Genetic and biological characterization of feline foamy virus isolated from a leopard cat (Prionailurus bengalensis) in Vietnam

Foamy viruses have been isolated from various mammals and show long-term co-speciation with their hosts. However, the frequent inter-species transmission of feline foamy viruses (FFVs) from domestic cats to wild cats across genera has been reported. Because infectious molecular clones of FFVs derived from wild cats have not been available, whether there are specific characteristics enabling FFVs to adapt to the new host species is still unknown. Here, we obtained the complete genome sequences of two FFV isolates (strains NV138 and SV201) from leopard cats (Prionailurus bengalensis) in Vietnam and constructed an infectious molecular clone, named pLC960, from strain NV138. The growth kinetics of the virus derived from pLC960 were comparable to those of other FFVs derived from domestic cats. Phylogenetic analysis revealed that these two FFVs from leopard cats are clustered in the same clade as FFVs from domestic cats in Vietnam. Comparisons of the amino acid sequences of Env and Bet proteins showed more than 97% identity among samples and no specific amino acid substitutions between FFVs from domestic cats and ones from leopard cats. These results indicate the absence of genetic constraint of FFVs for interspecies transmission from domestic cats to leopard cats

Monotreme-Specific Conserved Putative Proteins Derived from Retroviral Reverse Transcriptase

Endogenous retroviruses (ERVs) have played an essential role in the evolution of mammals. ERV-derived genes are reported in the therians, many of which are involved in placental development; however, the contribution of the ERV-derived genes in monotremes, which are oviparous mammals, remains to be uncovered. Here, we conducted a comprehensive search for possible ERV-derived genes in platypus and echidna genomes and identified three reverse transcriptase-like genes named RTOM1, RTOM2, and RTOM3 clustered in the GRIP2 intron. Comparative genomic analyses revealed that RTOM1, RTOM2, and RTOM3 are strongly conserved and are under purifying selection between these species. These could be generated by tandem duplications before the divergence of platypus and echidna. All RTOM transcripts were specifically expressed in the testis, possibly suggesting their physiological importance. This is the first study reporting monotreme-specific de novo gene candidates derived from ERVs, which provides new insights into the unique evolution of monotremes

An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation

哺乳類のゲノムに隠された古代ウイルス --古代ウイルス特有の遺伝子制御機構の発見--. 京都大学プレスリリース. 2021-11-10.[Background] Retroviruses utilize multiple unique RNA elements to control RNA processing and translation. However, it is unclear what functional RNA elements are present in endogenous retroviruses (ERVs). Gene co-option from ERVs sometimes entails the conservation of viral cis-elements required for gene expression, which might reveal the RNA regulation in ERVs. [Results] Here, we characterized an RNA element found in ERVs consisting of three specific sequence motifs, called SPRE. The SPRE-like elements were found in different ERV families but not in any exogenous viral sequences examined. We observed more than a thousand of copies of the SPRE-like elements in several mammalian genomes; in human and marmoset genomes, they overlapped with lineage-specific ERVs. SPRE was originally found in human syncytin-1 and syncytin-2. Indeed, several mammalian syncytin genes: mac-syncytin-3 of macaque, syncytin-Ten1 of tenrec, and syncytin-Car1 of Carnivora, contained the SPRE-like elements. A reporter assay revealed that the enhancement of gene expression by SPRE depended on the reporter genes. Mutation of SPRE impaired the wild-type syncytin-2 expression while the same mutation did not affect codon-optimized syncytin-2, suggesting that SPRE activity depends on the coding sequence. [Conclusions] These results indicate multiple independent invasions of various mammalian genomes by retroviruses harboring SPRE-like elements. Functional SPRE-like elements are found in several syncytin genes derived from these retroviruses. This element may facilitate the expression of viral genes, which were suppressed due to inefficient codon frequency or repressive elements within the coding sequences. These findings provide new insights into the long-term evolution of RNA elements and molecular mechanisms of gene expression in retroviruses

Characterization of ferret Pit1 as a receptor of feline leukemia virus subgroup B

