Molecular and genetic characterization of an Alcaligenes eutrophus insertion element

Kung, Shieh-Shiuh; Chen, Jychien; Chow, Wei-Yuan

doi:10.1128/jb.174.24.8023-8029.1992

Cited by 17 publications

(12 citation statements)

References 22 publications

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“…Three copies of the insertion sequence ISAE1 are located on chromosome 1 and the other two on pHG1 (ref. 16). One of the plasmid-borne copies of ISAE1 and one chromosomal copy create in-frame fusions of ORF2 of the mobile element and a CDS at the target site.…”

Section: Organization and General Features Of The Genomementioning

confidence: 99%

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

et al. 2006

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Section: Organization and General Features Of The Genomementioning

confidence: 99%

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

et al. 2006

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“…The function of ORF 2 remains unknown (26). Several other insertion sequences, such as IS30 (2), IS10 (8,9,33), and pot2 (25), have been shown to encode antisense RNA on the opposite strand to the TPase.…”

Section: Discussionmentioning

confidence: 99%

ISAfe1, an ISL3 Family Insertion Sequence fromAcidithiobacillus ferrooxidansATCC 19859

Holmes¹,

Zhao²,

Levicán³

et al. 2001

J Bacteriol

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Acidithiobacillus ferrooxidans, formerly Thiobacillus ferrooxidans (24), is a gram-negative bacterium that has been shown to be active in the solubilization of copper and in the processing of refractory gold ores in bioleaching operations (reviewed in references 21 and 36). It is also a major contributor to acid mine drainage in copper and coal mines and in certain natural environments. It is a chemolithotroph, deriving energy and electrons from the oxidation of ferrous iron and/or sulfur and various reduced sulfur compounds at pH 2 to 4, using oxygen as the ultimate electron acceptor (22). It fixes CO 2 by the Calvin-Bassham scheme. It can also anaerobically oxidize hydrogen at pH 5.5 (15). Recently, the almost complete genome sequence of A. ferrooxidans was used to detect and inventory the genes involved in amino acid metabolism (40).A mutant of A. ferrooxidans ATCC 19859 has been isolated that is able to switch reversibly, and with high frequency, between a wild-type state, in which it can oxidize both ferrous iron and sulfur compounds, and a mutant state, in which it has lost the capacity to oxidize iron (39). This phenomenon resembles other states of instability associated with the transposition of insertion sequences that have been described in other organisms and led us to investigate whether phenotypic switching might similarly be explained in A. ferrooxidans.Evidence was recently presented (5) that implicated a member of the so-called family 1 repetitive elements (50) in phenotypic switching. This repetitive element was tentatively identified as an insertion sequence and termed IST1 (renamed ISAfe1 here). Phenotypic switching was shown to be correlated with the high frequency insertion and excision of ISAfe1 into, and out of, the resB gene (5). ResB encodes a cytochrome c-type maturation protein (reviewed in reference 45), and a model was proposed in which insertion of ISAfe1 into resB eliminated the capacity of ResB to satisfactorily mature a c-type cytochrome and that this resulted, in turn, in the loss of the ability to oxidize iron but not sulfur (5).In order to describe and explain the phenomenon of phenotypic switching, we carried out a partial molecular characterization of ISAfe1. We further demonstrate that ISAfe1 can promote plasmid integration and resolution in E. coli, opening up the future possibility of exploiting E. coli to test experimentally certain characteristics of this insertion sequence. MATERIALS AND METHODSBacterial strains and media. Strains and plasmids used in this study are listed in Table 1. A. ferrooxidans ATCC 19859 was grown on Mackintosh medium or in modified 9K-ferrous iron medium (50). E. coli was grown in Luria-Bertani (LB) medium (30).Construction of plasmids. Construction of pTf85. A member of family 1 repeated DNA from A. ferrooxidans ATCC 19859 was cloned into pBR322, and the resulting plasmid was designated pTf11 (50). An internal SphI fragment of pTf1 1 was subcloned into pBR322 and termed pTf1 1-sph. pTf1 1-sph was subsequently used as a probe in a Southern blot...

