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pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements.

Xiang X, Huang X, Wang H, Huang L - Life (Basel) (2015)

Bottom Line: However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful.The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner.These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China. xiangxiaoyu@yahoo.com.

ABSTRACT
Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

No MeSH data available.


Related in: MedlinePlus

Patterns of deletion at the sites of transposition by ISSte1 (a) and MITE (b). Total DNAs or plasmid DNAs were isolated from enrichment cultures established with various hot spring and mud hole samples. PCR targeting the ISSte1 site or the MITE site was carried out. Fragments shorter than expected for the insertion of full-length ISStel or MITE into the pTC1 DNA were sequenced. Repeating sequences are labeled in color and specified. ORFs are shown with blank arrows. An additional deletion (AGGGGCTCT) occurred at 88 bp upstream of LDR in type 2 deletion variants, whereas an additional deletion (AGAGACCGAGAATGATA) was 86 bp downstream of RDR in types 3 and 8 deletion variants. The percentage of each deletion type for ISStel in all samples is indicated.
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life-05-00506-f004: Patterns of deletion at the sites of transposition by ISSte1 (a) and MITE (b). Total DNAs or plasmid DNAs were isolated from enrichment cultures established with various hot spring and mud hole samples. PCR targeting the ISSte1 site or the MITE site was carried out. Fragments shorter than expected for the insertion of full-length ISStel or MITE into the pTC1 DNA were sequenced. Repeating sequences are labeled in color and specified. ORFs are shown with blank arrows. An additional deletion (AGGGGCTCT) occurred at 88 bp upstream of LDR in type 2 deletion variants, whereas an additional deletion (AGAGACCGAGAATGATA) was 86 bp downstream of RDR in types 3 and 8 deletion variants. The percentage of each deletion type for ISStel in all samples is indicated.

Mentions: The insertion sequence (IS), denoted ISSte1 [17], is 762 bp in length and located in the intergenic region between ORF107 and ORF104 (Figure 4a). It contains a transposase (Tpase) gene (ORF204) flanked by 16-bp perfect inverted repeats (IR: GTGTGTGTCCAACAAT). Notably, there is a pair of perfect inverted repeats (IR': GGGTCAGGACGGG) between the left IR and ORF204. The insertion of ISSte1 has led to the duplication of the target site of 8 bp (DR: ATCACAAA). Sequence analysis shows that ORF204-encoded Tpase contains the conserved DDE domain (Figure S1) [17]. This, together with the size and sequence of the IRs, places ISSte1 in the IS6 family [17].


pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements.

Xiang X, Huang X, Wang H, Huang L - Life (Basel) (2015)

Patterns of deletion at the sites of transposition by ISSte1 (a) and MITE (b). Total DNAs or plasmid DNAs were isolated from enrichment cultures established with various hot spring and mud hole samples. PCR targeting the ISSte1 site or the MITE site was carried out. Fragments shorter than expected for the insertion of full-length ISStel or MITE into the pTC1 DNA were sequenced. Repeating sequences are labeled in color and specified. ORFs are shown with blank arrows. An additional deletion (AGGGGCTCT) occurred at 88 bp upstream of LDR in type 2 deletion variants, whereas an additional deletion (AGAGACCGAGAATGATA) was 86 bp downstream of RDR in types 3 and 8 deletion variants. The percentage of each deletion type for ISStel in all samples is indicated.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390865&req=5

life-05-00506-f004: Patterns of deletion at the sites of transposition by ISSte1 (a) and MITE (b). Total DNAs or plasmid DNAs were isolated from enrichment cultures established with various hot spring and mud hole samples. PCR targeting the ISSte1 site or the MITE site was carried out. Fragments shorter than expected for the insertion of full-length ISStel or MITE into the pTC1 DNA were sequenced. Repeating sequences are labeled in color and specified. ORFs are shown with blank arrows. An additional deletion (AGGGGCTCT) occurred at 88 bp upstream of LDR in type 2 deletion variants, whereas an additional deletion (AGAGACCGAGAATGATA) was 86 bp downstream of RDR in types 3 and 8 deletion variants. The percentage of each deletion type for ISStel in all samples is indicated.
Mentions: The insertion sequence (IS), denoted ISSte1 [17], is 762 bp in length and located in the intergenic region between ORF107 and ORF104 (Figure 4a). It contains a transposase (Tpase) gene (ORF204) flanked by 16-bp perfect inverted repeats (IR: GTGTGTGTCCAACAAT). Notably, there is a pair of perfect inverted repeats (IR': GGGTCAGGACGGG) between the left IR and ORF204. The insertion of ISSte1 has led to the duplication of the target site of 8 bp (DR: ATCACAAA). Sequence analysis shows that ORF204-encoded Tpase contains the conserved DDE domain (Figure S1) [17]. This, together with the size and sequence of the IRs, places ISSte1 in the IS6 family [17].

Bottom Line: However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful.The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner.These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China. xiangxiaoyu@yahoo.com.

ABSTRACT
Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

No MeSH data available.


Related in: MedlinePlus