scholarly journals A New Bacteroides Conjugative Transposon That Carries an ermB Gene

2003 ◽  
Vol 69 (11) ◽  
pp. 6455-6463 ◽  
Author(s):  
Anamika Gupta ◽  
Hera Vlamakis ◽  
Nadja Shoemaker ◽  
Abigail A. Salyers
Keyword(s):  
Antibiotic Resistance Genes ◽  
Open Reading Frames ◽  
Rrna Gene ◽  
Erythromycin Resistance ◽  
Gram Positive ◽  
Amino Acid Sequence Level ◽  
Conjugative Transposon ◽  
Pulsed Field ◽  
Gram Positive Bacteria ◽  
Ermb Gene

ABSTRACT The erythromycin resistance gene ermB has been found in a variety of gram-positive bacteria. This gene has also been found in Bacteroides species but only in six recently isolated strains; thus, the gene seems to have entered this genus only recently. One of the six Bacteroides ermB-containing isolates, WH207, could transfer ermB to Bacteroides thetaiotaomicron strain BT4001 by conjugation. WH207 was identified as a Bacteroides uniformis strain based on the sequence of its 16S rRNA gene. Results of pulsed-field gel electrophoresis experiments demonstrated that the transferring element was normally integrated into the Bacteroides chromosome. The element was estimated from pulsed-field gel data to be about 100 kb in size. Since the element appeared to be a conjugative transposon (CTn), it was designated CTnBST. CTnBST was able to mobilize coresident plasmids and the circular form of the mobilizable transposon NBU1 to Bacteroides and Escherichia coli recipients. A 13-kb segment that contained ermB was cloned and sequenced. Most of the open reading frames in this region had little similarity at the amino acid sequence level to any proteins in the sequence databases, but a 1,723-bp DNA segment that included a 950-bp segment downstream of ermB had a DNA sequence that was virtually identical to that of a segment of DNA found previously in a Clostridium perfringens strain. This finding, together with the finding that ermB is located on a CTn, supports the hypothesis that CTnBST could have entered Bacteroides from some other genus, possibly from gram-positive bacteria. Moreover, this finding supports the hypothesis that many transmissible antibiotic resistance genes in Bacteroides are carried on CTns.

scholarly journals A Newly Discovered Bacteroides Conjugative Transposon, CTnGERM1, Contains Genes Also Found in Gram-Positive Bacteria

2003 ◽  
Vol 69 (8) ◽  
pp. 4595-4603 ◽  
Author(s):  
Yanping Wang ◽  
Gui-Rong Wang ◽  
Aikiesha Shelby ◽  
Nadja B. Shoemaker ◽  
Abigail A. Salyers
Keyword(s):  
Amino Acid Sequence Identity ◽  
Efflux Pump ◽  
Antibiotic Resistance Genes ◽  
Pulsed Field Gel Electrophoresis ◽  
Erythromycin Resistance ◽  
Gram Positive ◽  
Conjugative Transposon ◽  
Gram Positive Bacteria ◽  
Sequence Identity ◽  
Predominant Type

ABSTRACT Results of a recent study of antibiotic resistance genes in human colonic Bacteroides strains suggested that gene transfer events between members of this genus are fairly common. The identification of Bacteroides isolates that carried an erythromycin resistance gene, ermG, whose DNA sequence was 99% identical to that of an ermG gene found previously only in gram-positive bacteria raised the further possibility that conjugal elements were moving into Bacteroides species from other genera. Six of seven ermG-containing Bacteroides strains tested were able to transfer ermG by conjugation. One of these strains was chosen for further investigation. Results of pulsed-field gel electrophoresis experiments showed that the conjugal element carrying ermG in this strain is an integrated element about 75 kb in size. Thus, the element appears to be a conjugative transposon (CTn) and was designated CTnGERM1. CTnGERM1 proved to be unrelated to the predominant type of CTn found in Bacteroides isolates—CTns of the CTnERL/CTnDOT family—which sometimes carry another type of erm gene, ermF. A 19-kbp segment of DNA from CTnGERM1 was cloned and sequenced. A 10-kbp portion of this segment hybridized not only to DNA from all the ermG-containing strains but also to DNA from strains that did not carry ermG. Thus, CTnGERM1 seems to be part of a family of CTns, some of which have acquired ermG. The percentage of G+C content of the ermG region was significantly lower than that of the chromosome of Bacteroides species—an indication that CTnGERM1 may have entered Bacteroides strains from some other bacterial genus. A survey of strains isolated before 1970 and after 1990 suggests that the CTnGERM1 type of CTn entered Bacteroides species relatively recently. One of the genes located upstream of ermG encoded a protein that had 85% amino acid sequence identity with a macrolide efflux pump, MefA, from Streptococcus pyogenes. Our having found >90% sequence identity of two upstream genes, including mefA, and the remnants of two transposon-carried genes downstream of ermG with genes found previously only in gram-positive bacteria raises the possibility that gram-positive bacteria could have been the origin of CTnGERM1.

