Edited by John M. Coffin, Tufts University School of Medicine, Boston, MA, and approved February 13, 2007 (received for review January 17, 2007)
Lentiviral genome organizations. The genome organization of the consensus RELIK provirus is shown in comparison to representative genome organizations of other lentiviral subgroups: equine (equine infectious anemia virus, EIAV), feline (feline immunodeficiency virus, FIV), bovine (bovine immunodeficiency virus, BIV), caprine/ovine (caprine arthritis–encephalitis virus, CAEV; ovine maedi–visna virus, OMVV), and primate lineages. Most primate lineages lack a vpu gene.
Alignment of the putative RELIK Tat protein with the Tat proteins of other lentiviruses. Numbers refer to the relative positions aligned. Boxes denote identical amino acid residues, and bold type indicates residues with similar properties. Lentiviral Rev proteins share little sequence similarity, but we did identify putative nuclear localization and nuclear export signals (34), which are underlined in SI Fig. 5.
Phylogenetic relationships of RELIK to other retroviruses. (a) Phylogeny of RELIK and other lentiviruses together with a sample of nonlentiviral exogenous retroviruses, rooted on BLV, HTLV1, and HTLV2. Support for the ML trees was assessed via 1,000 nonparametric bootstrap replicates, and posterior clade probabilities were assessed for the Bayesian phylogeny. Both support indices are indicated as values out of 100, with posterior clade probabilities indicated above the branches and bootstrap scores below. Branches with posterior probabilities <95% were collapsed. The RELIK sequences are indicated by their accession numbers. (b) Unrooted phylogeny showing the relationships of the lentiviruses. Bootstrap scores and Bayesian posterior probabilities are indicated to the left and right of the forward slash, respectively, and nodes with only 100 indicated showed maximal support under both measures.
Schematic of the three segmental duplications used for dating RELIK insertions. Open boxes show RELIK LTRs and the location of the single short interspersed nuclear element insertion, and flanking sequences are indicated by thinner lines. Indels between the sequences are represented by solid triangles, with the number of inserted/deleted bases involved below. Thirty bases of flanking sequences are shown for each segmentally duplicated pair. Percentage divergence was calculated by using the GTR model with all parameters estimated from the data.
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Katzourakis et al. 10.1073/pnas.0700471104. |
Fig. 5. The RELIK consensus sequence. The inverted repeats at the ends of both LTRs are highlighted in light gray with the putative promoter and polyadenylation signals indicated in bold type. Regions of nucleic acid secondary structure, the slippery sequence at the 5' end of pol, and the PPT and P.B.S. are highlighted in dark gray. The locations of the proteins encoded by the gag, pol and env genes were determined by homology to the HIV-1 reference sequence HXB2 (1), by searches against the pFAM database(2), or from alignments of retroviral envelope sequences (3). The identities of the two accessory genes were determined using the pFAM database (Tat) or from Pollard and Malim (4) (Rev). Some lentiviruses contain short Rev and Tat domains toward the 5' and 3' ends of the env gene respectively (see Fig. 1). The general lack of sequence similarity of these regions within the lentiviruses meant that it was not possible to determine whether or not RELIK encodes such domains. The consensus sequence contained one in-frame TGA stop-codon at position 2555 that has been removed from the figure. Analysis of the proviruses from which the RELIK consensus was derived indicated that some had CGA codons in this position. Thus this stop-codon most likely arose from independent, host-mediated mutation of a CG nucleotide hotspot (i.e., CGA-TGA) in many of the sequences.
1. Petropoulos C (1997) in Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor , NY), pp 757-805.
2. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al. (2006) Nucleic Acids Res 34:D247-D251.
3. Bénit L, Dessen P, Heidmann T (2001) J Virol 75:11709-11719.
4. Pollard VW, Malim MH (1998) Annu Rev Microbiol 52:491-532.
Fig. 6. Secondary structure motifs within the RELIK sequence. Secondary structures were predicted using the MFOLD thermodynamic folding algorithm (1), and assessed by comparison to well-characterized examples in other lentiviruses. (a) The putative TAR (transactivation responsive region) downstream of the viral promoter is a well-defined and consistently predicted two-finger structure similar to the TAR found in HIV-2 (2). (b) The putative RRE (Rev responsive element) contains a consistently predicted three-finger structure. The precise boundaries of the RRE are uncertain. (c) The predicted ribosomal frameshift site at the gag-pol junction comprises a simple 8bp stem loop downstream of a heptameric slippery sequence.
1. Zuker M, Mathews DH, Turner DH (1999) in RNA Biochemistry and Biotechnology, eds Barciszewski J, Clark BFC (Kluwer Academic).
2. Rabson AB, Graves BJ (1997) in Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor , NY), p 226.
Fig. 7. Nucleotide compositional bias across the first 6,000 bp of the coding regions of the consensus RELIK genome (Top), and the genomes of two other representative lentiviruses, EIAV (Middle) and FIV (Bottom). Biases were calculated using a sliding window of 500 nt and a step size of 100 nt.
Fig. 8. Alignment of the 5' 2500bp of the upper segmental duplication shown in Fig. 4. Flanking sequences are indicated in dark gray, LTRs in light gray and the SINE insertion in green. Transitions and transversions are shown in blue and red, respectively.
