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Study of the HIV-2 Env cytoplasmic tail variability and its impact on Tat, Rev and Nef.

Bakouche N, Vandenbroucke AT, Goubau P, Ruelle J - PLoS ONE (2013)

Bottom Line: A 70% reduction of the length of the CT region affected the HIV-2 ROD and EHO strains in vitro due to a premature stop codon in the env gene.These regions don't affect the rev and Nef amino acids composition which evolves independently.In contrast, Tat co-evolves with the Env CT.

View Article: PubMed Central - PubMed

Affiliation: Institut de recherche expérimentale et clinique, Université catholique de Louvain, Brussels, Belgium.

ABSTRACT

Background: The HIV-2 env's 3' end encodes the cytoplasmic tail (CT) of the Env protein. This genomic region also encodes the rev, Tat and Nef protein in overlapping reading frames. We studied the variability in the CT coding region in 46 clinical specimens and in 2 reference strains by sequencing and by culturing. The aims were to analyse the variability of Env CT and the evolution of proteins expressed from overlapping coding sequences.

Results: A 70% reduction of the length of the CT region affected the HIV-2 ROD and EHO strains in vitro due to a premature stop codon in the env gene. In clinical samples this wasn't observed, but the CT length varied due to insertions and deletions. We noted 3 conserved and 3 variable regions in the CT. The conserved regions were those containing residues involved in Env endocytosis, the potential HIV-2 CT region implicated in the NF-kB activation and the potential end of the lentiviral lytic peptide one. The variable regions were the potential HIV-2 Kennedy region, the potential lentiviral lytic peptide two and the beginning of the potential lentiviral lytic peptide one. A very hydrophobic region was coded downstream of the premature stop codon observed in vitro, suggesting a membrane spanning region. Interestingly, the nucleotides that are responsible for the variability of the CT don't impact rev and Nef. However, in the Kennedy-like coding region variability resulted only from nucleotide changes that impacted Env and Tat together.

Conclusion: The HIV-2 Env, Tat and Rev C-terminal part are subject to major length variations in both clinical samples and cultured strains. The HIV-2 Env CT contains variable and conserved regions. These regions don't affect the rev and Nef amino acids composition which evolves independently. In contrast, Tat co-evolves with the Env CT.

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SE plots of the CT coding nucleotides.We created a SE plot for all the nucleotides (A) or for each nucleotide by codon (B). In graph A and B, the line represents moving averages (30 positions for total sequence in black; 10 positions for the separated nucleotides): blue for the first nucleotides of each codon in the Env reading frame (env N1), red for the second nucleotides (env N2) and green for the third nucleotides (env N3). The N1 variability has a major impact on Env and Rev and a small impact on Tat/Nef, the N2 variability has a major impact on Env and Tat/Nef and a small impact on Rev and finally the env N3 variability has a major impact on Tat/Nef and Rev and a small impact on Env. Above each plot are shown key regions of the different proteins. A: The first conserved region containing the endocytosis signal. B: The region containing the Kennedy-like sequences. C: The hydrophobic region. D: LLP-2 region. E: LLP-3 region. F: LLP-3 / LLP-1 interegion. G: LLP-1 region + position 166 for the stop codon.
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pone-0079129-g003: SE plots of the CT coding nucleotides.We created a SE plot for all the nucleotides (A) or for each nucleotide by codon (B). In graph A and B, the line represents moving averages (30 positions for total sequence in black; 10 positions for the separated nucleotides): blue for the first nucleotides of each codon in the Env reading frame (env N1), red for the second nucleotides (env N2) and green for the third nucleotides (env N3). The N1 variability has a major impact on Env and Rev and a small impact on Tat/Nef, the N2 variability has a major impact on Env and Tat/Nef and a small impact on Rev and finally the env N3 variability has a major impact on Tat/Nef and Rev and a small impact on Env. Above each plot are shown key regions of the different proteins. A: The first conserved region containing the endocytosis signal. B: The region containing the Kennedy-like sequences. C: The hydrophobic region. D: LLP-2 region. E: LLP-3 region. F: LLP-3 / LLP-1 interegion. G: LLP-1 region + position 166 for the stop codon.

Mentions: Figures 3a and 3b show the SE of the entire CT DNA/RNA coding region at the nucleotide level. In the first graph, we plotted all the SE for all 498 DNA/RNA positions (Figure 3a). To know which nucleotide(s) was the driver of the DNA/RNA variability, we plotted the 166 first nucleotides of the env codon (called env N1; rev N2; tat/nef N3), the 166 second nucleotides of the env codon (called env N2; rev N3; tat/nef N1) and 166 third nucleotides of the env codon (env N3; rev N1; tat/nef N2;) in a separate graph (Figure 3b). We then plotted the SE of each polypeptide sequence at their equivalent expressed positions in a single graph (Figure 4). Finally, we analysed region by region the impact of this high concentration of overlapping ORF.


