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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

Restriction patterns of pTC plasmids. Plasmid DNAs were extracted from various isolates by alkaline lysis and purified using a plasmid purification kit. The DNAs were digested with EcoRI. The restriction digests 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, pTC1 DNA from S. tengchongensis RT8-4; lane 2, plasmid DNA from isolate H7; lane 3, plasmid DNA from isolate H7; lane 4, plasmid DNA from isolate H3; lane 5, plasmid DNA from isolate D2; lane 6, plasmid DNA from isolate D4; lane 7, plasmid DNA from isolate H5. Restriction fragments containing a deletion are indicated by arrows.
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life-05-00506-f005: Restriction patterns of pTC plasmids. Plasmid DNAs were extracted from various isolates by alkaline lysis and purified using a plasmid purification kit. The DNAs were digested with EcoRI. The restriction digests 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, pTC1 DNA from S. tengchongensis RT8-4; lane 2, plasmid DNA from isolate H7; lane 3, plasmid DNA from isolate H7; lane 4, plasmid DNA from isolate H3; lane 5, plasmid DNA from isolate D2; lane 6, plasmid DNA from isolate D4; lane 7, plasmid DNA from isolate H5. Restriction fragments containing a deletion are indicated by arrows.

Mentions: To determine the distribution of pTC1 and its variants in acidic hot springs and mud holes in Tengchong, we collected 35 samples at various spots in a general area of ~0.1 km2. Enrichment cultures from 27 of the samples were successfully established in Zillig’s medium supplemented with 0.2% tryptone [3]. Plasmid DNAs were isolated from 11 of the enrichment cultures by using the alkaline lysis method. Restriction analysis showed that the EcoRI cleavage patterns of seven of the plasmids resembled that of pTC1, whereas those of the other four were also indistinguishable from that of pTC1 except for one fragment (Figure 5). An additional fragment of ~400 bp appeared in one of the pTC variants, whereas the 6.8-kb EcoRI fragment, which harbored ISStel, was shortened to 6.0, 5.5 and 5.2 kb, respectively, in the other three variants. The ~400-bp EcoRI fragment of the former pTC variant, denoted pTC2, was sequenced. As shown in Figure 4 and Figure S2b in supplementary, pTC2 was 163 bp shorter than pTC1 in that fragment, and the MITE found in pTC1 was absent from pTC2 except for a single DR of the element. Therefore, pTC1 appears to have resulted from the insertion of the MITE in pTC2. These results suggest that pTC plasmids were widely distributed in the geothermal area of Tengchong, and pTC1 was likely a predominant species of these plasmids.


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)

Restriction patterns of pTC plasmids. Plasmid DNAs were extracted from various isolates by alkaline lysis and purified using a plasmid purification kit. The DNAs were digested with EcoRI. The restriction digests 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, pTC1 DNA from S. tengchongensis RT8-4; lane 2, plasmid DNA from isolate H7; lane 3, plasmid DNA from isolate H7; lane 4, plasmid DNA from isolate H3; lane 5, plasmid DNA from isolate D2; lane 6, plasmid DNA from isolate D4; lane 7, plasmid DNA from isolate H5. Restriction fragments containing a deletion are indicated by arrows.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00506-f005: Restriction patterns of pTC plasmids. Plasmid DNAs were extracted from various isolates by alkaline lysis and purified using a plasmid purification kit. The DNAs were digested with EcoRI. The restriction digests 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, pTC1 DNA from S. tengchongensis RT8-4; lane 2, plasmid DNA from isolate H7; lane 3, plasmid DNA from isolate H7; lane 4, plasmid DNA from isolate H3; lane 5, plasmid DNA from isolate D2; lane 6, plasmid DNA from isolate D4; lane 7, plasmid DNA from isolate H5. Restriction fragments containing a deletion are indicated by arrows.
Mentions: To determine the distribution of pTC1 and its variants in acidic hot springs and mud holes in Tengchong, we collected 35 samples at various spots in a general area of ~0.1 km2. Enrichment cultures from 27 of the samples were successfully established in Zillig’s medium supplemented with 0.2% tryptone [3]. Plasmid DNAs were isolated from 11 of the enrichment cultures by using the alkaline lysis method. Restriction analysis showed that the EcoRI cleavage patterns of seven of the plasmids resembled that of pTC1, whereas those of the other four were also indistinguishable from that of pTC1 except for one fragment (Figure 5). An additional fragment of ~400 bp appeared in one of the pTC variants, whereas the 6.8-kb EcoRI fragment, which harbored ISStel, was shortened to 6.0, 5.5 and 5.2 kb, respectively, in the other three variants. The ~400-bp EcoRI fragment of the former pTC variant, denoted pTC2, was sequenced. As shown in Figure 4 and Figure S2b in supplementary, pTC2 was 163 bp shorter than pTC1 in that fragment, and the MITE found in pTC1 was absent from pTC2 except for a single DR of the element. Therefore, pTC1 appears to have resulted from the insertion of the MITE in pTC2. These results suggest that pTC plasmids were widely distributed in the geothermal area of Tengchong, and pTC1 was likely a predominant species of these plasmids.

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