Journal of Microbiology

Volume 46(5); October 2008

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

Turkey Fecal Microbial Community Structure and Functional Gene Diversity Revealed by 16S rRNA Gene and Metagenomic Sequences: Jingrang Lu , Jorge Santo Domingo; J. Microbiol. 2008;46(5):469-477. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0117-z

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Abstract: The primary goal of this study was to better understand the microbial composition and functional genetic diversity associated with turkey fecal communities. To achieve this, 16S rRNA gene and metagenomic clone libraries were sequenced from turkey fecal samples. The analysis of 382 16S rRNA gene sequences showed that the most abundant bacteria were closely related to Lactobacillales (47%), Bacillales (31%), and Clostridiales (11%). Actinomycetales, Enterobacteriales, and Bacteroidales sequences were also identified, but represented a smaller part of the community. The analysis of 379 metagenomic sequences showed that most clones were similar to bacterial protein sequences (58%). Bacteriophage (10%) and avian viruses (3%) sequences were also represented. Of all metagenomic clones potentially encoding for bacterial proteins, most were similar to low G+C Gram-positive bacterial proteins, particularly from Lactobacillales (50%), Bacillales (11%), and Clostridiales (8%). Bioinformatic analyses suggested the presence of genes encoding for membrane proteins, lipoproteins, hydrolases, and functional genes associated with the metabolism of nitrogen and sulfur containing compounds. The results from this study further confirmed the predominance of Firmicutes in the avian gut and highlight the value of coupling 16S rRNA gene and metagenomic sequencing data analysis to study the microbial composition of avian fecal microbial communities.

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

The Identification of CTX-M-14, TEM-52, and CMY-1 Enzymes in Escherichia coli Isolated from the Han River in Korea: Jungmin Kim , Hee Young Kang , Yeonhee Lee; J. Microbiol. 2008;46(5):478-481. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0150-y

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Abstract

From water samples collected monthly between 2000 and 2001 from the Han River in Seoul, sixteen strains of Escherichia coli which confer resistance to at least 10 kinds of antimicrobial agents were isolated. From these isolates, 2 kinds of extended-spectrum β-lactamases (ESBLs) and one plasmid-mediated AmpC β-lactamase were detected; CTX-M-14 from 10 isolates, TEM-52 from 5 isolates, and CMY-1 from one isolate. Class 1 integron gene cassettes, such as aadA1, dfr12-orfF-aadA2, and dfr17-aadA5, were also detected and the integrons are the same as those found in E. coli isolated from swine, poultry, and humans in Korea. The result of this study indicated the importance of river water as a reservoir for antimicrobial resistance genes and resistant bacteria.

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Occurrence of Multidrug-Resistant (MDR) Extended-Spectrum Beta-lactamase (ESBL)-Producing Escherichia coli in Wastewater and Natural Water Sources from the Eastern Part of Uttar Pradesh, India
Kaushik Satyaprakash, Pavan Kumar Pesingi, Annada Das, M. R. Vineeth, Satya Veer Singh Malik, Sukhadeo B. Barbuddhe, Deepak Bhiwa Rawool
Water, Air, & Soil Pollution.2024;[Epub] CrossRef
Freshwater environment as a reservoir of extended-spectrum β-lactamase-producing Enterobacteriaceae
Sohyun Cho, Charlene R Jackson, Jonathan G Frye
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Hetty Blaak, Angela H.A.M. van Hoek, Christiaan Veenman, Arieke E. Docters van Leeuwen, Gretta Lynch, Wendy M. van Overbeek, Ana Maria de Roda Husman
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Research Support, U.S. Gov't, Non-P.H.S.

