scholarly journals A proposal to rename the hyperthermophilePyrococcus woeseiasPyrococcus furiosussubsp.woesei

Archaea ◽  
2004 ◽  
Vol 1 (4) ◽  
pp. 277-283 ◽  
Author(s):  
Wirojne Kanoksilapatham ◽  
Juan M. González ◽  
Dennis L. Maeder ◽  
Jocelyne DiRuggiero ◽  
Frank T. Robb
Keyword(s):  
Intergenic Spacer ◽  
Optimal Growth ◽  
23S Rrna ◽  
Type I ◽  
Vulcano Island ◽  
Is Element ◽  
Is Elements ◽  
Pyrococcus Woesei ◽  
Genomic Markers ◽  
Beach Site

Pyrococcusspecies are hyperthermophilic members of the order Thermococcales, with optimal growth temperatures approaching 100 °C. All species grow heterotrophically and produce H2or, in the presence of elemental sulfur (S°), H2S.Pyrococcus woeseiandP. furiosuswere isolated from marine sediments at the same Vulcano Island beach site and share many morphological and physiological characteristics. We report here that the rDNA operons of these strains have identical sequences, including their intergenic spacer regions and part of the 23S rRNA. Both species grow rapidly and produce H2in the presence of 0.1% maltose and 10–100 µM sodium tungstate in S°-free medium. However,P. woeseishows more extensive autolysis thanP. furiosusin the stationary phase.PyrococcusfuriosusandP. woeseishare three closely related families of insertion sequences (ISs). A Southern blot performed with IS probes showed extensive colinearity between the genomes ofP. woeseiandP. furiosus.Cloning and sequencing of ISs that were in different contexts inP. woeseiandP. furiosusrevealed that thenapAgene inP. woeseiis disrupted by a type III IS element, whereas inP. furiosus, this gene is intact. A type I IS element, closely linked to thenapAgene, was observed in the same context in bothP. furiosusandP. woeseigenomes. Our results suggest that the IS elements are implicated in genomic rearrangements and reshuffling in these closely related strains. We propose to renameP. woeseia subspecies ofP. furiosusbased on their identical rDNA operon sequences, many common IS elements that are shared genomic markers, and the observation that allP. woeseinucleotide sequences deposited in GenBank to date are > 99% identical toP. furiosussequences.

Genomic fingerprinting ofFrankiamicrosymbionts fromCeanothuscopopulations using repetitive sequences and polymerase chain reactions

1999 ◽  
Vol 77 (9) ◽  
pp. 1220-1230 ◽  
Author(s):  
Soon-Chun Jeong ◽  
David D Myrold
Keyword(s):  
Dna Sequencing ◽  
Dna Analysis ◽  
Repetitive Sequences ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Genomic Fingerprinting ◽  
Chain Reactions ◽  
Intergenic Spacer Region ◽  
Polymerase Chain

Specificity between Ceanothus species and their microsymbionts, Frankia, were investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequencing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyzed by genomic fingerprinting using repetitive sequences and PCR. A newly designed direct repeat (DR) sequence and a BOX sequence were used as PCR primers after justification that these primers can generate Frankia-specific fingerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR showed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geographic separation plays a more important role for divergence of Ceanothus-microsymbiotic Frankia than host plant.Key words: Frankia, Ceanothus, rep-PCR, diversity.

scholarly journals PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species

2010 ◽  
Vol 10 (1) ◽  
pp. 90 ◽  
Author(s):  
Maria Hoffmann ◽  
Eric W Brown ◽  
Peter CH Feng ◽  
Christine E Keys ◽  
Markus Fischer ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Vibrio Species ◽  
23S Rrna

scholarly journals Presence of a novel 16S–23S rRNA gene intergenic spacer insert in Bradyrhizobium canariense strains

2007 ◽  
Vol 269 (2) ◽  
pp. 207-212 ◽  
Author(s):  
Vera Safronova ◽  
Elena Chizhevskaya ◽  
Simonetta Bullitta ◽  
Evgeny Andronov ◽  
Andrei Belimov ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
23S Rrna Gene

scholarly journals Elucidation of Insertion Elements Carried on Plasmids andIn VitroConstruction of Shuttle Vectors from the Toxic Cyanobacterium Planktothrix

2014 ◽  
Vol 80 (16) ◽  
pp. 4887-4897 ◽  
Author(s):  
Guntram Christiansen ◽  
Alexander Goesmann ◽  
Rainer Kurmayer
Keyword(s):  
Homologous Recombination ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Gene Clusters ◽  
Content Type ◽  
Shuttle Vectors ◽  
Is Element ◽  
Toxic Cyanobacterium ◽  
Is Elements

