Evidence for endogenous retroviruses in human chemokine receptor gene introns: possible evolutionary inferences and biological roles

The human chemokine receptor (CKR) genes CCR2, CCR6, CCR7, CCR9, CCR10, CXCR4, and CXCR5 harbor one or two introns. CCR7, CCR9, CCR10, and CXCR5 introns, (but not CCR2, CCR6, and CXCR4 introns) encompass retrovirus-like inserts with the characteristics of SINEs (short interspersed nuclear elements) up to 300 nucleotides (nt) long. Other characteristic elements of the retroviral genome, such as long terminal repeats and gag, pol, and env genes, are lacking. The inserts likely derived from one (or more) of the following retroviruses: XA34 (NCBI GenBank Nucleotides, U29659), HERV-P-T47D (AF087913), ERV FTD (U27241), HERV-K (Y17832), HML6p (U86698), HERV-H/env60 (AJ289710), XA38 (U37066). Virus-like inserts are remarkably homogeneous in all CKR introns, with nt identities of about 80%. Percentages of nt identities between the CKR inserts and the corresponding viral sequences are also about 80%. With reference to the CKR sequence, the viral sequence aligns in some instances Plus/Plus (XA34, HML6p, HERV-H/env60, and XA38) and in other instances Plus/Minus (HERV-P-T47D, ERV FTD, and HERV-K). Some aspects of the evolution of retroviruses and CKRs as well as hypotheses on the biological significance of the SINE inserts are discussed

Viral sequence integration into introns of chemokine receptor genes

Viral DNA sequences are able to integrate into the non-coding DNA sections of the genome of human cells which have been infected, either spontaneously or experimentally. We have made a data-base search for integration events of non-endogenous viruses into the introns of chemokine receptor sequences. A BLAST search of all viral DNA sequences, using the intronic sequences as "Query," returned several significant alignments. However, due to the high reiteration rate of the non-coding sequences in the human genome, it became necessary to re-examine the individual alignments to verify whether the virus-flanking intronic sequence was really located in a chemokine receptor intron. We found only one unquestionable event of viral insertion of a section of a long terminal repeat of the murine leukemia virus within the first intron of the CC chemokine receptor 7 gene. Possible biological effects of such an insertion are discussed. Further experimental or clinical research could demonstrate the occurrence of other intronic viral insertions in human chemokine receptor genes

Mutation, selection and the amino acid hydropathic character: a study on receptor genes involved in immune and non-immune functions

In some mRNA sequences, namely those of formyl peptide receptors and chemokine CXC receptors 4, it has been observed that the second nucleotide (nt) of the coding triplets is significantly more highly conserved than the first nt and the correlation between the conservation indexes of the first two nt is positive and significantly higher than the "basic" correlation usually found between adjacent nt. A theoretical analysis demonstrated that random mutations in the first nt preserve hydrophobicity in 73 % of triplets coding for hydrophobic amino acids (aa) and hydrophilicity in 77 % of triplets coding for hydrophilic aa, while random mutations in the second nt preserve hydrophobicity in 18 % of triplets coding for hydrophobic aa and hydrophilicity in 53 % of triplets coding for hydrophilic aa. When the triplets which had changed their hydropathic aa coding character underwent a second random mutation in the previously unmutated first or second nt, an additional 11 % of the originally hydrophobic-coding triplets reverted to hydrophobicity and an additional 14 % of the originally hydrophilic-coding triplets reverted to hydrophilicity. This analysis provides a rationale for why a higher number of mutations in the second nt are presumably negatively selected and a number of double mutations in the first and second nt presumably are positively selected, in cases when a mutation in one of the two is not reverted

The HIV-1 Rev Binding Family of Proteins - The Dog Proteins as a Study Model

Various proteins that are required for the building of new complete human immunodeficiency type 1 virions (HIV-1) are coded by unspliced or partly spliced virus-derived mRNAs. HIV-1 has developed special strategies for moving these mRNAs to the cytoplasm to be translated. In the nucleus of the infected cell the virus-derived protein Regulator of expression of viral proteins (Rev) can bind both the viral intron-containing mRNAs and the cellular co-factor HIV-1 Rev binding protein (HRB) and this complex may be shuttled through the nuclear pores. HRB genes have been relatively well conserved during evolution, from Drosophila to humans. However, as a consequence of reading-frame shifts due to nt insertions/deletions, the protein products generated may differ considerably from the prototypal HRB protein, which comprises one Arf-GAP zinc finger domain, several Phenylalanine-Glycine (FG) motifs and four Asparagine-Proline-Phenylalanine (NPF) motifs. This variability is best exemplified by four HRB proteins of the dog, which are discussed here in more detail. The hypothesis is advanced that atypical HRB proteins may not be able to bind Rev and possibly have other, still undetermined, functions. Since the cellular co-factor HRB is essential for viral replication and spread but is not required for cell viability and main bodily functions, it might be an attractive candidate for anti-HIV-1 drug targeting

Mutation, selection, and functional repair in formyl peptide receptor genes: a view on the selection processes occurring in this gene subfamily

Formyl peptides (FPs) released by some bacteria are powerful chemoattractants and activators of granulocytes, monocytes, and macrophages, acting through the members of a subfamily of specific seven-transmembrane G-protein-coupled formyl peptide receptors (FPRs), which are expressed only in mammals. Upon stimulation, granulocytes chemotactically move towards sites of maximal FP concentration, and release different bactericidal lytic enzymes and reactive oxygen species (ROI). In some instances, such as ischemia/reperfusion, the proinflammatory mediators released by the injured tissues and the intestinal bacteria and endotoxins, which may permeate across the damaged mucosal barrier, prime the inflowing granulocytes for an enhanced ROI production, resulting in severe damage to the host tissues. In this investigation 16 representative FPR and FPR-like mRNAs were selected to study the pattern of mutation/conservation of the individual nucleotides (nt) in the coding sequences. Mutations occur in 56.7%, 46.4%, and 87.5 % of cases in the first, second, and third nt, respectively, of the coding triplets. A probabilistic analysis demonstrated a significant nonrandom linkage between mutations in the first and second nt. Furthermore, the triplets that are variously double-mutated in the first two nt code, on average, for more hydrophobic amino acids (AA) in the transmembrane segments and more hydrophilic AA in the external and intracytoplasmic segments, thus preserving the general structure of the receptor. The authors hypothesize that when in one of the first two nt a mutation leading to a nonfunctioning protein product occurred, the mutated gene was eventually eliminated; however, a second mutation occurring in the other previously unmutated nt may have led to a protein product that is compatible with functional activity, although mutated in one (noncritical) AA. Such double mutations effecting a "functional repair" have thus survived and are retained among the extant sequences. Moreover, the combined mutation of all three nt in coding triplets occurs with a significantly higher than random frequency and this finding may be interpreted in a similar way