scholarly journals Distribution of the ermG Gene among Bacterial Isolates from Porcine Intestinal Contents

2005 ◽  
Vol 71 (8) ◽  
pp. 4930-4934 ◽  
Author(s):  
Yanping Wang ◽  
Gui-Rong Wang ◽  
Nadja B. Shoemaker ◽  
Terence R. Whitehead ◽  
Abigail A. Salyers
Keyword(s):  
Insertion Sequence ◽  
Bacillus Sphaericus ◽  
Gram Positive ◽  
Sequence Element ◽  
Conjugative Transposon ◽  
Gram Positive Bacteria ◽  
First Finding ◽  
Intestinal Contents ◽  
Porcine Feces ◽  
Insertion Sequence Element

ABSTRACT The ermG gene was first found in the soil bacterium Bacillus sphaericus. More recently, it was found in several human intestinal Bacteroides species. We report here the first finding of ermG genes in gram-positive bacteria isolated from porcine feces and from under-barn manure pits used to store porcine wastes. The porcine ermG sequences were identical to the sequence of the B. sphaericus ermG gene except that six of the seven ermG-containing strains contained an insertion sequence element insertion in the C-terminal end of the gene. The porcine ermG genes were found in three different gram-positive genera, an indication that it is possible that the gene is being spread by horizontal gene transfer. A segment of a Bacteroides conjugative transposon that carries an ermG gene cross-hybridized with DNA from six of the seven porcine isolates, but the restriction patterns in the porcine strains were different from that of the Bacteroides conjugative transposon.

scholarly journals Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments

2007 ◽  
Vol 73 (10) ◽  
pp. 3272-3282 ◽  
Author(s):  
Erin A. Gontang ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
New Taxa ◽  
Marine Sediments ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Operational Taxonomic Units ◽  
The Republic ◽  
Republic Of Palau ◽  
High Degree

ABSTRACT Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of ≥98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.

scholarly journals Microarray-Based Detection of 90 Antibiotic Resistance Genes of Gram-Positive Bacteria

2005 ◽  
Vol 43 (5) ◽  
pp. 2291-2302 ◽  
Author(s):  
V. Perreten ◽  
L. Vorlet-Fawer ◽  
P. Slickers ◽  
R. Ehricht ◽  
P. Kuhnert ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Gram Positive ◽  
Gram Positive Bacteria

scholarly journals Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-glucose

2008 ◽  
Vol 410 (1) ◽  
pp. 187-194 ◽  
Author(s):  
Andreas Pföstl ◽  
Sonja Zayni ◽  
Andreas Hofinger ◽  
Paul Kosma ◽  
Christina Schäffer ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Biosynthesis Pathway ◽  
Subsequent Reaction ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Thermoanaerobacterium Thermosaccharolyticum ◽  
Thermophilic Organism ◽  
O Antigens ◽  
Derivatives Of ◽  
Reading Frames

