sMMO is discussed with recent progress that is critical for understanding the microbial applications of C-H activation in one-carbon substrates.

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

Bacillus coreaensis sp. nov.: a xylan-hydrolyzing bacterium isolated from the soil of Jeju Island, Republic of Korea: Won-Jae Chi , Young Sang Youn , Jae-Seon Park , Soon-Kwang Hong; J. Microbiol. 2015;53(7):448-453. Published online June 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5140-2

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Abstract: A xylan-degrading bacterium, designated as MS5T strain, was isolated from soil collected from the Jeju Island, Republic of Korea. Strain MS5T was Gram-stain-positive, aerobic, and motile by polar flagellum. The major fatty acids identified in this bacterium were iso-C15:0 (32.3%), C16:0 (27.3%), and anteiso-C15:0 (10.2%). A similarity search based on the 16S rRNA gene sequence revealed that the strain belongs to the class Bacilli and shared the highest similarity with the type strains Bacillus beringensis BR035T (98.7%) and Bacillus korlensis ZLC-26T (98.6%) which form a coherent cluster in a neighbor-joining phylogenetic tree. The DNA G+C content of strain MS5T was 43.0 mol%. The major menaquinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNADNA relatedness values between strain MS5T and two closely related species, B. beringensis BR035T and B. korlensis ZLC- 26T, were less than 70%. DNA-DNA relatedness analysis and 16S rRNA sequence similarity, as well as phenotypic and chemotaxonomic characteristics suggest that the strain MS5T constitutes a novel Bacillus species, for which the name Bacillus coreaensis sp. nov. is proposed. The type strain is MS5T (=DSM25506T =KCTC13895T).

Biocatalytic Properties and Substrate-binding Ability of a Modular GH10 β-1,4-Xylanase from an Insect-symbiotic Bacterium, Streptomyces mexicanus HY-14: Do Young Kim , Dong-Ha Shin , Sora Jung , Jong Suk Lee , Han-Young Cho , Kyung Sook Bae , Chang-Keun Sung , Young Ha Rhee , Kwang-Hee Son , Ho-Yong Park; J. Microbiol. 2014;52(10):863-870. Published online October 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4390-8

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Abstract: The gene (1350-bp) encoding a modular β-1,4-xylanase (XylU), which consists of an N-terminal catalytic GH10 domain and a C-terminal carbohydrate-binding module 2 (CBM 2), from Streptomyces mexicanus HY-14 was cloned and functionally characterized. The purified His-tagged recombinant enzyme (rXylU, 44.0 kDa) was capable of efficiently hydrolyze diverse xylosidic compounds, p-nitrophenyl-cellobioside, and pnitrophenyl- xylopyranoside when incubated at pH 5.5 and 65°C. Especially, the specific activities (649.8 U/mg and 587.0 U/mg, respectively) of rXylU toward oat spelts xylan and beechwood xylan were relatively higher than those (<500.0 U/mg) of many other GH10 homologs toward the same substrates. The results of enzymatic degradation of birchwood xylan and xylooligosaccharides (xylotriose to xylohexaose) revealed that rXylU preferentially hydrolyzed the substrates to xylobiose (>75%) as the primary degradation product. Moreover, a small amount (4%<) of xylose was detected as the degradation product of the evaluated xylosidic substrates, indicating that rXylU was a peculiar GH10 β-1,4- xylanase with substrate specificity, which was different from its retaining homologs. A significant reduction of the binding ability of rXylU caused by deletion of the C-terminal CBM 2 to various insoluble substrates strongly suggested that the additional domain might considerably contribute to the enzyme-substrate interaction.

Molecular Characterization of the Alpha Subunit of Multicomponent Phenol Hydroxylase from 4-Chlorophenol-Degrading Pseudomonas sp. Strain PT3: Wael S. El-Sayed , Mohamed K. Ibrahim , Salama A. Ouf; J. Microbiol. 2014;52(1):13-19. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3250-x

