How old is the immunodeficiency virus?

Eigen, Manfred; Nieselt-Struwe, Katja

doi:10.1097/00002030-199001001-00014

Cited by 37 publications

(18 citation statements)

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“…A particular mutation that appears to occur very frequently may be either neutral or, if it involves a ''strategic'' position, deleterious, or under certain environmental changes, such as those produced by the immune response of the host, it may be advantageous for the virus. These situations cause quite dramatic differences for different viruses, as is known for polio virus and HIV (15). The equivalent importance of m and Q m is obvious from the symmetric condition m Q m Ͼ 1.…”

Section: (Ii) the Error Threshold Is Not Solely Determined By The Avementioning

confidence: 99%

Error catastrophe and antiviral strategy

Eigen

2002

Proc. Natl. Acad. Sci. U.S.A.

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Section: (Ii) the Error Threshold Is Not Solely Determined By The Avementioning

confidence: 99%

Error catastrophe and antiviral strategy

Eigen

2002

Proc. Natl. Acad. Sci. U.S.A.

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317

256

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“…The mutational spectra of in vitro polymerisation [1][2][3][4][5][6][7][8][9] for DNA polymerases belonging to families found in at least two of the three living kingdoms [10] are considered here as relevant with respect to a primordial polymerase; we will not take into account DNA polymerases ß, as they are family X DNA polymerases so far only found among eukaryotes [11], and HIV reverse transcriptases, which emerged very 'late' in evolution [12].…”

Section: Assumptionsmentioning

confidence: 99%

Chain termination codons and polymerase‐induced frameshift mutations

Jestin

Kempf

1997

FEBS Letters

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The consensus sequence for single-base deletions in non-reiterated runs during in vitro DNA-dependent DNA polymerisation is refined using data available in the literature. This leads to the observation that chain termination codons are hotspots for single-base deletions. The evolutionary implications are discussed in two models which differ in whether polymerases evolved while the genetic code emerged or after the genetic code was fixed. A possible answer to the question 'Why are stop codons just what they are?' is suggested.© 1997 Federation of European Biochemical Societies.Key words: Genetic code; Stop codon; Deletion; Polymerase AssumptionsThe mutational spectra of in vitro polymerisation [1-9] for DNA polymerases belonging to families found in at least two of the three living kingdoms [10] are considered here as relevant with respect to a primordial polymerase; we will not take into account DNA polymerases ß, as they are family X DNA polymerases so far only found among eukaryotes [11], and HIV reverse transcriptases, which emerged very 'late' in evolution [12].As it is believed that RNA preceded DNA in evolution [13], data for RNA replicases would be more relevant but are not available; recent evidence shows, however, that DNA and RNA replicases are very closely related [14][15][16]: a single substitution of a hydroxyl group by a hydrogen atom in the Y639F mutant of T7 RNA polymerase allows a DNA replicase to function as a RNA replicase [17], and a single mutation confers on Moloney murine leukaemia virus reverse transcriptase the ability to replicate RNA [18]; we also note that Escherichia coli DNA polymerase I is an accurate RNA-dependent DNA polymerase [19]. Polymerase errorsPolymerase-induced mutations are mainly substitutions and frameshifts [1][2][3][4][5][6][7]. For the Klenow polymerase domain [1], which has no nuclease domain, as can be assumed for a primordial polymerase, the frameshift error rate is about half the substitution error rate: frameshift mutations therefore represent a significant proportion of the mutations in such systems. Frameshifts result mostly from deletions and additions of one base [1][2][3][4][5]. Crucially, these are highly deleterious by preventing translation in the correct reading frame of the codons »Corresponding author. Fax: (44) (1223) 402 140. E-mail: jlj@mrc-lmb.cam.ac.uk downstream of the mutation. Frameshifts occurring in directly repeated and palindromic sequences [8] will be addressed in the discussion. Here, we will focus on frameshifts in non-reiterated runs, where single-base deletions occur far more frequently than single-base additions [1,2,4,7]. Additions will therefore be neglected in the following. For polymerases with and without nuclease domains, the data indicate no significant differences in the consensus sequence for single-base deletions in non-reiterated runs. It has been defined as YR [1], TTR [9], YTG [6] and TR [8]. Using the current data [1-9] we here refine it as YTRV (V = C, A or G; Table 1). These singlebase deletions are found to...

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“…While the description of this diagram is straightforward if sequences consist only of purines and pyrimidines, it gets difficult if more complex alphabets (nucleic acids, amino acids) are used (7). Statistical geometr y in sequence space has been successfully applied to study the evolution of tRNAs (8) or HIV (9).…”

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confidence: 99%

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment

Strimmer¹,

Haeseler²

1997

Proc. Natl. Acad. Sci. U.S.A.

847

684

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We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three fully resolved tree topologies that can be computed for four sequences. The three likelihoods are represented as one point inside an equilateral triangle. The triangle is partitioned in different regions. One region represents star-like evolution, three regions represent a well-resolved phylogeny, and three regions ref lect the situation where it is difficult to distinguish between two of the three trees. The location of the likelihoods in the triangle defines the mode of sequence evolution. If n sequences are analyzed, then the likelihoods for each subset of four sequences are mapped onto the triangle. The resulting distribution of points shows whether the data are suitable for a phylogenetic reconstruction or not.

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How old is the immunodeficiency virus?

Cited by 37 publications

References 0 publications

Error catastrophe and antiviral strategy

Error catastrophe and antiviral strategy

Chain termination codons and polymerase‐induced frameshift mutations

Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment

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