| Literature DB >> 29695285 |
Juemin Xi1,2,3, Junying Chen1,2,3, Miaoling Xu4, Hongying Yang5, Songjiao Wen1,2,3, Yue Pan1,2,3, Xiaodan Wang1,2,3, Chao Ye1,2,3,6, Lijuan Qiu1,2,3,7, Qiangming Sun8,9,10.
Abstract
BACKGROUD: Variations in HPV LCR/E6/E7 have been shown to be associated with the viral persistence and cervical cancer development. So far, there are few reports about the polymorphisms of the HPV-58 LCR/E6/E7 sequences in Southwest China. This study aims to characterize the gene polymorphisms of the HPV-58 LCR/E6/E7 sequences in women of Southwest China, and assess the effects of variations on the immune recognition of viral E6 and E7 antigens.Entities:
Keywords: E6; E7; HPV-58; LCR; MHC binding peptides; Phylogenetic analysis; Polymorphism; Selection pressure; Transcription factor binding site
Mesh:
Substances:
Year: 2018 PMID: 29695285 PMCID: PMC5918753 DOI: 10.1186/s12985-018-0986-7
Source DB: PubMed Journal: Virol J ISSN: 1743-422X Impact factor: 4.099
HPV-58 variants based on the LCR/E6/E7 sequences
| HPV-58 variable sites | |||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GenBank Acession | Variant ID | LCR | E6 | E7 | Lineage | ||||||||||||||||||||||||
| 7172 | 7194 | 7265 | 7266 | 7304 | 7440 | 7525 | 7540 | 7556 | 7714 | 7749 | 7755 | 7784 | 7793 | 7807 | 24 | 52 | 54 | 307 | 321 | 388 | 632 | 694 | 744 | 760 | 761 | 803 | |||
| D90400.1 | T | G | C | C | A | T | A | A | C | A | C | A | T | A | T | T | C | G | C | C | A | C | G | T | G | G | T | A1 | |
| MF741321 | 1 | – | – | – | – | – | G | – | – | – | – | – | – | – | – | – | – | – | A | – | – | – | – | – | – | – | – | – | A1 |
| MF741322 | 2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | A1 |
| MF741323 | 3 | – | – | – | – | – | – | – | – | – | – | – | – | – | G | – | – | – | – | – | – | C | – | – | G | – | – | C | A1 |
| MF741324 | 4 | – | – | – | – | – | – | – | G | – | – | G | – | C | – | – | – | – | – | – | – | – | – | – | – | – | – | – | A1 |
| MF741325 | 5 | – | – | G | T | – | – | – | – | – | G | – | – | – | – | – | – | – | – | T | – | – | – | A | G | – | A | – | A2 |
| MF741326 | 6 | – | – | G | T | – | – | – | – | – | – | – | – | – | G | – | – | – | – | – | T | C | – | – | G | – | – | C | A1 |
| MF741327 | 7 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | C | – | – | – | – | – | – | A1 |
| MF741328 | 8 | C | – | G | T | – | – | – | – | – | G | – | – | – | – | G | – | – | – | T | – | – | – | A | G | – | A | – | A2 |
| MF741329 | 9 | – | C | – | – | G | – | C | – | T | C | – | G | – | C | – | – | T | – | T | – | – | T | – | G | A | – | – | A3 |
| MF741330 | 10 | – | C | – | – | G | – | – | – | – | C | – | G | – | – | – | – | T | – | T | – | – | T | – | G | A | – | – | A3 |
| MF741331 | 11 | – | – | – | – | – | – | – | – | – | – | – | – | – | G | – | G | – | – | – | – | C | – | – | G | – | – | C | A1 |
| AA changes | C66C | S71F | K93 N | T20I | G41R | T57 T | G63S | G63D | V77A | ||||||||||||||||||||
| Secondary structure | H | S | H | ||||||||||||||||||||||||||
The nucleotides matching the reference sequence (GenBank: D90400.1) are marked with a dash (−). The H and S in the row of secondary structure designate “helix” and “sheet”, respectively
Tests for the positive selected sites in HPV-58 E6 and E7
| Regions | Models | lnL | 2ΔlnL | Positively selected sites |
|---|---|---|---|---|
| E6 | M1 | − 675.08 | 2.18 | NA |
| M2 | − 673.99 | NS | ||
| M7 | −675.13 | 2.28 | NA | |
| M8 | −673.99 | NS | ||
| E7 | M1 | − 499.87 | 18.92 | NA |
| M2 | − 490.41 | 63G** | ||
| M7 | −499.84 | 18.86 | NA | |
| M8 | −490.41 | 63G** |
lnL designates the log-likelihood; 2ΔlnL designates 2-fold as the lnL difference between the two models. Two asterisks (**) indicate the posterior probability ≥99% by BEB analysis and to be a positively selected site. NA designates not allowed, and NS designates the sites not reaching the significant level
The putative MHC binding peptides of HPV-58 E6 and E7 proteins
| Protein | Position of amino acid | Peptide sequence | MHC binding |
|---|---|---|---|
| E6 | 64–72 | KVCLRLLSK | Class-I |
| 91–99 | TLKKCLNEI | Class-I | |
| 67–75 | LRLLSKISE | Class-II | |
| E7 | 16–24 | HPEPTDLFC | Class-I |
| 35–43 | DEIGLDGPD | Class-I | |
| 59–67 | CYTCGTTVR | Class-I | |
| 74–82 | TTDVRTLQQ | Class-I | |
| 15–22 | LHPEPTDL | Class-II | |
| 37–45 | IGLDGPDGQ | Class-II | |
| 77–85 | VRTLQQLLM | Class-II |