Isolation and Molecular Characterization of Xylella fastidiosa from Coffee Plants in Costa Rica: Mauricio Montero-Astua , Carlos Chacon-Diaz , Estela Aguilar , Carlos Mario Rodriguez , Laura Garita , William Villalobos , Lisela Moreira , John S. Hartung , Carmen Rivera; J. Microbiol. 2008;46(5):482-490. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0072-8

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Abstract: Coffee plants exhibiting a range of symptoms including mild to severe curling of leaf margins, chlorosis and deformation of leaves, stunting of plants, shortening of internodes, and dieback of branches have been reported since 1995 in several regions of Costa Rica''s Central Valley. The symptoms are referred to by coffee producers in Costa Rica as ''crespera'' disease and have been associated with the presence of the bacterium Xylella fastidiosa. Coffee plants determined to be infected by the bacterium by enzyme linked immunosorbent assay (ELISA), were used for both transmission electron microscopy (TEM) and for isolation of the bacterium in PW broth or agar. Petioles examined by TEM contained rod-shaped bacteria inside the xylem vessels. The bacteria measured 0.3 to 0.5 um in width and 1.5 to 3.0 um in length, and had rippled cell walls 10 to 40 nm in thickness, typical of X. fastidiosa. Small, circular, dome-shaped colonies were observed 7 to 26 days after plating of plant extracts on PW agar. The colonies were comprised of Gram-negative rods of variable length and a characteristic slight longitudinal bending. TEM of the isolated bacteria showed characteristic rippled cell walls, similar to those observed in plant tissue. ELISA and PCR with specific primer pairs 272-1-int/272-2-int and RST31/RST33 confirmed the identity of the isolated bacteria as X. fastidiosa. RFLP analysis of the amplification products revealed diversity within X. fastidiosa strains from Costa Rica and suggest closer genetic proximity to strains from the United States of America than to other coffee or citrus strains from Brazil.

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

Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People: Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0199-7

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Abstract

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

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Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination
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Generation of Infectious Transcripts from Korean Strain and Mild Mottle Strain of Potato Virus X: Sun Hee Choi , Ki Hyun Ryu; J. Microbiol. 2008;46(5):502-507. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0078-2

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Abstract: Full-length cDNAs of two different strains of Potato virus X (PVX-Kr and PVX-Mo) have been directly amplified by long template reverse transcription polymerase chain reaction (RT-PCR) using the 5’-end primer containing a SP6 or T7 RNA promoter sequence and the virus-specific 3’-end primer, and then constructed in plasmid vectors. Capped in vitro transcripts from cloned full-length cDNAs as well as those RTPCR amplicons proved to be infectious systemically on tobacco plants. Symptom expression on tobacco plants from PVX-Mo transcripts was faster and severer than that from PVX-Kr. In replication stability test of transcripts derived from PVX clones, progeny viruses showed stable replication according to sequencing through passages. This highly infectious transcript system from the full-length cDNA clones for PVX can be useful for recombinant molecules for functional analysis of viral proteins in plant-virus interaction study as well as for expression of foreign protein in planta.

Ponticoccus gilvus gen. nov., sp. nov., a Novel Member of the Family Propionibacteriaceae from Seawater: Dong Wan Lee , Soon Dong Lee; J. Microbiol. 2008;46(5):508-512. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0096-0

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Abstract

A novel actinobacterium, designated strain MSW-19T, was isolated from a seawater sample in Republic of Korea. Cells were aerobic, Gram-positive, non-endospore-forming, and non-motile cocci. Colonies were circular, convex, opaque, and vivid yellow in colour. A phylogenetic tree based on 16S rRNA gene sequences exhibited that the organism formed a distinct clade within the radius encompassing representatives of the family Propionibacteriaceae. The phylogenetic neighbors were the type strains of the genera Friedmanniella, Microlunatus, Micropruina, Propionicicella, and Propionicimonas. Levels of 16S rRNA gene sequence similarity between the isolate and members of the family were less than 95.3%. The cell wall peptidoglycan of the organism contained LL-diaminopimelic acid as the diagnostic diamino acid. The isolate contained MK-9(H4) as the predominant menaquinone, ai-C15:0 as the major fatty acid and polar lipids including phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. The G+C content of the DNA was 69.6 mol%. On the basis of the phenotypic and phylogenetic data presented here, the isolate is considered to represent a novel genus and species in the family Propionibacteriaceae, for which the name Ponticoccus gilvus gen. nov., sp. nov. is proposed. The type strain is strain MSW-19T (= KCTC 19476T= DSM 21351T).

