Two families of repeated DNA sequences in Thiobacillus ferrooxidans

Yates, James R.; Holmes, David S.

doi:10.1128/jb.169.5.1861-1870.1987

Cited by 71 publications

(44 citation statements)

References 25 publications

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“…AF322013). Significant similarities were also observed with transposases of IS1632 of B. japonicum (30), IS6120 of Mycobacterium smegmatis (25), IS1166 of Rhodococcus zopfii (13), IST2 of Thiobacillus ferrooxidans (54), and IS666 of Mycobacterium avium (44). All of the elements listed above are classified as members of a distinct closely homologous subclass within the family IS256; however, for the majority of them, the transposition activity has not been experimentally determined (http://www-is.biotoul.fr/is .html).…”

Section: Vol 185 2003 Transposable Elements Of Paracoccus Pantotropmentioning

confidence: 73%

Identification and Characterization of Transposable Elements of Paracoccus pantotrophus

2003

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We studied diversity and distribution of transposable elements residing in different strains (DSM 11072, DSM 11073, DSM 65, and LMD 82.5) of a soil bacterium Paracoccus pantotrophus (␣-Proteobacteria). With application of a shuttle entrapment vector pMEC1, several novel insertion sequences (ISs) and transposons (Tns) have been identified. They were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, terminal inverted repeats, as well as target sequences) and classification into the appropriate IS or Tn families. The frequency of transposition of these elements varied and ranged from 10 ؊6 to 10 ؊3 depending on the strain. The copy number, localization (plasmid or chromosome), and distribution of these elements in the Paracoccus species P. pantotrophus, P. denitrificans, P. methylutens, P. solventivorans, and P. versutus were analyzed. This allowed us to distinguish elements that are common in paracocci (ISPpa2, ISPpa3-both of the IS5 family-and ISPpa5 of IS66 family) as well as strain-specific ones (ISPpa1 of the IS256 family, ISPpa4 of the IS5 family, and Tn3434 and Tn5393 of the Tn3 family), acquired by lateral transfer events. These elements will be of a great value in the design of new genetic tools for paracocci, since only one element (IS1248 of P. denitrificans) has been described so far in this genus.

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Section: Vol 185 2003 Transposable Elements Of Paracoccus Pantotropmentioning

confidence: 73%

Identification and Characterization of Transposable Elements of Paracoccus pantotrophus

2003

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“…Even the most statistically significant clusters of these dendrograms do not coincide with genomovars determined by DNA-DNA hybridization. This can be accounted for by the fact that PFGE is able to detect point mutations at restriction sites, changes in the locations of IST elements (insertion sequences; Yates & Holmes, 1987) and plasmid-chromosome recombinations, i.e. events that do not alter significantly the nucleotide sequence of the total genome.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic heterogeneity of the species Acidithiobacillus ferrooxidans

Karavaiko

Turova

et al. 2003

International Journal of Systematic and Evolutionary Microbiology

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Polyphasic genotypic analysis of 25 Acidithiobacillus ferrooxidans strains isolated from ores and ore concentrates collected in different regions of the world showed considerable strain heterogeneity. Restriction patterns of the chromosomal DNA of these strains obtained by PFGE were specific for each strain. According to the degree of DNA relatedness, 17 of the 23 strains studied were divided into four genomovars. Six independent, considerably divergent strains could not be assigned to any of the genomovars. A comparison of nearly complete nucleotide sequences of the 16S rDNA of five representatives of the genomovars (including the type strain of A. ferrooxidans, ATCC 23270 T ) with those of species of the genus Acidithiobacillus available from GenBank showed that most of the A. ferrooxidans strains, together with the type strain and some other strains of the species Acidithiobacillus thiooxidans, comprised a monophyletic cluster. Within this major cluster, A. ferrooxidans strains fell into four phylogenetic groups that were equidistant from the phylogenetic group of A. thiooxidans strains. In general, the distribution of strains among the phylogenetic groups correlated with their distribution among the genomovars, except that the representatives of two different genomovars fell into one phylogenetic group. Thus, at least two levels of phylogenetic heterogeneity for A. ferrooxidans have been found. The phylogenetic heterogeneity of A. ferrooxidans strains, which are phenotypically indistinguishable, suggests the occurrence of microevolutionary processes in different econiches. This should be taken into account in the biohydrometallurgical applications of A. ferrooxidans strains.

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“…Acidithiobacillus ferrooxidans ATCC 23270 was grown in 9K salts medium (pH 2.4) supplemented with elemental sulfur or iron (FeSO 4 ) as described by Yates and Holmes (1988). Escherichia coli JM109 was grown in Luria-Bertani (LB) medium.…”

Section: Bacterial Strains Plasmids and Mediamentioning

confidence: 99%

A Lux-like Quorum Sensing System in the Extreme Acidophile Acidithiobacillus ferrooxidans

Rivas

Seeger²,

Holmes

et al. 2005

Biol. Res.

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The genome of the acidophilic, proteobacterium Acidithiobacillus ferrooxidans, contains linked but divergently oriented genes, termed afeI and afeR, whose predicted protein products are significantly similar to the LuxI and LuxR families of proteins. A possible promoter and Lux box are predicted upstream of afeI. A cloned copy of afeI, expressed in E. coli, encodes an enzyme that catalyzes the production of a diffusible compound identified by gas chromatography and mass spectrometry as an unsubstituted N-acyl homoserine lactone (AHL) of chain length C 14 . This AHL can be detected by a reporter strain of Sinorhizobium meliloti Rm41 suggesting that it is biologically active. The reporter strain also responds to extracts of the supernatant of A. ferrooxidans grown to early stationary phase in sulfur medium indicating that a diffusible AHL is produced by this microorganism. Semi-quantitative RT-PCR experiments indicate that afeI and afeR are expressed maximally in early stationary phase and are more expressed when A. ferrooxidans is grown in sulfur-rather than iron-containing medium. Given the predicted amino acid sequence and functional properties of AfeI and AfeR it is proposed that A. ferrooxidans has a quorum sensing system similar to the LuxI-LuxR paradigm.

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Two families of repeated DNA sequences in Thiobacillus ferrooxidans

Cited by 71 publications

References 25 publications

Identification and Characterization of Transposable Elements of Paracoccus pantotrophus

Identification and Characterization of Transposable Elements of Paracoccus pantotrophus

Phylogenetic heterogeneity of the species Acidithiobacillus ferrooxidans

A Lux-like Quorum Sensing System in the Extreme Acidophile Acidithiobacillus ferrooxidans

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