ABSTRACTSeveral gene clusters that are responsible for toxin synthesis in bloom-forming cyanobacteria have been found to be associated with transposable elements (TEs). In particular, insertion sequence (IS) elements were shown to play a role in the inactivation or recombination of the genes responsible for cyanotoxin synthesis. Plasmids have been considered important vectors of IS element distribution to the host. In this study, we aimed to elucidate the IS elements propagated on the plasmids and the chromosome of the toxic cyanobacteriumPlanktothrix agardhiiNIVA-CYA126/8 by means of high-throughput sequencing. In total, five plasmids (pPA5.5, pPA14, pPA50, pPA79, and pPA115, of 5, 6, 50, 79, and 120 kbp, respectively) were elucidated, and two plasmids (pPA5.5, pPA115) were found to propagate full IS element copies. Large stretches of shared DNA information between plasmids were constituted of TEs. Two plasmids (pPA5.5, pPA14) were used as candidates to engineer shuttle vectors (named pPA5.5SV and pPA14SV, respectively)in vitroby PCR amplification and the subsequent transposition of the Tn5 cattransposon containing the R6Kγ origin of replication ofEscherichia coli. While pPA5.5SV was found to be fully segregated, pPA14SV consistently co-occurred with its wild-type plasmid even under the highest selective pressure. Interestingly, the Tn5 cattransposon became transferred by homologous recombination into another plasmid, pPA50. The availability of shuttle vectors is considered to be of relevance in investigating genome plasticity as a consequence of homologous recombination events. Combining the potential of high-throughput sequencing andin vitroproduction of shuttle vectors makes it simple to produce species-specific shuttle vectors for many cultivable prokaryotes.

scholarly journals Molecular Detection and Characterization of Borrelia garinii (Spirochaetales: Borreliaceae) in Ixodes nipponensis (Ixodida: Ixodidae) Parasitizing a Dog in Korea

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 289 ◽  
Author(s):  
Seung-Hun Lee ◽  
Youn-Kyoung Goo ◽  
Paul John L. Geraldino ◽  
Oh-Deog Kwon ◽  
Dongmi Kwak
Keyword(s):  
Molecular Detection ◽  
Single Gene ◽  
Protein A ◽  
Intergenic Spacer ◽  
Surface Protein ◽  
23S Rrna ◽  
Borrelia Garinii ◽  
Intergenic Spacer Region ◽  
Individual Level ◽  
Pcr Targeting

The present study aimed to detect and characterize Borrelia spp. in ticks attached to dogs in Korea. Overall, 562 ticks (276 pools) attached to dogs were collected and tested for Borrelia infection by PCR targeting the 5S-23S rRNA intergenic spacer region (rrf-rrl). One tick larva (pool level, 0.4%; individual level, 0.2%) was confirmed by sequencing Borrelia garinii, a zoonotic pathogen. For molecular characterization, the outer surface protein A (ospA) and flagellin genes were analyzed. Phylogenetic ospA analysis distinguished B. garinii from B. bavariensis, which has been recently identified as a novel Borrelia species. On the other hand, phylogenetic analysis showed that single gene analysis involving rrf-rrl or flagellin was not sufficient to differentiate B. garinii from B. bavariensis. In addition, the B. garinii-infected tick was identified as Ixodes nipponensis by sequencing according to mitochondrial 16S rRNA and the second transcribed spacer region. To our knowledge, this is the first study to report the molecular detection of B. garinii in I. nipponensis parasitizing a dog in Korea. Continuous monitoring of tick-borne pathogens in ticks attached to animals is required to avoid disease distribution and possible transmission to humans.

Differentiation of group VIII Spiroplasma strains with sequences of the 16S–23S rDNA intergenic spacer region

2004 ◽  
Vol 50 (12) ◽  
pp. 1061-1067 ◽  
Author(s):  
Laura B Regassa ◽  
Kimberly M Stewart ◽  
April C Murphy ◽  
Frank E French ◽  
Tao Lin ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Analytical Models ◽  
23S Rrna ◽  
Rrna Gene ◽  
Group Viii ◽  
Similarity Coefficients ◽  
Intergenic Spacer Region ◽  
Intergenic Sequences ◽  
The Stability ◽  
The 16S Rrna Gene

Spiroplasma species (Mollicutes: Spiroplasmataceae) are associated with a wide variety of insects, and serology has classified this genus into 34 groups, 3 with subgroups. The 16S rRNA gene has been used for phylogenetic analysis of spiroplasmas, but this approach is uninformative for group VIII because the serologically distinct subgroups generally have similarity coefficients >0.990. Therefore, we investigated the utility of the 16S–23S rRNA spacer region as a means to differentiate closely related subgroups or strains. We generated intergenic sequences and detailed serological profiles for 8 group VIII Spiroplasma strains. Sequence analyses using Maximum Parsimony, Neighbor Joining, and Maximum Likelihood placed the strains into 2 clades. One clade consisted of strains BARC 2649 and GSU5367. The other clade was divided into clusters containing representatives of the 3 designated group VIII subgroups (EA-1, DF-1, and TAAS-1) and 3 previously unclassified strains. The stability of the positions of the strains in various analytical models and the ability to provide robust support for groupings tentatively supported by serology indicates that the 16S–23S intergenic rDNA sequence will prove useful in intragroup analysis of group VIII spiroplasmas.Key words: Mollicutes, Spiroplasma, phylogeny, Tabanidae.