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Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov., novel taxa assignable to the family Propionibacteriaceae and derived from human clinical samples
Kathryn A. Bernard, Tamara Burdz, Ana Luisa Pacheco, Deborah Wiebe, Nisha B. Patel, Paul A. Lawson, Marc-Christian Domingo, Jean Longtin, Anne-Marie Bernier
International Journal of Systematic and Evolutionary Microbiology .2020; 70(11): 5676. CrossRef
Systematic review of descriptions of novel bacterial species: evaluation of the twenty-first century taxonomy through text mining
Fernando Hayashi Sant’Anna, Keli Cristine Reiter, Patrícia de Fátima Almeida, Luciane Maria Pereira Passaglia
International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2925. CrossRef
Culturable rare Actinomycetes: diversity, isolation and marine natural product discovery
Ramesh Subramani, William Aalbersberg
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Taxonomic Revision of the Nematode-Trapping Fungus Arthrobotrys multisecundaria: Juan Li , Jinkui Yang , Lianming Liang , Ke-Qin Zhang; J. Microbiol. 2008;46(5):513-518. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-007-0115-6

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Abstract: The gene encoding an extracellular serine protease was cloned from Arthrobotrys multisecundaria using degenerate primers. The gene was highly similar (99.26%) to protease Mlx from Monacrosporium microscaphoides. To clarify the taxonomic relationship between these species, genes encoding the internal transcribed spacer (ITS) and β-tubulin were also cloned and sequenced from A. multisecundaria and M. microscaphoides, respectively. Homologous analysis of the nuclear (ITS) and protein (β-tubulin) encoding genes showed that the two species of nematode-trapping fungi also shared extensive identity (99.82 and 99.63%, respectively), although they exhibited obvious differences in secondary conidia morphology. Accordingly, a taxonomic revision is recommended, with A. multisecundaria being revised as A. microscaphoides var. multisecundaria. In addition, the identified mutation may better facilitate the study of the sporulation of nematode-trapping fungi.

Lysobacter daecheongensis sp. nov., Isolated from Sediment of Stream Near the Daechung Dam in South Korea: Leonid N. Ten , Hae-Min Jung , Wan-Taek Im , Soon-Ae Yoo , Sung-Taik Lee; J. Microbiol. 2008;46(5):519-524. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0047-9

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Abstract

A Gram-negative, aerobic, rod shaped, non-spore-forming bacterial strain, designated Dae08T, was isolated from sediment of the stream near Daechung dam in South Korea, and was characterized in order to determine its taxonomic position, using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Dae08T belongs to the family Xanthomonadaceae of the Gammaproteobacteria, and is related to Lysobacter brunescens ATCC 29482T (97.3%). The phylogenetic distances from any other species with validly published names within the genus Lysobacter were greater than 3.7%. The G+C contents of the genomic DNA of strain Dae08T was 69.3 mol%. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with iso-C15:0, iso-C17:1 ω9c, iso-C17:0, iso-C16:0, and iso-C11:0 3-OH as the major acids supported the affiliation of strain Dae08T to the genus Lysobacter. DNA-DNA relatedness between strain Dae08T and its phylogenetically closest neighbour was 28%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Dae08T (= KCTC 12600T) should be classified in the genus Lysobacter as the novel species, for which the name Lysobacter daecheongensis sp. nov. is proposed.

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Luteimonas aestuarii sp. nov., Isolated from Tidal Flat Sediment: Seong Woon Roh , Kyoung-Ho Kim , Young-Do Nam , Ho-Won Chang , Min-Soo Kim , Jung-Hoon Yoon , Hee-Mock Oh , Jin-Woo Bae; J. Microbiol. 2008;46(5):525-529. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0189-9

