Journal of Microbiology

Volume 55(6); June 2017

Review

[Minireview] Unraveling new functions of superoxide dismutase using yeast model system: Beyond its conventional role in superoxide radical scavenging: Woo-Hyun Chung ,; J. Microbiol. 2017;55(6):409-416. Published online March 9, 2017; DOI: https://doi.org/10.1007/s12275-017-6647-5

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39 Citations

Abstract: To deal with chemically reactive oxygen molecules constantly threatening aerobic life, cells are readily equipped with elabo-rate biological antioxidant systems. Superoxide dismutase is a metalloenzyme catalytically eliminating superoxide radi-cal as a first-line defense mechanism against oxidative stress. Multiple different SOD isoforms have been developed through-out evolution to play distinct roles in separate subcellular com-partments. SOD is not essential for viability of most aerobic organisms and intriguingly found even in strictly anaerobic bacteria. Sod1 has recently been known to play important roles as a nuclear transcription factor, an RNA binding pro-tein, a synthetic lethal interactor, and a signal modulator in glucose metabolism, most of which are independent of its canonical function as an antioxidant enzyme. In this review, recent advances in understanding the unconventional role of Sod1 are highlighted and discussed with an emphasis on its genetic crosstalk with DNA damage repair/checkpoint path-ways. The budding yeast Saccharomyces cerevisiae has been successfully used as an efficient tool and a model organism to investigate a number of novel functions of Sod1.

Journal Articles

Nocardioides suum sp. nov. isolated from the air environment in an indoor pig farm: Siwon Lee , Wonseok Lee , Hyen-Mi Chung , Sangjung Park; J. Microbiol. 2017;55(6):417-420. Published online April 20, 2017; DOI: https://doi.org/10.1007/s12275-017-6313-y

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Abstract: A bacterial strain PBT33-2T was isolated from the air environ-ment in an indoor pig farm. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PBT33-2T be-longed to the genus Nocardioides in the phylum Actinobac-teria, and was most closely related to Nocardioides daphnia D287T in a maximum-likelihood and neighbor-joining phy-logenetic trees. Strain PBT33-2T shared 95.3% sequence iden-tity with N. daphnia D287T. However, the highest sequence similarity was shown with N. sediminis MSL-01T (96.0%). It had less than 96.0% sequence identities with other type spe-cies of the genus Nocardioides. Strain PBT-33-2T grew at 15–45°C (optimum 20–35°C), pH 5.0–11.0 (optimum pH 7.0) and 0–4.0% (w/v) NaCl (optimum 0%). The major fatty acid and quinone were iso-C16:0 and MK-8, and the DNA G+C content of strain PBT33-2T was 69.3 mol%. On the basis of poly-phasic results, strain PBT33-2T represents a novel spe-cies of the genus Nocardioides, for which the name Nocar-dioides suum sp. nov. is proposed. Its type strain is PBT33-2T (=KCTC 39558T =DSM 102833T).

Jindonia aestuariivivens gen. nov., sp. nov., isolated from a tidal flat on the south-western sea in Republic of Korea: Sooyeon Park , Sun Young Yoon , Min-Ji Ha , Jung-Hoon Yoon; J. Microbiol. 2017;55(6):421-427. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6621-2

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Abstract: A Gram-stain-negative, aerobic, non-flagellated, and coccoid, ovoid or rod-shaped bacterium, designated JDTF-65T, was isolated from a tidal flat on the south-western sea in Republic of Korea. Strain JDTF-65T grew optimally at 25°C, at pH 7.0– 8.0 and in the presence of 2.0% (w/v) NaCl. Strain JDTF-65T exhibited 16S rRNA gene sequence similarities of 97.1–97.6% to the type strains of ‘Aliisedimentitalea scapharcae’, Phaeo-bacter gallaeciensis, Phaeobacter inhibens, Leisingera aqui-marina, Tropicibacter litoreus, Sulfitobacter pseudonitzschiae, and Pseudoseohaeicola caenipelagi. Phylogenetic trees based on 16S rRNA gene sequences showed that strain JDTF-65T forms an independent lineage within the radiation enclosed by the family Rhodobacteraceae. Strain JDTF-65T contained Q-10 as the predominant ubiquinone and C18:1 ω7c as the major fatty acid. The major polar lipids of strain JDTF-65T were phosphatidylcholine, phosphatidylethanolamine, phos-phatidylglycerol, one unidentified aminolipid, and one un-identified lipid. The DNA G+C content of strain JDTF-65T was 56.8 mol% and its DNA-DNA relatedness values with the type strains of the phylogenetically related species were 13– 27%. Differential phenotypic properties revealed that strain JDTF-65T is separated from representatives of some phylo-genetically related taxa. On the basis of the data presented, strain JDTF-65T represents a new genus and species within the family Rhodobacteraceae, for which the name Jindonia aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Jindonia aestuariivivens is JDTF-65T (=KCTC 52564T =NBRC 112534T).

