About: HIV-1 tolerates changes in A-count in a small segment of the pol gene

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About: HIV-1 tolerates changes in A-count in a small segment of the pol gene Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	HIV-1 tolerates changes in A-count in a small segment of the pol gene
Creator	Berkhout, Ben Klaver, Bep Van Hemert, Formijn Van Der Kuyl, Antoinette Van Der Velden, Yme
Source	Medline; PMC
abstract	BACKGROUND: 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 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. RESULTS: To 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. CONCLUSIONS: Extrapolating 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.
has issue date	2017-09-05(xsd:dateTime)
bibo:doi	10.1186/s12977-017-0367-0
bibo:pmid	28870251
has license	cc-by
sha1sum (hex)	aa5c3ba1a343c13446ce37073c2e03cf91032f28
schema:url	https://doi.org/10.1186/s12977-017-0367-0
resource representing a document's title	HIV-1 tolerates changes in A-count in a small segment of the pol gene
has PubMed Central identifier	PMC5583962
has PubMed identifier	28870251
schema:publication	Retrovirology
resource representing a document's body	covid:aa5c3ba1a343c13446ce37073c2e03cf91032f28#body_text
is schema:about of	named entity 'SMALL' named entity 'segment' named entity 'RNA' named entity 'biased' named entity 'manipulated' named entity 'HIV-1' named entity 'RNA GENOME' named entity 'POL GENE' named entity 'CHANGES' named entity 'TO EXPLAIN' named entity 'BUT' named entity 'FAR' named entity 'KNOWN' named entity 'MASSIVE' named entity 'REPLICATION' named entity 'SEQUENCE MOTIFS' named entity 'RESULTING IN' named entity 'APPROACH' named entity 'AFFECTED' named entity 'PHENOMENON' named entity 'ATTEMPT' named entity 'SMALL' named entity 'HIV-1 RNA' named entity 'MUTANTS' named entity 'PRESENT' named entity 'BACKGROUND' named entity 'NUCLEOTIDE' named entity 'BIASED' named entity 'HIV-1' named entity 'SEGMENT' named entity 'COUNT' named entity 'IMPAIRED' named entity 'RESERVATION' named entity 'HIV-1' named entity 'DECREASE' named entity 'TO INCREASE' named entity 'FORWARD' named entity 'HAVE' named entity 'GENE SEGMENT' named entity 'COUNT' named entity 'UNKNOWN SEQUENCE' named entity 'LIKELIHOOD' named entity 'COMPOSITION' named entity 'POLYMERASE' named entity 'STRIKING' named entity 'VIRUS' named entity 'REASON FOR' covid:arg/aa5c3ba1a343c13446ce37073c2e03cf91032f28 named entity 'striking' named entity 'gene' named entity 'likelihood' named entity 'genome' named entity 'HIV-1' named entity 'mutants' named entity 'RNA' named entity 'genome' named entity 'RPMI 1640' named entity 'mutagenesis' named entity 'lymphocytes' named entity 'viral genome' named entity 'codon' named entity 'Gly' named entity 'virus' named entity 'phylogenetic analysis' named entity 'virus' named entity 'Gag protein' named entity 'HIV-1' named entity 'HIV' named entity 'infectivity' named entity 'codons' named entity 'HIV-1' named entity 'HIV-1 genome' named entity 'virus' named entity 'HIV-1' named entity 'naturally occurring' named entity 'viral proteome' named entity 'RNA'

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