A putative transposase gene in the 16S–23S rRNA intergenic spacer region of Mycoplasma imitans

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 1023-1029 ◽  
Author(s):  
Ryô Harasawa ◽  
David G. Pitcher ◽  
Ana S. Ramírez ◽  
Janet M. Bradbury
Keyword(s):  
Relative Size ◽  
Intergenic Spacer ◽  
Its Region ◽  
23S Rrna ◽  
Mycoplasma Species ◽  
Insertion Element ◽  
Transposase Gene ◽  
Intergenic Spacer Region ◽  
Pcr Products ◽  
Type Strains

Examination of the nucleotide sequences of the 16S–23S intergenic transcribed spacer (ITS) region of Mycoplasma imitans and Mycoplasma gallisepticum identified a putative transposase gene located only in the ITS of M. imitans, which can be used as a genetic marker to distinguish these two species. The relative size of the PCR products of the ITS region allowed a clear distinction to be made between strains of M. imitans and M. gallisepticum, both of which could be readily discriminated from the type strains of all the other recognized avian Mycoplasma species. In addition, the putative transposase gene assigned in the ITS of M. imitans was shown to include a sequence homologous to that of the P75 gene of M. gallisepticum. This is believed to be the first description of an insertion element in the rRNA operon region of a mycoplasma species.

scholarly journals Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array

2009 ◽  
Vol 58 (5) ◽  
pp. 596-605 ◽  
Author(s):  
Siou Cing Su ◽  
Mario Vaneechoutte ◽  
Lenie Dijkshoorn ◽  
Yu Fang Wei ◽  
Ya Lei Chen ◽  
...  
Keyword(s):  
Clinical Importance ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Oligonucleotide Array ◽  
Rrna Genes ◽  
Universal Primers ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nylon Membrane ◽  
Gram Negative

Many species of non-fermenting Gram-negative bacilli (non-fermenters) are important opportunistic and nosocomial pathogens. Identification of most species of non-fermenters by phenotypic characteristics can be difficult. In this study, an oligonucleotide array was developed to identify 38 species of clinically relevant non-fermenters. The method consisted of PCR-based amplification of 16S–23S rRNA gene intergenic spacer (ITS) regions using bacterial universal primers, followed by hybridization of the digoxigenin-labelled PCR products with oligonucleotide probes immobilized on a nylon membrane. A total of 398 strains, comprising 276 target strains (i.e. strains belonging to the 38 species to be identified) and 122 non-target strains (i.e. strains not included in the array), were analysed by the array. Four target strains (three reference strains and one clinical isolate) produced discrepant identification by array hybridization. Three of the four discordant strains were found to be correctly identified by the array, as confirmed by sequencing of the ITS and 16S rRNA genes, with the remaining one being an unidentified species. The sensitivity and specificity of the array for identification of non-fermenters were 100 and 96.7 %, respectively. In summary, the oligonucleotide array described here offers a very reliable method for identification of clinically relevant non-fermenters, with results being available within one working day.

scholarly journals Diversity of Toxic and Nontoxic Nodularia Isolates (Cyanobacteria) and Filaments from the Baltic Sea

2001 ◽  
Vol 67 (10) ◽  
pp. 4638-4647 ◽  
Author(s):  
Maria J. Laamanen ◽  
Muriel F. Gugger ◽  
Jaana M. Lehtimäki ◽  
Kaisa Haukka ◽  
Kaarina Sivonen
Keyword(s):  
Baltic Sea ◽  
Dna Sequences ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
The Baltic Sea ◽  
Field Samples ◽  
Digestion Pattern ◽  
Internally Transcribed Spacer ◽  
The Baltic ◽  
Flanking Regions

ABSTRACT Cyanobacteria of the genus Nodularia form toxic blooms in brackish waters worldwide. In addition,Nodularia spp. are found in benthic, periphytic, and soil habitats. The majority of the planktic isolates produce a pentapeptide hepatotoxin nodularin. We examined the morphologic, toxicologic, and molecular characters of 18 nodularin-producing and nontoxic Nodularia strains to find appropriate markers for distinguishing the toxic strains from the nontoxic ones in field samples. After classical taxonomy, the examined strains were identified as Nodularia sp., Nodularia spumigena,N. baltica, N. harveyana, and N. sphaerocarpa. Morphologic characters were ambiguous in terms of distinguishing between the toxic and the nontoxic strains. DNA sequences from the short 16S-23S rRNA internally transcribed spacer (ITS1-S) and from the phycocyanin operon intergenic spacer and its flanking regions (PC-IGS) were different for the toxic and the nontoxic strains. Phylogenetic analysis of the ITS1-S and PC-IGS sequences from strains identified as N. spumigena, and N. baltica, and N. litorea indicated that the division of the planktic Nodularia into the three species is not supported by the ITS1-S and PC-IGS sequences. However, the ITS1-S and PC-IGS sequences supported the separation of strains designated N. harveyana and N. sphaerocarpa from one another and the planktic strains.HaeIII digestion of PCR amplified PC-IGS regions of all examined 186 Nodularia filaments collected from the Baltic Sea produced a digestion pattern similar to that found in toxic isolates. Our results suggest that only one plankticNodularia species is present in the Baltic Sea plankton and that it is nodularin producing.

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