Journal of Microbiology

Volume 52(2); February 2014

Review

MINIREVIEW] To Peep into Pif1 Helicase: Multifaceted All the Way from Genome Stability to Repair-Associated DNA Synthesis: Woo-Hyun Chung; J. Microbiol. 2014;52(2):89-98. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3524-3

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26 Citations

Abstract: Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.

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

Comparative Phylogenetic Relationships and Genetic Structure of the Caterpillar Fungus Ophiocordyceps sinensis and Its Host Insects Inferred from Multiple Gene Sequences: Qing-Mei Quan , Qing-Xia Wang , Xue-Li Zhou , Shan Li , Xiao-Ling Yang , Yun-Guo Zhu , Zhou Cheng; J. Microbiol. 2014;52(2):99-105. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3391-y

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26 Citations

Abstract: Ophiocordyceps sinensis (Ascomycota: Ophiocordycipitaceae) is a native fungal parasite of Hepialidae caterpillars and one of the most economically important medicinal caterpillar fungi in China. However, little is known about the phylogenetic and evolutionary relationships between O. sinensis and its host insects. In this study, nuclear ITS and β-tubulin sequences from O. sinensis and mitochondrial COI, COII, and Cytb sequences from its hosts were analyzed across 33 populations sampled from five regions in China. Phylogenetically, both O. sinensis and its hosts were divided into three geographically correlated clades, and their phylogenies were congruent. Analysis of molecular variance and calculated coefficients of genetic differentiation revealed significant genetic divergence among the clades within both O. sinensis (FST=0.878, NST=0.842) and its hosts (FST=0.861, NST=0.816). Estimated gene flow was very low for O. sinensis (Nm=0.04) and the host insects (Nm=0.04) among these three clades. Mantel tests demonstrated a significant correlation (P<0.01) between the genetic distances for O. sinensis and its hosts, as well as a significant association (P<0.05) between geographic and genetic distances in both. The similar phylogenetic relationships, geographic distributions, and genetic structure and differentiation between O. sinensis and its hosts imply that they have coevolved.

Paenibacillus swuensis sp. nov., a Bacterium Isolated from Soil: Jae-Jin Lee , Da-Hye Yang , Ye-Sil Ko , Jae-Kyoung Park , Eun-Young Im , Ju-Yeon Kim , Ka-Young Kwon , Yu-Jung Lee , Hyung-Mi Kim , Myung Kyum Kim; J. Microbiol. 2014;52(2):106-110. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3546-x

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6 Citations

Abstract: Strain DY6T, a Gram-positive endospore-forming motile rodshaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6T revealed that strain DY6T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6T were found with Paenibacillus gansuensis B518T (97.9%), P. chitinolyticus IFO 15660T (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173T (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C15:0 (38.7%) and C16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6T (=KCTC 33026T =JCM 18491T) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.

Microbial Communities in Semi-consolidated Carbonate Sediments of the Southwest Indian Ridge: Jiwei Li , Xiaotong Peng , Huaiyang Zhou , Jiangtao Li , Zhilei Sun , Shun Chen; J. Microbiol. 2014;52(2):111-119. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3133-1

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15 Citations

Abstract: White semi-consolidated carbonate sediments attached to black ferromanganese oxide films were collected approximately 50 km west of a newly discovered hydrothermal field near the Southwest Indian Ridge (SWIR). The biodiversity of the prokaryotic communities within the field was examined using clone library-based culture-independent analysis of the exterior black oxides and the interior white carbonates. Subsequent 16S rRNA gene analysis suggested that Gammaproteobacteria, Acidobacteria, and Thaumarchaeota members dominated the bacterial and archaeal clone libraries. To further characterize the metabolic processes within the microbial community, analyses of the amoA (coding the alpha subunit of the ammonia monooxygenase for Archaea) and aprA (coding the alpha subunit of the dissimilatory adenosine-5'-phosphosulfate reductase for the sulfate-reducing and sulfur-oxidizing prokaryotes) functional genes were conducted. The functional gene analysis results suggested that Thaumarchaeota and Alphaproteobacteria members were the potential players that participated in N and S cycles in this marine carbonate sedimentary environment. This paper is the first to describe the microbial communities and their potential metabolic pathways within the semi-consolidated carbonate sediments of the SWIR.