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Abstract

A novel bacterium B9T was isolated from tidal flat sediment. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow and the cells are Gram-negative, rod-shaped, and do not require NaCl for growth. The 16S rRNA gene sequence similarity indicated that strain B9T is associated with the genus Lysobacter (≤ 97.2%), Xanthomonas (≤ 96.8%), Pseudomonas (≤ 96.7%), and Luteimonas (≤ 96.0%). However, within the phylogenetic tree, this novel strain shares a branching point with the species Luteimonas composti CC-YY255T (96.0%). The DNA-DNA hybridization experiments showed a DNA-DNA homology of 23.0% between strain B9T and Luteimonas mephitis B1953/27.1T. The G+C content of genomic DNA of the type strain is 64.7 mol% (SD, 1.1). The predominant fatty acids are iso-C11:0, iso-C15:0, iso-C16:0, iso-C17:0, iso-C17:1 ω9c, and iso-C11:0 3-OH. Combined analysis of the 16S rRNA gene sequences, fatty acid profile, and results from physiological and biochemical tests indicated that there is genotypic and phenotypic differentiation of the isolate from other Luteimonas species. For these reasons, strain B9T was proposed as a novel species, named Luteimonas aestuarii. The type strain of the new species is B9T (= KCTC 22048T, DSM 19680T).

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Paenibacillus camelliae sp. nov., Isolated from Fermented Leaves of Camellia sinensis: Hyun-Woo Oh , Byung-Chun Kim , Kang Hyun Lee , Do Young Kim , Doo-Sang Park , Hee-Moon Park , Kyung Sook Bae; J. Microbiol. 2008;46(5):530-534. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0233-9

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Abstract

A novel bacterium, strain b11s-2T was isolated from Pu’er tea. The isolate was Gram-positive, endosporeforming motile rod that grew at 15~42°C and pH 6.0~10.2. The DNA G+C content was 48.3 mol%, the predominant isoprenoid quinone was MK-7, and the predominant cellular fatty acid was anteiso-C15:0 (54.2%) followed by C16:0 (15.5%) and iso-C16:0 (8.2%). The polar lipid pattern of b11s-2T was characterized by the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain was affiliated within the Paenibacillaceae. The strain was most closely related to Paenibacillus granivorans A30T, with a similarity of 97.1%. Based on the phylogenetic and phenotypic characteristics of strain b11s-2T, the isolate is thought to represent a novel taxon in the genus Paenibacillus. The name Paenibacillus camelliae sp. nov. is proposed for the fermented tea isolate; the type strain is b11s-2T (= KCTC 13220T= CECT 7361T).

Citations

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Characterization of Exopolysaccharide (EPS) Produced by Weissella hellenica SKkimchi3 Isolated from Kimchi: Min Ju Kim , Ha Na Seo , Tae Sik Hwang , Sung Hun Lee , Doo Hyun Park; J. Microbiol. 2008;46(5):535-541. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0134-y

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Abstract: Weissella hellenica SKkimchi3 produces the higher exopolysaccharide (EPS) on sucrose than lactose, glucose, and fructose at pH 5 and 20°C. Sucrose was exclusively used to cultivate SKkimchi3 in all experiments base on the EPS production tests. The molecular mass of EPS, as determined by gel permeation chromatography, was 203,000. 1H and 13C NMR analysis indicated that the identity of EPS may be a glucan. When EPS, starch, and cellulose was treated with α-amylase, glucoamylase, glucosidase, and cellulase, glucose was produced from starch and cellulose but was not produced from EPS. Based on HPLC analysis, elemental analysis, 1H and 13C NMR analysis, and enzymatic hydrolysis tests, EPS was estimated to be a glucan. EPS suspension was not precipitated even by centrifugation at 10,000×g for 60 min, and EPS made the fermented milk and bacterial culture viscous.

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

Genome-Wide Transcriptional Responses to Sulfite in Saccharomyces cerevisiae: Hoon Park , Yoon-Sun Hwan; J. Microbiol. 2008;46(5):542-548. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0053-y

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Abstract: Sulfite is a commonly used preservative in foods, beverages, and pharmaceuticals because it is toxic to many microorganisms. In order to understand the global response of Saccharomyces cerevisiae to sulfite, genome-wide transcript profiling following sulfite exposure was obtained. The transcription levels of 21 genes were increased more than 2-fold, while those of 37 genes decreased to a similar extent. Genes involved in carbohydrate metabolism represented the highest proportion of induced genes, which may account for the easily acquired resistance to sulfite. Most of down-regulated genes are involved in transcription, protein biosynthesis, and cell growth. The down-regulation of these genes is thought to reflect growth arrest which occurs during sulfite treatment, allowing cells to save energy. Cells treated with sulfite generated more than 70% of acetaldehyde than untreated cells, suggesting that the increased acetaldehyde production is correlated with the induction of PDC1 gene encoding pyruvate decarboxylase.