Derivatives of 3-amino-3,6-dideoxyhexoses are widespread in Nature. They are part of the repeating units of lipopolysaccharide O-antigens, of the glycan moiety of S-layer (bacterial cell surface layer) glycoproteins and also of many antibiotics. In the present study, we focused on the elucidation of the biosynthesis pathway of dTDP-α-D-Quip3NAc (dTDP-3-acetamido-3,6-dideoxy-α-D-glucose) from the Gram-positive, anaerobic, thermophilic organism Thermoanaerobacterium thermosaccharolyticum E207-71, which carries Quip3NAc in its S-layer glycan. The biosynthesis of dTDP-α-D-Quip3NAc involves five enzymes, namely a transferase, a dehydratase, an isomerase, a transaminase and a transacetylase, and follows a pathway similar to that of dTDP-α-D-Fucp3NAc (dTDP-3-acetamido-3,6-dideoxy-α-D-galactose) biosynthesis in Aneurinibacillus thermoaerophilus L420-91T. The ORFs (open reading frames) of interest were cloned, overexpressed in Escherichia coli and purified. To elucidate the enzymatic cascade, the different products were purified by HPLC and characterized by NMR spectroscopy. The initiating reactions catalysed by the glucose-1-phosphate thymidylyltransferase RmlA and the dTDP-D-glucose-4,6-dehydratase RmlB are well established. The subsequent isomerase was shown to be capable of forming a dTDP-3-oxo-6-deoxy-D-glucose intermediate from the RmlB product dTDP-4-oxo-6-deoxy-D-glucose, whereas the isomerase involved in the dTDP-α-D-Fucp3NAc pathway synthesizes dTDP-3-oxo-6-deoxy-D-galactose. The subsequent reaction steps of either pathway involve a transaminase and a transacetylase, leading to the specific production of nucleotide-activated 3-acetamido-3,6-dideoxy-α-D-glucose and 3-acetamido-3,6-dideoxy-α-D-galactose respectively. Sequence comparison of the ORFs responsible for the biosynthesis of dTDP-α-D-Quip3NAc revealed homologues in Gram-negative as well as in antibiotic-producing Gram-positive bacteria. There is strong evidence that the elucidated biosynthesis pathway may also be valid for LPS (lipopolysaccharide) O-antigen structures and antibiotic precursors.

Bacterial diversity associated with subalpine fir (Abies lasiocarpa) ectomycorrhizae following wildfire and salvage-logging in central British Columbia

2002 ◽  
Vol 48 (7) ◽  
pp. 611-625 ◽  
Author(s):  
Madhukar B Khetmalas ◽  
Keith N Egger ◽  
Hugues B Massicotte ◽  
Linda E Tackaberry ◽  
M Jill Clapperton
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Abies Lasiocarpa ◽  
Gram Positive ◽  
Salvage Logging ◽  
Gram Positive Bacteria ◽  
Significant Difference

To assess the effect of fire and salvage logging on the diversity of mycorrhizal–bacterial communities, bacteria associated with Cenococcum, Thelephora, Tomentella, Russulaceae, and E-strain ectomycorrhizae (ECM) of Abies lasiocarpa seedlings were characterized using two approaches. First, bacteria were isolated and characterized by Biolog©, gas chromatography fatty acid methyl ester (GC-FAME), and amplified 16S rDNA restriction analysis (ARDRA). The bacterial communities retrieved from ECM from both sites were dominated by Proteobacteria (groups gamma and beta). Pseudomonas was the most common genus isolated, followed by Variovorax, Burkholderia, and Xanthomonas. Gram-positive isolates (mostly high-G+C Gram-positive bacteria) were more frequently retrieved on the burned-salvaged site, many commonly associated with the two ascomycete ECM, Cenococcum and E-strain. Pseudomonas species were retrieved more frequently from Thelephora. Although actinomycetes were isolated from all sites, almost no actinomycetes or other Gram-positive bacteria were isolated from either Thelephora or Tomentella. Second, amplified 16S rRNA gene sequences were amplified directly from root tips and then cloned into the plasmid vector pAMP1, followed by restriction analysis. This technique distinguished more genotypes than isolates retrieved by culturing methods, but generally, results were similar in that the largest proportion of the bacteria were putatively Gram-negative; putative Gram-positive bacteria were fewer and most were from the burned–salvaged site. Direct cloning resulted in many patterns that did not match any identified isolates, suggesting that a large proportion of clones were unique or not culturable by the methods used. Analysis for both protocols showed no significant difference in bacterial diversity between the burned–salvaged and unburned sites. Key words: rhizosphere bacteria, ARDRA, 16S rDNA, Biolog©, GC-FAME.

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