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Abstract: Multicomponent phenol hydroxylases (mPHs) are diiron enzymes that use molecular oxygen to hydroxylate a variety of phenolic compounds. The DNA sequence of the alpha subunit (large subunit) of mPH from 4-chlorophenol (4-CP)- degrading bacterial strain PT3 was determined. Strain PT3 was isolated from oil-contaminated soil samples adjacent to automobile workshops and oil stations after enrichment and establishment of a chlorophenol-degrading consortium. Strain PT3 was identified as a member of Pseudomonas sp. based on sequence analysis of the 16S rRNA gene fragment. The 4-CP catabolic pathway by strain PT3 was tentatively proposed to proceed via a meta-cleavage pathway after hydroxylation to the corresponding chlorocatechol. This hypothesis was supported by polymerase chain reaction (PCR) detection of the LmPH encoding sequence and UV/VIS spectrophotometric analysis of the culture filtrate showing accumulation of 5-chloro-2-hydroxymuconic semialdehyde (5-CHMS) with λmax 380. The detection of catabolic genes involved in 4-CP degradation by PCR showed the presence of both mPH and catechol 2,3-dioxygenase (C23DO). Nucleotide sequence analysis of the alpha subunit of mPH from strain PT3 revealed specific phylogenetic grouping to known mPH. The metal coordination encoding regions from strain PT3 were found to be conserved with those from the homologous dinuclear oxo-iron bacterial monooxygenases. Two DE(D)XRH motifs was detected in LmPH of strain PT3 within an approximate 100 amino acid interval, a typical arrangement characteristic of most known PHs.

NOTE] Isolation and Characterization of Histamine-Producing Bacteria from Fermented Fish Products: Jin Seok Moon , So-Young Kim , Kyung-Ju Cho , Seung-Joon Yang , Gun-Mook Yoon , Hyun-Ju Eom , Nam Soo Han; J. Microbiol. 2013;51(6):881-885. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3333-0

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Abstract: Histamine is mainly produced by microorganisms that are found in fermented foods, and is frequently involved in food poisoning. Two histamine-producing bacteria were isolated from fermented fish products, anchovy sauce, and sand lance sauce by using a histidine decarboxylating medium. The species were identified as Bacillus licheniformis A7 and B. coagulans SL5. Multiplex PCR analysis showed the presence of the conserved histidine decarboxylase (hdc) gene in the chromosome of these bacteria. B. licheniformis A7 and B. coagulans SL5 produced the maximum amount of histamine (22.3±3.5 and 15.1±1.5 mg/L, respectively). As such, they were determined to be potential histamine-producing bacteria among the tested cultures.

Paenibacillus xylaniclasticus sp. nov., a Xylanolytic-Cellulolytic Bacterium Isolated from Sludge in an Anaerobic Digester: Chakrit Tachaapaikoon , Somboon Tanasupawat , Patthra Pason , Somphit Sornyotha , Rattiya Waeonukul , Khin Lay Kyu , Khanok Ratanakhanokchai; J. Microbiol. 2012;50(3):394-400. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1480-3

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Abstract: A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1T, was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C15:0, iso-C16:0, anteiso-C17:0, and C16:0 were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1T belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232T, P. curdlanolyticus KCTC 3759T, and P. kobensis KCTC 3761T with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232T, P. curdlanolyticus KCTC 3759T, and P. kobensis KCTC 3761T were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1T were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1T should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1T (=NBRC 106381T =KCTC 13719T =TISTR 1914T).

Biochemical Characteristization of Propionyl-Coenzyme A Carboxylase Complex of Streptomyces toxytricini: Atanas V. Demirev , Anamika Khanal , Nguyen Phan Kieu Hanh , Kyung Tae Nam , Doo Hyun Nam; J. Microbiol. 2011;49(3):407-412. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-1122-1

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Abstract: Acyl-CoA carboxylases (ACC) are involved in important primary or secondary metabolic pathways such as fatty acid and/or polyketides synthesis. In the 6.2 kb fragment of pccB gene locus of Streptomyces toxytricini producing a pancreatic inhibitor lipstatin, 3 distinct subunit genes of presumable propionyl-CoA carboxylase (PCCase) complex, assumed to be one of ACC responsible for the secondary metabolism, were identified along with gene for a biotin protein ligase (Bpl). The subunits of PCCase complex were α subunit (AccA3), β subunit (PccB), and auxiliary ε subunit (PccE). In order to disclose the involvement of the PCCase complex in secondary metabolism, some biochemical characteristics of each subunit as well as their complex were examined. In the test of substrate specificity of the PCCase complex, it was confirmed that this complex showed much higher conversion of propionyl-CoA rather than acetyl-CoA. It implies the enzyme complex could play a main role in the production of methylmalonyl-CoA from propionyl-CoA, which is a precursor of secondary polyketide biosynthesis.