Genetic Diversity and Structure of Cordyceps sinensis Populations from Extensive Geographical Regions in China as Revealed by Inter-Simple Sequence Repeat Markers: Hong-Hui Liang , Zhou Cheng , Xiao-Ling Yang , Shan Li , Zu-Quan Ding , Tong-Shui Zhou , Wen-Ju Zhang , Jia-Kuan Chen; J. Microbiol. 2008;46(5):549-556. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0107-1

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41 Scopus

Abstract: Cordyceps sinensis is one of the most valuable medicinal caterpillar fungi native to China. However, its productivity is extremely limited and the species is becoming endangered. The genetic diversity of eighteen C. sinensis populations across its major distributing regions in China was evaluated by inter-simple sequence repeat (ISSR) markers. A total of 141 markers were produced in 180 individuals from the 18 populations, of which 99.3% were polymorphic. The low average of Shannon (0.104) and Nei index (0.07) of the 18 populations indicates that there are little genetic variations within populations. For all 18 populations, estimates of total gene diversity (HT), gene diversity within populations (HS), coefficient of genetic differentiation (GST), and gene flow (Nm) were 0.170, 0.071, 0.583, and 0.357, respectively. This pattern suggests that the genetic diversity of C. sinensis is low and most of the ISSR variations are found among populations with little gene exchange. The 18 populations are divided into five groups based on the genetic distance and the grouping pattern matches with the geographic distribution along the latitudinal gradient. The five groups show obvious difference in the GST and Nm values. Therefore, the genetic diversification of C. sinensis populations may be determined by geographic isolation and the combined effects of life history characters and the interaction with host insect species. The information illustrated by this study is useful for selecting in situ conservation sites of C. sinensis.

DNA Microarray-Based Global Transcriptional Profiling of Yersinia pestis in Multicellularity: Jingfu Qiu , Zhaobiao Guo , Haihong Liu , Dongsheng Zhou , Yanping Han , Ruifu Yang; J. Microbiol. 2008;46(5):557-563. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0140-0

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4 Scopus

Abstract: Yersinia pestis, the causative agent of plague, has a feature of forming multicellular aggregates at liquid-air interface around the wall of glass tube. In this study, we employed the whole-genome DNA microarray of Y. pestis to investigate the global transcriptional profile in multicellularity compared with that in its planktonic growth. A total of 177 genes were differentially expressed in Y. pestis during early stage of multicellular formation; Seventy genes of them were up-regulated while 107 down-regulated. In addition to a large number of genes encoding unknown functions, most of the induced genes encode cell envelope and transport/binding proteins. The up-regulation of amino acid biosynthesis, the differentially altered genes that are involved in virulence, and the cold shock protein genes were for the first time reported to be associated with the multicellular formation. Our results revealed the global gene expression of Y. pestis were changed in the formation of multicellularity, providing insights into the molecular mechanism of multicellular behaviour, which need investigating further.

Journal Article

DNA Adenine Methylation of sams1 Gene in Symbiont-Bearing Amoeba proteus: Taeck J. Jeon; J. Microbiol. 2008;46(5):564-570. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0129-8

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Abstract: The expression of amoeba sams genes is switched from sams1 to sams2 when amoebae are infected with Legionella jeonii. To elucidate the mechanism for the inactivation of host sams1 gene by endosymbiotic bacteria, methylation states of the sams1 gene of D and xD amoebae was compared in this study. The sams1 gene of amoebae was methylated at an internal adenine residue of GATC site in symbiont-bearing xD amoebae but not in symbiont-free D amoebae, suggesting that the modification might have caused the inactivation of sams1 in xD amoebae. The sams1 gene of xD amoebae was inactivated at the transcriptional level. Analysis of DNA showed that adenine residues in L. jeonii sams were also methylated, implying that L. jeonii bacteria belong to a Dam methylase-positive strain. In addition, both SAM and Met appeared to act as negative regulators for the expression of sams1 whereas the expression of sams2 was not affected in amoebae.

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