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Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.

Santos AF, Lengruber RB, Soares EA, Jere A, Sprinz E, Martinez AM, Silveira J, Sion FS, Pathak VK, Soares MA - PLoS ONE (2008)

Bottom Line: One third of RT C-terminal residues were found to be conserved among group M variants.Three mutations were found exclusively in NRTI-treated isolates.Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Virologia Humana, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.

ABSTRACT

Background: Although extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H) is poorly understood.

Methods and findings: We wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI.

Conclusions: This is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.

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Related in: MedlinePlus

Three-dimensional structure of HIV-1 RT connection (A) and RNase H (B) domains in contact with template viral DNA showing codons significantly associated with NRTI treatment.The atomic coordinates of HIV-1 RT isolate BH10 (entry 1HYS of the Brookhanven Protein Data Bank) was downloaded into the visualization software ViewerLite v. 5.0 and then manually colored. Subtype B-related substitutions with statistical significance are shown in red. Amino acid residues with asterisks denote those which interact with nucleic acid. Additional residues which interact with nucleic acid, but not found to be selected by treatment in our analysis, are shown in green. Amino acid residues depicted in orange in panel (B) represent the RNase H catalytic site.
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pone-0001781-g004: Three-dimensional structure of HIV-1 RT connection (A) and RNase H (B) domains in contact with template viral DNA showing codons significantly associated with NRTI treatment.The atomic coordinates of HIV-1 RT isolate BH10 (entry 1HYS of the Brookhanven Protein Data Bank) was downloaded into the visualization software ViewerLite v. 5.0 and then manually colored. Subtype B-related substitutions with statistical significance are shown in red. Amino acid residues with asterisks denote those which interact with nucleic acid. Additional residues which interact with nucleic acid, but not found to be selected by treatment in our analysis, are shown in green. Amino acid residues depicted in orange in panel (B) represent the RNase H catalytic site.

Mentions: Mutations subjected to selective pressure were highlighted onto the structural C-terminal domains of HIV-1 RT (Figure 4). In the connection domain, nine mutations were selected by treatment in subtype B. The RNase H domain harbored 6 mutations selected by treatment in this subtype. Interestingly, some of these residues lie in motifs known to contact the nucleic acid (G359S, A360T/V and K390R). As expected, the seven amino acid residues that comprise the RNase H catalytic site (D443, E478, D498, S499, H539, N545 and D549) were highly conserved and remained unchanged under NRTI treatment.


Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.

Santos AF, Lengruber RB, Soares EA, Jere A, Sprinz E, Martinez AM, Silveira J, Sion FS, Pathak VK, Soares MA - PLoS ONE (2008)

Three-dimensional structure of HIV-1 RT connection (A) and RNase H (B) domains in contact with template viral DNA showing codons significantly associated with NRTI treatment.The atomic coordinates of HIV-1 RT isolate BH10 (entry 1HYS of the Brookhanven Protein Data Bank) was downloaded into the visualization software ViewerLite v. 5.0 and then manually colored. Subtype B-related substitutions with statistical significance are shown in red. Amino acid residues with asterisks denote those which interact with nucleic acid. Additional residues which interact with nucleic acid, but not found to be selected by treatment in our analysis, are shown in green. Amino acid residues depicted in orange in panel (B) represent the RNase H catalytic site.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2262134&req=5

pone-0001781-g004: Three-dimensional structure of HIV-1 RT connection (A) and RNase H (B) domains in contact with template viral DNA showing codons significantly associated with NRTI treatment.The atomic coordinates of HIV-1 RT isolate BH10 (entry 1HYS of the Brookhanven Protein Data Bank) was downloaded into the visualization software ViewerLite v. 5.0 and then manually colored. Subtype B-related substitutions with statistical significance are shown in red. Amino acid residues with asterisks denote those which interact with nucleic acid. Additional residues which interact with nucleic acid, but not found to be selected by treatment in our analysis, are shown in green. Amino acid residues depicted in orange in panel (B) represent the RNase H catalytic site.
Mentions: Mutations subjected to selective pressure were highlighted onto the structural C-terminal domains of HIV-1 RT (Figure 4). In the connection domain, nine mutations were selected by treatment in subtype B. The RNase H domain harbored 6 mutations selected by treatment in this subtype. Interestingly, some of these residues lie in motifs known to contact the nucleic acid (G359S, A360T/V and K390R). As expected, the seven amino acid residues that comprise the RNase H catalytic site (D443, E478, D498, S499, H539, N545 and D549) were highly conserved and remained unchanged under NRTI treatment.

Bottom Line: One third of RT C-terminal residues were found to be conserved among group M variants.Three mutations were found exclusively in NRTI-treated isolates.Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Virologia Humana, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.

ABSTRACT

Background: Although extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H) is poorly understood.

Methods and findings: We wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI.

Conclusions: This is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.

Show MeSH
Related in: MedlinePlus