Achromobacter panacis sp. nov., isolated from rhizosphere of Panax ginseng: Priyanka Singh , Yeon Ju Kim , Hina Singh , Mohamed El-Agamy Farh , Deok-Chun Yang; J. Microbiol. 2017;55(6):428-434. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-6612-3

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Abstract: A novel strain DCY105T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Re-public of Korea. Strain DCY105T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5–7.0 and in the absence of NaCl. Phylogenetically, strain DCY105T is most closely related to Achromobacter marplatensis LMG 26219T (96.81%). The DNA G+C content of strain DCY105T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and dipho-sphatidylglycerol were amongst the major polar lipids. C16:00, C8:03OH and iso-C17:03OH were identified as the major fatty acids present in DCY105T. The results of physiological and biochemical tests allowed strain DCY105T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105T (=CCTCCAB 2015193T =KCTC 42751T).

Corynebacterium defluvii sp. nov., isolated from Sewage: Qiu-Li Yu , Zheng-Fei Yan , Feng-Hua Tian , Chuan-Wen Jia , Chang-Tian Li; J. Microbiol. 2017;55(6):435-439. Published online April 20, 2017; DOI: https://doi.org/10.1007/s12275-017-6592-3

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Abstract: A Gram-positive, aerobic, non-motile, rod-shapeds, cata-lase-positive, and oxidase-negative strain, designated Y49T, was isolated from sewage collected from Jilin Agricultural University, China. It grew at 20–40°C (optimum at 30°C), at pH 6.0–8.0 (optimum at 7.0) and at 0–1.0% sodium chlo-ride (optimum at 0%). The major isoprenoid quinone was menaquinone-8 (MK-8) and the polar lipids were diphos-phatidylglycerol, phosphatidylglycerol, phosphatidylmethy-lethanolamine, four unidentified lipids, and two unidenti-fied aminolipids. The peptidoglycan was meso-diaminopi-melic acid. The cell-wall sugars were galactose, arabinose, and glucose. The fatty acids were C9:0, C16:0, C16:1 ω9c, C17:1 ω9c, C18:3 ω6c (6,9,12), C18:1 ω9c, and C18:0. The DNA G+C content was 51.4 mol%. Based on the 16S rRNA gene se-quence analysis, the nearest phylogenetic neighbors of strain Y49T were Corynebacterium efficiens DSM 44549T (97.5%), Corynebacterium callunae DSM 20147T (97.2%), Coryne-bacterium deserti GIMN 1.010T (96.8%), Corynebacterium glutamicum ATCC 13032T (96.4%), and other species belong-ing to this genus (92.3–95.4%). The DNA-DNA relatedness value between strain Y49T and C. efficiens DSM 44549T, C. callunae DSM 20147T, C. deserti GIMN1.010T, and C. gluta-micum ATCC 13032T was 25.5±2.0%, 21.1±1.0%, 16.5±0.5%, and 13.5±0.9%, respectively. Based on the phylogenetic an-alysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain Y49T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium defluvii sp nov. is proposed. The type strain is Y49T (= KCTC 39731T =CGMCC 1.15506T).

Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus: Yun Suk Lee , Hyun Jung Kim , Woojun Park; J. Microbiol. 2017;55(6):440-447. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7086-z

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Abstract: Although microbially induced calcium carbonate precipita-tion (MICP) through ureolysis has been widely studied in en-vironmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium car-bonate-precipitating bacteria that induced an alkaline envi-ronment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to pre-cipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy disper-sive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning elec-tron microscopy analysis indicated the formation of morpho-logically distinct minerals around cells under these condi-tions. Monitoring of bacterial growth, pH changes, and Ca2+ concentrations under aerobic, hypoxia, and anaerobic con-ditions suggested that strain YS11 could induce alkaline con-ditions up to a pH of 8.9 and utilize 95% of free Ca2+ only under aerobic conditions. Unusual Ca2+ binding and its re-lease from cells were observed under hypoxia conditions. Bio-film and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore- forming ability, which supports its potential application for self-healing concrete.

ZntR positively regulates T6SS4 expression in Yersinia pseudotuberculosis: Tietao Wang , Keqi Chen , Fen Gao , Yiwen Kang , Muhammad Tausif Chaudhry , Zhuo Wang , Yao Wang , Xihui Shen; J. Microbiol. 2017;55(6):448-456. Published online March 10, 2017; DOI: https://doi.org/10.1007/s12275-017-6540-2

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Abstract: The type VI secretion system (T6SS) is a widespread and versatile protein secretion system found in most Gram- negative bacteria. Studies of T6SS have mainly focused on its role in virulence toward host cells and inter-bacterial inter-actions, but studies have also shown that T6SS4 in Yersinia pseudotuberculosis participates in the acquisition of zinc ions to alleviate the accumulation of hydroxyl radicals induced by multiple stressors. Here, by comparing the gene expression patterns of wild-type and zntR mutant Y. pseudotubercu-losis cells using RNA-seq analysis, T6SS4 and 17 other bio-logical processes were found to be regulated by ZntR. T6SS4 was positively regulated by ZntR in Y. pseudotuberculosis, and further investigation demonstrated that ZntR regulates T6SS4 by directly binding to its promoter region. T6SS4 ex-pression is regulated by zinc via ZntR, which maintains in-tracellular zinc homeostasis and controls the concentration of reactive oxygen species to prevent bacterial death under oxidative stress. This study provides new insights into the regulation of T6SS4 by a zinc-dependent transcriptional regu-lator, and it provides a foundation for further investigation of the mechanism of zinc transport by T6SS.

The inability of Bacillus licheniformis perR mutant to grow is mainly due to the lack of PerR-mediated fur repression: Jung-Hoon Kim , Yoon-Mo Yang , Chang-Jun Ji , Su-Hyun Ryu , Young-Bin Won , Shin-Yeong Ju , Yumi Kwon , Yeh-Eun Lee , Hwan Youn , Jin-Won Lee; J. Microbiol. 2017;55(6):457-463. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-7051-x

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Abstract: PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes in-volved in peroxide stress response. Industrially important bac-terium Bacillus licheniformis contains three PerR-like pro-teins (PerRBL, PerR2, and PerR3) compared to its close rela-tive Bacillus subtilis. Interestingly, unlike other bacteria in-cluding B. subtilis, no authentic perRBL null mutant could be established for B. licheniformis. Thus, we constructed a con-ditional perRBL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL. PerRBL regulon genes include katA, mrgA, ahpC, pfeT, hemA, fur, and perR as observed for PerRBS. However, there is some variation in the expression levels of fur and hemA genes be-tween B. subtilis and B. licheniformis in the derepressed state. Furthermore, katA, mrgA, and ahpC are strongly induced, whereas the others are only weakly or not induced by H2O2 treatment. In contrast to the B. subtilis perR null mutant which frequently gives rise to large colony phenotype mainly due to the loss of katA, the suppressors of B. licheniformis perR mutant, which can form colonies on LB agar, were all cata-lase-positive. Instead, many of the suppressors showed in-creased levels of siderophore production, suggesting that the suppressor mutation is linked to the fur gene. Consistent with this, perR fur double mutant could grow on LB agar without Fe supplementation, whereas perR katA double mutant could only grow on LB agar with Fe supplementation. Taken toge-ther, our data suggest that in B. licheniformis, despite the si-milarity in PerRBL and PerRBS regulon genes, perR is an essen-tial gene required for growth and that the inability of perR null mutant to grow is mainly due to elevated expression of Fur.