Effect of Fumarate Reducing Bacteria on In Vitro Rumen Fermentation, Methane Mitigation and Microbial Diversity: Lovelia Mamuad , Seon Ho Kim , Chang Dae Jeong , Yeon Jae Choi , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2014;52(2):120-128. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3518-1

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29 Citations

Abstract: The metabolic pathways involved in hydrogen (H2) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH4) emissions by ruminants. H2 as one of the major substrate for CH4 production is therefore should be controlled. One of the strategies on reducing CH4 is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH4 production, diversity and quantity. M. jalaludinii significantly reduced CH4 at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH4 production and quantity, increases succinate and changes the rumen microbial diversity.

Functional Analysis of a Subtilisin-like Serine Protease Gene from Biocontrol Fungus Trichoderma harzianum: Haijuan Fan , Zhihua Liu , Rongshu Zhang , Na Wang , Kai Dou , Gulijimila Mijiti , Guiping Diao , Zhiying Wang; J. Microbiol. 2014;52(2):129-138. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3308-9

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24 Citations

Abstract: The subtilisin-like serine protease gene ThSS45 has been cloned from Trichoderma harzianum ACCC30371. Its coding region is 1302 bp in length, encoding 433 amino acids, with a predicted protein molecular weight of 44.9 kDa and pI of 5.91. ThSS45 was shown by RT-qPCR analysis to be differentially transcribed in response to eight different treatments. The transcription of ThSS45 was up-regulated when grown in mineral medium, under carbon starvation, and nitrogen starvation, and in the presence of 1% root powder, 1% stem powder, and 1% leaf powder derived from Populus davidiana × P. bolleana (Shanxin poplar) aseptic seedlings. The highest increase in transcription approached 3.5-fold that of the control at 6 h under induction with 1% poplar root powder. The transcription of ThSS45 was also slightly up-regulated by 1% Alternaria alternata cell wall and 5% A. alternata fermentation liquid. Moreover, the analyses of coding and promoter regions of ThSS45 homologs indicated that serine protease may be involved in both mycoparasitism and antibiotic secretion. ThSS45 was cloned into the pGEX-4T-2 vector and then expressed in Escherichia coli BL21. The recombinant protein, with an expected molecular weight of approximately 69 kDa, was then purified. When transformant BL21-ss was induced with 1 mM IPTG for 6 h, the purified protease activity reached a peak of 18.25 U/ml at pH 7.0 and 40°C. In antifungal assays the purified protease obviously inhibited the growth of A. alternata mycelia.

Identification and Characterization of Ectoine Biosynthesis Genes and Heterologous Expression of the ectABC Gene Cluster from Halomonas sp. QHL1, a Moderately Halophilic Bacterium Isolated from Qinghai Lake: Derui Zhu , Jian Liu , Rui Han , Guoping Shen , Qifu Long , Xiaoxing Wei , Deli Liu; J. Microbiol. 2014;52(2):139-147. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3389-5