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“…Interestingly, no other gene encoding the biphenyl-degrading enzyme could be detected upstream of bphC1, indicating that this bphC1D cistron is not part of a complete bph operon, as found in other bacteria (Furukawa, 2000;Higson, 1992). Upstream of the bphC1 gene, there is a DNA region with 26.4% identity to ISAE1, an insertion element of Alcaligenes eutrophus strain H1 (Kung et al, 1992), including a 33-bp-long inverted repeat.…”

Section: Meta Cleavage Enzyme Involved In Df Mineral-mentioning

confidence: 99%

Bacterial degradation of aromatic compounds via angular dioxygenation.

Nojiri

Habe

Omori

2001

J. Gen. Appl. Microbiol.

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Dioxygenation is one of the important initial reactions of the bacterial degradation of various aromatic compounds. Aromatic compounds, such as biphenyl, toluene, and naphthalene, are dioxygenated at lateral positions of the aromatic ring resulting in the formation of cis-dihydrodiol. This "normal" type of dioxygenation is termed lateral dioxygenation. On the other hand, the analysis of the bacterial degradation of fluorene (FN) analogues, such as 9-fluorenone, dibenzofuran (DF), carbazole (CAR), and dibenzothiophene (DBT)-sulfone, and DF-related diaryl ether compounds, dibenzo-p-dioxin (DD) and diphenyl ether (DE), revealed the presence of the novel mode of dioxygenation reaction for aromatic nucleus, generally termed angular dioxygenation. In this atypical dioxygenation, the carbon bonded to the carbonyl group in 9-fluorenone or to heteroatoms in the other compounds, and the adjacent carbon in the aromatic ring are both oxidized. Angular dioxygenation of DF, CAR, DBT-sulfone, DD, and DE produces the chemically unstable hemiacetal-like intermediates, which are spontaneously converted to 2,2,3-trihydroxybiphenyl, 2-aminobiphenyl-2,3-diol, 2,3-dihydroxybiphenyl-2-sulfinate, 2,2,3-trihydroxydiphenyl ether, and phenol and catechol, respectively. Thus, angular dioxygenation for these compounds results in the cleavage of the three-ring structure or DE structure. The angular dioxygenation product of 9-fluorenone, 1-hydro-1,1a-dihydroxy-9-fluorenone is a chemically stable cis-diol, and is enzymatically transformed to 2-carboxy-2,3-dihydroxybiphenyl. 2-Substituted 2,3-dihydroxybiphenyls formed by angular dioxygenation of FN analogues are degraded to monocyclic aromatic compounds by meta cleavage and hydrolysis. Thus, after the novel angular dioxygenation, subsequent degradation pathways are homologous to the corresponding part of that of biphenyl. Compared to the bacterial strains capable of catalyzing lateral dioxygenation, few bacteria having angular dioxygenase have been reported. Only a few degradation pathways, CARdegradation pathway of Pseudomonas resinovorans strain CA10, DF/DD-degradation pathway of Sphingomonas wittichii strain RW1, DF/DD/FN-degradation pathway of Terrabacter sp. strain DBF63, and carboxylated DE-degradation pathway of P. pseudoalcaligenes strain POB310, have been investigated at the gene level. As a result of the phylogenetic analysis and the comparison of substrate specificity of angular dioxygenase, it is suggested that this atypical mode of dioxygenation is one of the oxygenation reactions originating from the relaxed substrate specificity of the Rieske nonheme iron oxygenase superfamily. Genetic characterization of the degradation pathways of these compounds suggests the possibility that the respective genetic elements constituting the entire catabolic pathway have been recruited from various other bacteria and/or other genetic loci, and that these pathways have not evolutionary matured.

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Molecular and genetic characterization of an Alcaligenes eutrophus insertion element

Cited by 17 publications

References 22 publications

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

ISAfe1, an ISL3 Family Insertion Sequence fromAcidithiobacillus ferrooxidansATCC 19859

Bacterial degradation of aromatic compounds via angular dioxygenation.

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