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.

Identification and characterization of a new agar-degrading strain with the novel properties of saccharides inhibition and nitrogen fixation: Hao Wu , Guiguang Chen , Yaxi Bian , Wei Zeng , Bihong Sun , Zhiqun Liang; J. Microbiol. 2017;55(6):475-482. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-6464-x

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Abstract: In this study, a new agar-degrading strain was isolated from soil with agar as a sole carbon source and energy. Based on its morphological, physiological, biochemical characterization and 16S rDNA sequence, the strain was identified as Strep-tomyces lavendulae UN-8. The extracellular agarase activity reached 0.03 U/ml after fermentation in shake flask (250 ml), which was close to other reported non-marine micro-organisms. Furthermore, it is interesting that the growth of UN-8 would be inhibited by glucose (40 g/L) and maltose (40 g/L) with the inhibitory rate of 100% and 70%, respec-tively. Besides, UN-8 could be grown on the solid medium without any nitrogen sources, then the possible nitrogen fix-ation gene nifU was cloned from its genomic DNA. The de-duced amino acid sequence of nifU has high similarity (98%) with nitrogen fixation protein NifU from Streptomyces sp. NRRL S-104 (KJY22454.1) and Streptomyces sp. NRRL F-4428 (KJK52526.1) based on NCBI blast. It is suggested that the nifU gene of UN-8 also encoded nitrogen fixation protein NifU. These results provided some new information for the further understanding of agar-degrading strain.

Bedaquiline susceptibility test for totally drug-resistant tuberculosis Mycobacterium tuberculosis: Ji-Chan Jang , Yong-Gyun Jung , Jungil Choi , Hyunju Jung , Sungweon Ryoo; J. Microbiol. 2017;55(6):483-487. Published online April 20, 2017; DOI: https://doi.org/10.1007/s12275-017-6630-1

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Abstract: This study aimed to provide information that bedaquilline is significantly effective for treatment of totally drug resistant (TDR) Mycobacterium tuberculosis that shows resistant to all first- and second-line drugs-using an innovative disc agarose channel (DAC) system. Time-lapse images of single bacterial cells under culture conditions with different concentrations of bedaquiline were analysed by image processing software to determine minimum inhibitory concentrations (MICs). Bedaquiline inhibited the growth of TDR M. tuberculosis strains, with MIC values ranging from 0.125 to 0.5 mg/L. The results of the present study demonstrate that bedaquiline, newly approved by the United States Food and Drug Admi-nistration (FDA), may offer therapeutic solutions for TDR -TB.

Coptidis Rhizoma extract inhibits replication of respiratory syncytial virus in vitro and in vivo by inducing antiviral state: Byeong-Hoon Lee , Kiramage Chathuranga , Md Bashir Uddin , Prasanna Weeratunga , Myun Soo Kim , Won-Kyung Cho , Hong Ik Kim , Jin Yeul Ma , Jong-Soo Lee; J. Microbiol. 2017;55(6):488-498. Published online May 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7088-x

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Abstract: Coptidis Rhizoma is derived from the dried rhizome of Ranun-culaceous plants and is a commonly used traditional Chinese medicine. Although Coptidis Rhizoma is commonly used for its many therapeutic effects, antiviral activity against respi-ratory syncytial virus (RSV) has not been reported in detail. In this study, we evaluated the antiviral activities of Coptidis Rhizoma extract (CRE) against RSV in human respiratory tract cell line (HEp2) and BALB/c mice. An effective dose of CRE significantly reduces the replication of RSV in HEp2 cells and reduces the RSV-induced cell death. This antiviral activity against RSV was through the induction of type I inter-feron-related signaling and the antiviral state in HEp2 cells. More importantly, oral administration of CRE exhibited prophylactic effects in BALB/c mice against RSV. In HPLC analysis, we found the presence of several compounds in the aqueous fraction and among them; we confirmed that pal-matine was related to the antiviral properties and immune- modulation effect. Taken together, an extract of Coptidis Rhi-zoma and its components play roles as immunomodulators and could be a potential source as promising natural antivirals that can confer protection to RSV. These outcomes should encourage further allied studies in other natural products.

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