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
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Screening for Plasmids
2.2. Electron Microscopy
2.3. DNA Sequencing and Genome Analysis
2.4. Detection of Transposition by ISSte1 and MITE at the Specific Sites
3. Results
3.1. Identification of Plasmid pTC1
3.2. Genomic Analysis of pTC1
Name | Predicted function | Conserved motifs | Homologues in other Sulfolobus CPs | Section |
---|---|---|---|---|
ORF62 | Transmembrane protein involved in conjugation | Signal peptide and transmembrane regions (1)1 | pAH1_p35, pARN3_p40, pARN4_p39, pHVE14_p53, pSOG1_p44, pSOG2_p41, pYN01_p2 | A |
ORF297 | Signal peptide involved in conjugation | Signal peptide | pAH1_p1, pARN3_p1, pARN4_p1, pLD8501_p25, pYN01_p50, pHVE14_p3, pING1_p34, pKEF9_p3, pNOB8_p33, pSOG1_p5, pSOG2_p4, pMGB1_p1 | A |
ORF144 | Unknown | - | pAH1_p1, pARN3_p1, pARN4_p1, pLD8501_p25, pYN01_p50, pMGB1_p1 | A |
ORF124 | Unknown | - | pAH1_p1, pARN3_p1, pARN4_p1, pLD8501_p25, pYN01_p50, pMGB1_p1 | A |
ORF213 | The transcription factor TFIIB | TF_Zn_Ribbon superfamily | pAH1_p2, pARN3_p2, pARN4_p2, pLD8501_p24, pYN01_p49, pSOG1_p45 | A |
ORF99c | Unknown | - | pAH1_p3, pARN3_p3, pARN4_p3, pLD8501_p23, pYN01_p48, pMGB1_p3 | A |
ORF621 | TrbE-like protein involved in conjugation transfer | AAA_10 | pAH1_p4, pARN3_p4, pARN4_p4, pHVE14_p1, pING1_p32, pKEF9_p1, pLD8501_p22, pNOB8_p31, pSOG1_p2, pSOG2_p2, pYN01_p47, pMGB1_p4 | A |
ORF458 | Transmembrane protein involved in conjugation | Signal peptide and transmembrane regions (9) | pAH1_p5, pARN3_p5, pARN4_p5, pLD8501_p6, pSOG1_p7, pYN01_p36, pMGB1_p5 | A |
ORF161 | Transmembrane protein involved in conjugation | Transmembrane regions (2) | pAH1_p6, pARN3_p6, pARN4_p6, pYN01_p35 | A |
ORF179 | Transmembrane protein involved in conjugation | Transmembrane regions (3) | pAH1_p9, pARN3_p7, pARN4_p8, pLD8501_p1, pYN01_p33 | A |
ORF92 | Transmembrane protein involved in conjugation | Transmembrane regions (2) | pAH1_p10, pARN3_p8, pARN4_p9, pYN01, pMGB1_p8 | A |
ORF189 | Transmembrane protein involved in conjugation | Signal peptide and transmembrane regions (1) | pAH1_p11, pARN3_p9, pARN4_p10, pSOG1_p4, pYN01_p31, pMGB1_p9 | A |
ORF129 | Transmembrane protein involved in conjugation | Signal peptide and transmembrane regions (2) | pAH1_p12, pARN3_p10, pARN4_p11, pYN01_p30, pMGB1_p10 | A |
ORF1019 | VirD/TraG-like protein | TraG_VirD4/AAA_10 | pAH1_p13, pARN3_p11, pARN4_p12, pHVE14_p14, pING1_p5, pKEF9_p12, pNOB8_p10, pSOG1_p12, pSOG1_p2, pSOG2_p12, pYN01_p29, pMGB1_p11 | A |
ORF142 | Unknown | - | pAH1_p14, pARN3_p12, pARN4_p13, pING1_p6, pKEF9_p13, pSOG1_p13, pSOG2_p13 | A |
ORF99a | Predicted transcriptional regulators | HTH_ARSR superfamily | pING_p18, pNOB8_p18, pNOB8_p44, pYN01_p41, pMGB1_p20 | C |
ORF107 | Predicted transcriptional regulators | HTH_MARR | pAH1_p22, pKEF9_p24, pNOB8_p18, pNOB8_p2, pNOB8_p19, pYN01_p42, pLD8501_p16, pMGB1_p20, pMGB1_21 | C |
ORF204 | Transposase | COG3316 | pARN4_p16 | C |
ORF104 | Unknown | - | pARN3_p27, pARN4_p25, pING1_p19, pNOB8_p20, pYN01_p17, pHVE14_p30, pKEF9_p25, pSOG1_p23, pSOG2_p26 | C |
ORF108 | Unknown | - | - | C |
ORF92a | Unknown | - | - | C |
ORF79 | Unknown | - | pSOG1_p24, pSOG2_p27, pMGB1_p7 | C |
ORF80 | PlrA-like protein | Sulfolobus_pRN | pING1_p26, pARN4_p33, pNOB8_p28, pKEF9_p33, pSOG1_p34, pLD8501_p29, pHVE14_p41, pAH1_p33, pYN01_p6 | C |
ORF56 | CopG family transcriptional regulator | PHA01748/RHH_1 superfamily | pAH1_p28, pKEF9_p28, pYN01_p11, pNOB8_24, pMGB1_p26 | C |
ORF162 | Unknown | - | C | |
ORF125 | Unknown | - | pARN3_p38, pARN4_p37, pKEF9_p38, pHVE14_p50, pSOG1_p42, pSOG2_p39, pYN01_p4 | C |
3.3. pTC Plasmids in the Geothermal Area of Tengchong
4. Discussion
Acknowledgments
Author Contributions
Supplementary Materials
Conflicts of Interest
References
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Xiang, X.; Huang, X.; Wang, H.; Huang, L. 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. Life 2015, 5, 506-520. https://doi.org/10.3390/life5010506
Xiang X, Huang X, Wang H, Huang L. 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. Life. 2015; 5(1):506-520. https://doi.org/10.3390/life5010506
Chicago/Turabian StyleXiang, Xiaoyu, Xiaoxing Huang, Haina Wang, and Li Huang. 2015. "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" Life 5, no. 1: 506-520. https://doi.org/10.3390/life5010506
APA StyleXiang, X., Huang, X., Wang, H., & Huang, L. (2015). 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. Life, 5(1), 506-520. https://doi.org/10.3390/life5010506