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17 Citations

Abstract: The moderately halophilic bacterium Halomonas sp. QHL1 was identified as a member of the genus Halomonas by 16S rRNA gene sequencing. HPLC analysis showed that strain QHL1 synthesizes ectoine in its cytoplasm. The genes involved in the ectoine biosynthesis pathway were identified on the chromosome in the order ectABC. Subsequently, the ectB gene from this strain was amplified by PCR, and the entire ectABC gene cluster (3,580 bp) was cloned using genome walking. Analysis showed that the ectA (579 bp), ectB (1269 bp), and ectC (390 bp) genes were organized in a single transcriptional unit and were predicted to encode three peptides of 21.2 kDa, 46.4 kDa, and 14.7 kDa, respectively. Two putative promoters, a δ70-dependent promoter and a δ38-controlled promoter, as well as several conserved motifs with unknown function were identified. Individual ectA, ectB, and ectC genes, and the entire ectABC gene cluster were inserted into the expression plasmid pET-28a(+) to generate the recombinant plasmids pET-28a(+)-ectA, pET-28a(+)-ectB, pET-28a(+)-ectC and pET-28a(+)-ectABC, respectively. Heterologous expression of these proteins in Escherichia coli BL21 (DE3) was confirmed by SDS-PAGE. The recombinant E. coli strain BL21 (pET-28a (+)-ectABC) displayed a higher salt tolerance than native E. coli cells but produced far less ectoine than the wild-type QHL1 strain.

Interaction between the α-Barrel Tip of Vibrio vulnificus TolC Homologs and AcrA Implies the Adapter Bridging Model: Seunghwa Lee , Saemee Song , Minho Lee , Soonhye Hwang , Ji-Sun Kim , Nam-Chul Ha , Kangseok Lee; J. Microbiol. 2014;52(2):148-153. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3578-2

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11 Citations

Abstract: The AcrAB-TolC multidrug efflux pump confers resistance to Escherichia coli against many antibiotics and toxic compounds. The TolC protein is an outer membrane factor that participates in the formation of type I secretion systems. The genome of Vibrio vulnificus encodes two proteins homologous to the E. coli TolC, designated TolCV1 and TolCV2. Here, we show that both TolCV1 and TolCV2 partially complement the E. coli TolC function and physically interact with the membrane fusion protein AcrA, a component of the E. coli AcrAB-TolC efflux pump. Using site-directed mutational analyses and an in vivo cross-linking assay, we demonstrated that the α-barrel tip region of TolC homologs plays a critical role in the formation of functional AcrAB-TolC efflux pumps. Our findings suggest the adapter bridging model as a general assembly mechanism for tripartite drug efflux pumps in Gram-negative bacteria.

Plasminogen Activator Inhibitor Type 1 Expression Induced by Lipopolysaccharide of Porphyromonas gingivalis in Human Gingival Fibroblast: Hee Sam Na , Eun J. Lim , So Y. Jeong , Mi H. Ryu , Mi Hee Park , Jin Chung; J. Microbiol. 2014;52(2):154-160. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3022-7

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9 Citations

Abstract: In the gingival tissues of patients with periodontitis, inflammatory responses are mediated by a wide variety of genes. In our previous screening study, plasminogen activator inhibitor type 1 (PAI-1) mRNA binding protein expression was increased in gingiva from periodontitis patients. In this study, we further investigated the signaling pathway involved in PAI-1 expression induced by Porphyromonas gingivalis LPS (Pg LPS) in human gingival fibroblasts (HGF). When HGFs were treated with Pg LPS, both PAI-1 mRNA expression and PAI-1 protein were induced in a dose-dependent manner. Pg LPS induced NF-κB activation and the expressions of PAI-1 mRNA and protein were suppressed by pretreating with a NF-κB inhibitor. Pg LPS also induced ERK, p38, and JNK activation, and Pg LPS-induced PAI-1 expression was inhibited by ERK/p38/JNK inhibitor pretreatment. In conclusion, Pg LPS induced PAI-1 expression through NF-κB and MAP kinases activation in HGF.