Study of the HIV-2 Env cytoplasmic tail variability and its impact on Tat, Rev and Nef.

Bakouche N, Vandenbroucke AT, Goubau P, Ruelle J - PLoS ONE (2013)

SE plots of the CT coding nucleotides.We created a SE plot for all the nucleotides (A) or for each nucleotide by codon (B). In graph A and B, the line represents moving averages (30 positions for total sequence in black; 10 positions for the separated nucleotides): blue for the first nucleotides of each codon in the Env reading frame (env N1), red for the second nucleotides (env N2) and green for the third nucleotides (env N3). The N1 variability has a major impact on Env and Rev and a small impact on Tat/Nef, the N2 variability has a major impact on Env and Tat/Nef and a small impact on Rev and finally the env N3 variability has a major impact on Tat/Nef and Rev and a small impact on Env. Above each plot are shown key regions of the different proteins. A: The first conserved region containing the endocytosis signal. B: The region containing the Kennedy-like sequences. C: The hydrophobic region. D: LLP-2 region. E: LLP-3 region. F: LLP-3 / LLP-1 interegion. G: LLP-1 region + position 166 for the stop codon.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3815105&req=5

pone-0079129-g003: SE plots of the CT coding nucleotides.We created a SE plot for all the nucleotides (A) or for each nucleotide by codon (B). In graph A and B, the line represents moving averages (30 positions for total sequence in black; 10 positions for the separated nucleotides): blue for the first nucleotides of each codon in the Env reading frame (env N1), red for the second nucleotides (env N2) and green for the third nucleotides (env N3). The N1 variability has a major impact on Env and Rev and a small impact on Tat/Nef, the N2 variability has a major impact on Env and Tat/Nef and a small impact on Rev and finally the env N3 variability has a major impact on Tat/Nef and Rev and a small impact on Env. Above each plot are shown key regions of the different proteins. A: The first conserved region containing the endocytosis signal. B: The region containing the Kennedy-like sequences. C: The hydrophobic region. D: LLP-2 region. E: LLP-3 region. F: LLP-3 / LLP-1 interegion. G: LLP-1 region + position 166 for the stop codon.
Mentions: Figures 3a and 3b show the SE of the entire CT DNA/RNA coding region at the nucleotide level. In the first graph, we plotted all the SE for all 498 DNA/RNA positions (Figure 3a). To know which nucleotide(s) was the driver of the DNA/RNA variability, we plotted the 166 first nucleotides of the env codon (called env N1; rev N2; tat/nef N3), the 166 second nucleotides of the env codon (called env N2; rev N3; tat/nef N1) and 166 third nucleotides of the env codon (env N3; rev N1; tat/nef N2;) in a separate graph (Figure 3b). We then plotted the SE of each polypeptide sequence at their equivalent expressed positions in a single graph (Figure 4). Finally, we analysed region by region the impact of this high concentration of overlapping ORF.

Bottom Line: A 70% reduction of the length of the CT region affected the HIV-2 ROD and EHO strains in vitro due to a premature stop codon in the env gene.These regions don't affect the rev and Nef amino acids composition which evolves independently.In contrast, Tat co-evolves with the Env CT.

View Article: PubMed Central - PubMed

Affiliation: Institut de recherche expérimentale et clinique, Université catholique de Louvain, Brussels, Belgium.

ABSTRACT

Background: The HIV-2 env's 3' end encodes the cytoplasmic tail (CT) of the Env protein. This genomic region also encodes the rev, Tat and Nef protein in overlapping reading frames. We studied the variability in the CT coding region in 46 clinical specimens and in 2 reference strains by sequencing and by culturing. The aims were to analyse the variability of Env CT and the evolution of proteins expressed from overlapping coding sequences.

Results: A 70% reduction of the length of the CT region affected the HIV-2 ROD and EHO strains in vitro due to a premature stop codon in the env gene. In clinical samples this wasn't observed, but the CT length varied due to insertions and deletions. We noted 3 conserved and 3 variable regions in the CT. The conserved regions were those containing residues involved in Env endocytosis, the potential HIV-2 CT region implicated in the NF-kB activation and the potential end of the lentiviral lytic peptide one. The variable regions were the potential HIV-2 Kennedy region, the potential lentiviral lytic peptide two and the beginning of the potential lentiviral lytic peptide one. A very hydrophobic region was coded downstream of the premature stop codon observed in vitro, suggesting a membrane spanning region. Interestingly, the nucleotides that are responsible for the variability of the CT don't impact rev and Nef. However, in the Kennedy-like coding region variability resulted only from nucleotide changes that impacted Env and Tat together.

Conclusion: The HIV-2 Env, Tat and Rev C-terminal part are subject to major length variations in both clinical samples and cultured strains. The HIV-2 Env CT contains variable and conserved regions. These regions don't affect the rev and Nef amino acids composition which evolves independently. In contrast, Tat co-evolves with the Env CT.

Show MeSH
Related in: MedlinePlus