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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

Identification of plasmid pTC1 from Sulfolobus tengchongensis RT8-4. (a) Restriction digestion of the total DNA from S. tengchongensis RT8-4 containing pTC1. The total DNA from the cells was digested with indicated restriction enzymes. Restriction fragments were subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder with sizes of 10, 8, 6, 5, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.75, 0.5, and 0.25 kb (from top to bottom); lane 1, EcoRI; lane 2, EcoRV; lane 3, PstI; lane 4, XhoI; lane 5 SalI; lane 6, total DNA; (b) Restriction digestion of pTC1 DNA. pTC1 DNA was extracted from the cells by alkaline lysis and purified using a plasmid purification kit. The DNA was digested with EcoRI. The restriction digest was subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder; lane 1, EcoRI digest of the total DNA from S. tengchongensis RT8-4 containing pTC1; lane 2, EcoRI digest of purified pTC1 DNA; lane 3, purified pTC1 DNA.
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life-05-00506-f001: Identification of plasmid pTC1 from Sulfolobus tengchongensis RT8-4. (a) Restriction digestion of the total DNA from S. tengchongensis RT8-4 containing pTC1. The total DNA from the cells was digested with indicated restriction enzymes. Restriction fragments were subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder with sizes of 10, 8, 6, 5, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.75, 0.5, and 0.25 kb (from top to bottom); lane 1, EcoRI; lane 2, EcoRV; lane 3, PstI; lane 4, XhoI; lane 5 SalI; lane 6, total DNA; (b) Restriction digestion of pTC1 DNA. pTC1 DNA was extracted from the cells by alkaline lysis and purified using a plasmid purification kit. The DNA was digested with EcoRI. The restriction digest was subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder; lane 1, EcoRI digest of the total DNA from S. tengchongensis RT8-4 containing pTC1; lane 2, EcoRI digest of purified pTC1 DNA; lane 3, purified pTC1 DNA.

Mentions: We previously reported the isolation and identification of Sulfolobus tengchongensis strain RT8-4 from a hot spring in Tengchong in Southwestern China [13]. In a subsequent study, we isolated total DNA from the strain and digested it with various restriction endonucleases. When the digests were subjected to agarose gel electrophoresis and ethidium bromide staining, a stoichiometric pattern of bands with intensity significantly higher than that of smearing bands derived from the genomic DNA of the host was observed, suggesting the presence of an extrachromasomal genetic element in the host cell (Figure 1). This suggestion was supported by the finding that extraction of episomal DNA from S. tengchongensis RT8-4 by using the alkaline lysis procedure yielded high molecular weight DNA species that migrated faster than the genomic DNA of the host. To determine whether the DNA was derived from a virus or a plasmid, we examined the culture supernatant of S. tengchongensis RT8-4, and no virus-like particles were observed under an electron microscope. Based on these results, we conclude that a plasmid existed in S. tengchongensis RT8-4, and designated this plasmid as pTC1.


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)

Identification of plasmid pTC1 from Sulfolobus tengchongensis RT8-4. (a) Restriction digestion of the total DNA from S. tengchongensis RT8-4 containing pTC1. The total DNA from the cells was digested with indicated restriction enzymes. Restriction fragments were subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder with sizes of 10, 8, 6, 5, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.75, 0.5, and 0.25 kb (from top to bottom); lane 1, EcoRI; lane 2, EcoRV; lane 3, PstI; lane 4, XhoI; lane 5 SalI; lane 6, total DNA; (b) Restriction digestion of pTC1 DNA. pTC1 DNA was extracted from the cells by alkaline lysis and purified using a plasmid purification kit. The DNA was digested with EcoRI. The restriction digest was subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder; lane 1, EcoRI digest of the total DNA from S. tengchongensis RT8-4 containing pTC1; lane 2, EcoRI digest of purified pTC1 DNA; lane 3, purified pTC1 DNA.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4390865&req=5

life-05-00506-f001: Identification of plasmid pTC1 from Sulfolobus tengchongensis RT8-4. (a) Restriction digestion of the total DNA from S. tengchongensis RT8-4 containing pTC1. The total DNA from the cells was digested with indicated restriction enzymes. Restriction fragments were subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder with sizes of 10, 8, 6, 5, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.75, 0.5, and 0.25 kb (from top to bottom); lane 1, EcoRI; lane 2, EcoRV; lane 3, PstI; lane 4, XhoI; lane 5 SalI; lane 6, total DNA; (b) Restriction digestion of pTC1 DNA. pTC1 DNA was extracted from the cells by alkaline lysis and purified using a plasmid purification kit. The DNA was digested with EcoRI. The restriction digest was subjected to electrophoresis in agarose gel. Lane M, 1-kb DNA ladder; lane 1, EcoRI digest of the total DNA from S. tengchongensis RT8-4 containing pTC1; lane 2, EcoRI digest of purified pTC1 DNA; lane 3, purified pTC1 DNA.
Mentions: We previously reported the isolation and identification of Sulfolobus tengchongensis strain RT8-4 from a hot spring in Tengchong in Southwestern China [13]. In a subsequent study, we isolated total DNA from the strain and digested it with various restriction endonucleases. When the digests were subjected to agarose gel electrophoresis and ethidium bromide staining, a stoichiometric pattern of bands with intensity significantly higher than that of smearing bands derived from the genomic DNA of the host was observed, suggesting the presence of an extrachromasomal genetic element in the host cell (Figure 1). This suggestion was supported by the finding that extraction of episomal DNA from S. tengchongensis RT8-4 by using the alkaline lysis procedure yielded high molecular weight DNA species that migrated faster than the genomic DNA of the host. To determine whether the DNA was derived from a virus or a plasmid, we examined the culture supernatant of S. tengchongensis RT8-4, and no virus-like particles were observed under an electron microscope. Based on these results, we conclude that a plasmid existed in S. tengchongensis RT8-4, and designated this plasmid as pTC1.

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