Feline leukemia virus (FeLV) is a retrovirus that causes immune suppression and immunodeficiency, leading to opportunistic infections and leukemia/lymphoma in cats. Today, a variety of domestic mammals are kept in houses, and it is important to evaluate the possibility of interspecies transmission of FeLV. In this study, we assessed the infectivity of FeLV-B in ferrets that belong to Mustelidae. By pseudotype virus infection assay, we revealed that a ferret cell line, Mpf cells, is resistant to FeLV-B infection. The mRNA expression level of the FeLV-B receptor, Pit-1, was approximately half that of cat FEA cells in ferret Mpf cells. There was no significant difference in receptor usage between ferret’s and cat’s Pit1. These data may indicate the presence of the post-transcriptional modification and/or the restriction factor(s) against the FeLV-B infection in ferrets

Potentially reduced fusogenicity of syncytin‐2 in New World monkeys

Syncytin-2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys. It is known that syncytin-2 is conserved between apes and Old World monkeys, suggesting its functional importance; however, syncytin-2 of common marmosets (Callithrix jacchus) exhibits lower fusogenic activity than those of humans and Old World monkeys in human cell lines. To obtain insight into the functional diversity of syncytin-2 genes in primates, we examined the syncytin-2 gene in New World monkeys. We experimentally evaluated the cell fusion ability of syncytin-2 in humans, C. jacchus, and tufted capuchins (Sapajus apella). We found that the cell fusion ability of S. apella was lower than that of human syncytin-2. Chimeric syncytin-2 constructs revealed that the amino acid differences in the surface unit of S. apella syncytin-2 were responsible for the weak cell fusion activity. In addition, genomic sequence analyses of syncytin-2 revealed that the open reading frames (ORFs) of syncytin-2 were highly conserved in 7 apes and 22 Old World monkeys; however, the syncytin-2 ORFs of three out of 12 New World monkey species were truncated. Our results suggest that syncytin-2 in several New World monkeys may be of less importance than in Old World monkeys and apes, and other syncytin-like genes may be required for placental development in various New World monkey species

Aire suppresses CTLA-4 expression from the thymic stroma to control autoimmunity

Impaired production of thymic regulatory T cells (Tregs) is implicated in the development of Aire-dependent autoimmunity. Because Tregs require agonistic T cell receptor stimuli by self-antigens to develop, reduced expression of self-antigens from medullary thymic epithelial cells (mTECs) has been considered to play a major role in the reduced Treg production in Aire deficiency. Here, we show that mTECs abnormally express co-inhibitory receptor CTLA-4 if Aire is non-functional. Upon binding with CD80/CD86 ligands expressed on thymic dendritic cells (DCs), the ectopically expressed CTLA-4 from Aire-deficient mTECs removes the CD80/CD86 ligands from the DCs. This attenuates the ability of DCs to provide co-stimulatory signals and to present self-antigens transferred from mTECs, both of which are required for Treg production. Accordingly, impaired production of Tregs and organ-specific autoimmunity in Aire-deficient mice are rescued by the depletion of CTLA-4 expression from mTECs. Our studies illuminate the significance of mTEC-DC interaction coordinated by Aire for the establishment of thymic tolerance

PHENOTYPIC ANALYSIS OF MICE DEFICIENT FOR Ly6C1/Ly6C2

Ly6C comprises two homologous components of Ly6C1 and Ly6C2, and the expression of either of the Ly6C molecules defines unique functional subsets of monocytes. Ly6C is also expressed by other immune cell types, including Aire-expressing medullary thymic epithelial cells. Because the role of Ly6C expression in determining the functional subsets remains unclear, we generated mice deficient for both Ly6C1 and Ly6C2 with CRISPR-Cas9–mediated deletion. Mice deficient for Ly6C1/Ly6C2 showed no major alterations in the subsets and function of monocyte and other immune cells, including the cells involved in the dextran sulfate sodium salt–induced colitis model. By generating the mice deficient for Ly6C1 alone, we have also investigated the expression pattern of Ly6C1 and Ly6C2 in immune cells. Except for medullary thymic epithelial cells and CD4 single-positive T cells, immune cells predominantly expressed Ly6C2. Thus, despite the importance as a marker with a unique differential expression pattern, the Ly6C molecules have no major impact on determining the functional subsets and maintaining immune homeostasis