The Role of Carbohydrate-Binding Module (CBM) Repeat of a Multimodular Xylanase (XynX) from Clostridium thermocellum in Cellulose and Xylan Binding: Thangaswamy Selvaraj , Sung Kyum Kim , Yong Ho Kim , Yu Seok Jeong , Yu-Jeong Kim , Nguyen Dinh Phuong , Kyung Hwa Jung , Jungho Kim , Han Dae Yun , Hoon Kim; J. Microbiol. 2010;48(6):856-861. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0285-5

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Abstract: A non-cellulosomal xylanase from Clostridium thermocellum, XynX, consists of a family-22 carbohydratebinding module (CBM22), a family-10 glycoside hydrolase (GH10) catalytic module, two family-9 carbohydrate-binding modules (CBM9-I and CBM9-II), and an S-layer homology (SLH) module. E. coli BL21(DE3) (pKM29), a transformant carrying xynX', produced several truncated forms of the enzyme. Among them, three major active species were purified by SDS-PAGE, activity staining, gel-slicing, and diffusion from the gel. The truncated xylanases were different from each other only in their C-terminal regions. In addition to the CBM22 and GH10 catalytic modules, XynX1 had the CBM9-I and most of the CBM9-II, XynX2 had the CBM9-I and about 40% of the CBM9-II, and XynX3 had about 75% of the CBM9-I. The truncated xylanases showed higher binding capacities toward Avicel than those toward insoluble xylan. XynX1 showed a higher affinity toward Avicel (70.5%) than XynX2 (46.0%) and XynX3 (42.1%); however, there were no significant differences in the affinities toward insoluble xylan. It is suggested that the CBM9 repeat, especially CBM9-II, of XynX plays a role in xylan degradation in nature by strengthening cellulose binding rather than by enhancing xylan binding.

Identification and Characterization of Acetyl-CoA Carboxylase Gene Cluster in Streptomyces toxytricini: Atanas V. Demirev , Ji Seon Lee , Bhishma R. Sedai , Ivan G. Ivanov , Doo Hyun Nam; J. Microbiol. 2009;47(4):473-478. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0135-5

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Abstract: The gene locus for acetyl-CoA carboxylase (ACC) involved in the primary metabolism was identified from the genomic library of Streptomyces toxytricini which produces a lipase inhibitor lipstatin. The 7.4 kb cloned gene was comprised of 5 ORFs including accD1, accA1, hmgL, fadST1, and stsF. In order to confirm the biochemical characteristics of AccA1, the gene was overexpressed in Escherichia coli cells, and the recombinant protein was purified through Ni2+ affinity chromatography. Because most of the expressed AccA1 was biotinylated by host E. coli BirA in the presence of D-biotin, the non-biotinylated apo-AccA1 was purified after gene induction without D-biotin, followed by exclusion of holo-AccA1 using streptavidin beads. The separated apo-AccA1 was post-translationally biotinylated by S. toxytricini biotin apo-protein ligase (BPL) in a time- and enzyme-dependent manner. This result supports that this gene cluster of S. toxytricini encodes the functional ACC enzyme subunits to be biotinylated.

Expression of c-Myc Is Related to Host Cell Death Following Salmonella typhimurium Infection in Macrophage: Jihyoun Seong , Hong Hua Piao , Phil Yeoul Ryu , Youn Uck Kim , Hyon E Choy , Yeongjin Hong; J. Microbiol. 2009;47(2):214-219. Published online May 2, 2009; DOI: https://doi.org/10.1007/s12275-008-0308-7

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Abstract: It has been known that ornithine decarboxylase (ODC) induced by the binding of c-Myc to odc gene is closely linked to cell death. Here, we investigated the relationship between their expressions and cell death in macrophage cells following treatment with Salmonella typhimurium or lipopolysaccharide (LPS). ODC expression was increased by bacteria or LPS and repressed by inhibitors against mitogen-activated protein kinases (MAPKs) in Toll-like receptor 4 (TLR4) signaling pathway. In contrast, c-Myc protein level was increased after treatment with bacteria, but not by treatment with LPS or heat-killed bacteria although both bacteria and LPS increased the levels of c-myc mRNA to a similar extent. c-Myc protein level is dependent upon bacterial invasion because treatment with cytochalasin D (CCD), inhibitors of endocytosis, decreased c-Myc protein level. The cell death induced by bacteria was significantly decreased after treatment of CCD or c-Myc inhibitor, indicating that cell death by S. typhimurium infection is related to c-Myc, but not ODC. Consistent with this conclusion, treatment with bacteria mutated to host invasion did not increase c-Myc protein level and cell death rate. Taken together, it is suggested that induction of c-Myc by live bacterial infection is directly related to host cell death.

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