Abstract
BackgroundThe HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA.ResultsTo minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV–SIV sequence space.ConclusionsExtrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures.
Highlights
The human immunodeficiency virus type 1 (HIV-1) RNA genome has a biased nucleotide composition with a surplus of As
phylogeny-instructed mutagenesis (PIM) used the sequence of 675 HIV-1 subtype B isolates present in the Los Alamos sequence compendium [33]
The Min/Max results described in this study indicate how far one can go in changing the A-count of the HIV-1 RNA genome without interfering with virus replication, despite the fact that significant repositioning occurred in the phylogeny of these mutants
Summary
The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has far not been systematically manipulated. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has far not been systematically manipulated The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, resulting in replication-impaired virus mutants. The A-numbers reach 35.1% and the C-count is low at 18.1% [2] This A-pressure is rather strong and even influences the amino acid composition of the HIV-1 proteins with a preference for residues that are encoded by A-rich codons [3]. HIV-1 Reverse Transcriptase copies the RNA genome and at least under some
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