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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

Alignment of the putative origins of replication of pARN3, pING1, pKEF9, pSOG1, pSOG2 and pTC1. Repeating sequences are indicated by arrows. Identical or similar sequences are shown in dark or grey background, respectively.
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life-05-00506-f003: Alignment of the putative origins of replication of pARN3, pING1, pKEF9, pSOG1, pSOG2 and pTC1. Repeating sequences are indicated by arrows. Identical or similar sequences are shown in dark or grey background, respectively.

Mentions: Section B contains multiple sequence repeats and no ORFs. Based on Z-curve and GC-skew analyses, the origin of replication for pTC1 is located in a 209-bp stretch, downstream of ORF142, in a large intergenic region (Figure 2). The 209-bp region shares limited sequence similarity to the replication origin of pSOG2, pKEF9, pING1, pARN3, and pSOG1 (Figure 3). However, the conserved sequence TCTATACCCCC, found in the putative origin of the other CPs [9], is not present in pTC1 (Figure 3). On the other hand, there are two perfect direct repeats (TCCCCGGAACT) and three imperfect direct repeats (TCTCTCCNNCT) in this region as well as four imperfect repeats (AGCAGCGCTTGYCCT) 529–959 bp downstream of this region. The presence of these direct and inverted repeating sequences supports the possibility that pTC1 initiates replication in this region [16].


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)

Alignment of the putative origins of replication of pARN3, pING1, pKEF9, pSOG1, pSOG2 and pTC1. Repeating sequences are indicated by arrows. Identical or similar sequences are shown in dark or grey background, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00506-f003: Alignment of the putative origins of replication of pARN3, pING1, pKEF9, pSOG1, pSOG2 and pTC1. Repeating sequences are indicated by arrows. Identical or similar sequences are shown in dark or grey background, respectively.
Mentions: Section B contains multiple sequence repeats and no ORFs. Based on Z-curve and GC-skew analyses, the origin of replication for pTC1 is located in a 209-bp stretch, downstream of ORF142, in a large intergenic region (Figure 2). The 209-bp region shares limited sequence similarity to the replication origin of pSOG2, pKEF9, pING1, pARN3, and pSOG1 (Figure 3). However, the conserved sequence TCTATACCCCC, found in the putative origin of the other CPs [9], is not present in pTC1 (Figure 3). On the other hand, there are two perfect direct repeats (TCCCCGGAACT) and three imperfect direct repeats (TCTCTCCNNCT) in this region as well as four imperfect repeats (AGCAGCGCTTGYCCT) 529–959 bp downstream of this region. The presence of these direct and inverted repeating sequences supports the possibility that pTC1 initiates replication in this region [16].

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