Sequential Immunosuppressive Activities of Bacterial Secondary Metabolites from the Entomopahogenic Bacterium Xenorhabdus nematophila: Seonghyeon Eom , Youngjin Park , Yonggyun Kim; J. Microbiol. 2014;52(2):161-168. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3251-9

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38 Citations

Abstract: The entomopathogenic bacterium Xenorhabdus nematophila secretes at least eight bacterial metabolites that play crucial roles suppressing target insect immune responses by inhibiting eicosanoid biosynthesis. We analyzed sequential changes in bacterial metabolite production during bacterial growth and analyzed their individual immunosuppressive activities against the insect host, Spodoptera exigua. X. nematophila exhibited a typical bacterial growth pattern in both insect host and culture medium, and eight metabolites were secreted at different time points. At the early growth phase (6–12 h), Ac-FGV and PHPP were detected in significant amounts in the culture broth. At this early phase, both Ac-FGV (18 μg/ml) and oxindole (110 μg/ml) levels significantly inhibited phenoloxidase and phospholipase A2 activities in S. exigua hemolymph. At the late growth phase (12–36 h), all eight metabolites were detected at significant levels (10–140 μg/ml) in the culture broth and were sufficient to induce hemocyte toxicity. These results suggest that X. nematophila sequentially produces immunosuppressive metabolites that might sequentially and cooperatively inhibit different steps of insect immune responses.

Journal Article

Predictive Modelling of Lactobacillus casei KN291 Survival in Fermented Soy Beverage: Zieli&# , Koło&# , Goryl Antoni , Ilona Motyl; J. Microbiol. 2014;52(2):169-178. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3045-0

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10 Citations

Abstract: The aim of the study was to construct and verify predictive growth and survival models of a potentially probiotic bacteria in fermented soy beverage. The research material included natural soy beverage (Polgrunt, Poland) and the strain of lactic acid bacteria (LAB) – Lactobacillus casei KN291. To construct predictive models for the growth and survival of L. casei KN291 bacteria in the fermented soy beverage we design an experiment which allowed the collection of CFU data. Fermented soy beverage samples were stored at various temperature conditions (5, 10, 15, and 20°C) for 28 days. On the basis of obtained data concerning the survival of L. casei KN291 bacteria in soy beverage at different temperature and time conditions, two non-linear models (r2= 0.68–0.93) and two surface models (r2=0.76–0.79) were constructed; these models described the behaviour of the bacteria in the product to a satisfactory extent. Verification of the surface models was carried out utilizing the validation data - at 7°C during 28 days. It was found that applied models were well fitted and charged with small systematic errors, which is evidenced by accuracy factor - Af, bias factor - Bf and mean squared error - MSE. The constructed microbiological growth and survival models of L. casei KN291 in fermented soy beverage enable the estimation of products shelf life period, which in this case is defined by the requirement for the level of the bacteria to be above 106 CFU/cm3. The constructed models may be useful as a tool for the manufacture of probiotic foods to estimate of their shelf life period.

Research Support, Non-U.S. Gov't

NOTE] Effects of Light Intensity on Components and Topographical Structures of Extracellular Polysaccharides from the Cyanobacteria Nostoc sp.: Hongmei Ge , Ling Xia , Xuping Zhou , Delu Zhang , Chunxiang Hu; J. Microbiol. 2014;52(2):179-183. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-2720-5

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52 Citations

Abstract: A study on the effects of light intensity (40 and 80 μE/m2/sec) on the components and topographical structures of extracellular polysaccharides (EPS) was carried out in cyanobacteria Nostoc sp.. EPS yield increased with light intensity. However, light intensity did not significantly affect the EPS fractions and monosaccharide composition. Higher light intensity generally resulted in higher protein content of EPS in similar fractions. The topographical structure of EPS, investigated by atomic force microscopy, appeared as spherical lumps, chains and networks. The long chains were observed at higher light intensity. Thus, light intensity affected the yield and nature of EPS.

Erratum] Inhibitory Effect of Chlorophyllin on the Propionibacterium acnes-Induced Chemokine Expression: Mi-Sun Kang , Jin-Hee Kim , Boo-Ahn Shin , Hyun-Chul Lee , Youn-Shin Kim , Hae-Soon Lim , Jong-Suk Oh; J. Microbiol. 2014;52(2):184-184.; DOI: https://doi.org/10.1007/s12275-014-0698-7

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Abstract: In the article by Kang et al. published in Journal of Microbiology 2013; 51, 844-849. Figure 4 on page 847 should be changed as below.

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