The genome of the lizard Anolis carolinensis (the green anole) is the first nonavian reptilian genome sequenced. It offers a unique opportunity to comparatively examine the evolution of amniote genomes. We analyzed the abundance and diversity of non-LTR (long terminal repeat) retrotransposons in the anole using the Genome Parsing Suite. We found that the anole genome contains an extraordinary diversity of elements. We identified 46 families of elements representing five clades (L1, L2, CR1, RTE, and R4). Within most families, elements are very similar to each other suggesting that they have been inserted recently. The rarity of old elements suggests a high rate of turnover, the insertion of new elements being offset by the loss of element-containing loci. Consequently, non-LTR retrotransposons accumulate in the anole at a low rate and are found in low copy number. This pattern of diversity shows some striking similarity with the genome of teleostean fish but contrasts greatly with the low diversity and high copy number of mammalian L1 elements, suggesting a fundamental difference in the way mammals and nonmammalian vertebrates interact with their genomic parasites. The scarcity of divergent elements in anoles suggests that insertions have a deleterious effect and are eliminated by natural selection. We propose that the low abundance of non-LTR retrotransposons in the anole is related directly or indirectly to a higher rate of ectopic recombination in the anole relative to mammals.

Encephalomyocarditis virus and

Features of human rhinovirus (RV)-C virions that allow them to use novel cell receptors and evade immune responses are unknown. Unlike the RV-A+B, these isolates cannot be propagated in typical culture systems or grown for structure studies. Comparative sequencing, I-TASSER, MODELLER, ROBETTA, and refined alignment techniques led to a structural approximation for C15 virions, based on the extensive, resolved RV-A+B datasets. The model predicts all RV-C VP1 proteins are shorter by 21 residues relative to the RV-A, and 35 residues relative to the RV-B, effectively shaving the RV 5-fold plateau from the particle. There are major alterations in VP1 neutralizing epitopes and the structural determinants for ICAM-1 and LDLR receptors. The VP2 and VP3 elements are similar among all RV, but the loss of sequence “words” contributing Nim1ab has increased the apparent selective pressure among the RV-C to fix mutations elsewhere in the VP1, creating a possible compensatory epitope.

Cardiovirus Leader (L) proteins induce potent antihost inhibition of active cellular nucleocytoplasmic trafficking by triggering aberrant hyperphosphorylation of nuclear pore proteins (Nup). To achieve this, L binds protein RanGTPase (Ran), a key trafficking regulator, and diverts it into tertiary or quaternary complexes with required kinases. The activity of L is regulated by two phosphorylation events not required for Ran binding. Matched NMR studies on the unphosphorylated, singly, and doubly phosphorylated variants of Mengovirus L (L M ) show both modifications act together to partially stabilize a short internal α-helix comprising L M residues 43-46. This motif implies that ionic and Van der Waals forces contributed by phosphorylation help organize downstream residues 48-67 into a new interface. The full structure of L M as bound to Ran (unlabeled) and Ran (216 aa

The interactions between retroviruses and their hosts can be of a beneficial or detrimental nature. Some endogenous retroviruses are involved in development, while others cause disease. The Genome Parsing Suite (GPS) is a software tool to track and trace all Retroid agents in any sequenced genome (M. A. McClure et al., Genomics 85:512-523, 2005). Using the GPS, the retroviral content was assessed in four model teleost fish. Eleven new species of fish retroviruses are identified and characterized. The reverse transcriptase protein sequences were used to reconstruct a fish retrovirus phylogeny, thereby, significantly expanding the epsilonretrovirus family. Most of these novel retroviruses encode additional genes, some of which are homologous to cellular genes that would confer viral advantage. Although the fish divergence is much more ancient, retroviruses began infecting fish genomes approximately 4 million years ago.All genetic entities that encode the reverse transcriptase (RT) enzyme are referred to as retroids (22). The formal retroid classification includes endogenous and exogenous retroviruses, as well as pararetroviruses (large DNA viruses), retrotransposons with long terminal repeats (LTRs), retroposons that lack LTRs, retroplasmids, retrointrons, and retrons (20,21,43,44). This classification is based on the phylogeny of the RT protein sequence, the slowest evolving of the retroid gene components (30). In a global analysis of the retroid content of the genomes of the teleost fish Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback), and Tetraodon nigroviridis (green spotted pufferfish), we identified several new retroviruses (7). Here, we expand those studies, report the genomic details of 11 new fish retroviral species, and provide a reconstruction of the evolutionary history of sequenced fish retroviruses.In general, retroviruses are classified as alpha-, beta-, gamma-, delta-, and epsilonretroviruses, lentiviruses, and spumaviruses. The current characterization of known exogenous and endogenous fish retroviruses places them in the epsilon family (http: //www.ncbi.nlm.nih.gov/ICTVdb/) or between this group and the gammaretroviruses (36). To date, only three members of the epsilon family have been conclusively identified, i.e., walleye dermal sarcoma virus (WDSV) and the walleye epidermal hyperplasia viruses 1 and 2 (WEHV1 and WEHV2), and tentative members include perch hyperplasia virus and snakehead fish retrovirus (SnRV), (http://www.ncbi.nlm.nih.gov/ICTVdb/). Other fish retroviruses include the Atlantic salmon swim bladder sarcoma virus (SSSV) and zebrafish endogenous retrovirus (ZFERV) from D. rerio; both appear to fall between the gamma and epsilon families (36). Studied in less detail is the ERV_Tet species in T. nigroviridis (15), and the retrovirusstickleback (RV-stickleback), RV-brook trout, RV-freshwater houting, and RV-pufferfish retroviruses only identified by using PCR (17).WDSV is associated with the development of seasonal tumors in walleye and, along w...

Cardiovirus infections inhibit nucleocytoplasmic trafficking by Leader protein-induced phosphorylation of Phe/Gly-containing nucleoporins (Nups). Recombinant Leader from encephalomyocarditis virus, Theiler’s murine encephalomyelitis virus and Saffold virus target the same subset of Nups, including Nup62 and Nup98, but not Nup50. Reporter cell lines with fluorescence mCherry markers for M9, RS and classical SV40 import pathways, as well as the Crm1-mediated export pathway, all responded to transfection with the full panel of Leader proteins, showing consequent cessation of path-specific active import/export. For this to happen, the Nups had to be presented in the context of intact nuclear pores and exposed to cytoplasmic extracts. The Leader phosphorylation cascade was not effective against recombinant Nup proteins. The findings support a model of Leader-dependent Nup phosphorylation with the purpose of disrupting Nup-transportin interactions.

Human rhinoviruses of the RV-C species are recently discovered pathogens with greater clinical significance than isolates in the RV-A+B species. The RV-C cannot be propagated in typical culture systems; so much of the virology is necessarily derivative, relying on comparative genomics, relative to the better studied RV-A+B. We developed a bioinformatics-based structural model for a C15 isolate. The model showed the VP1–3 capsid proteins retain their fundamental cores relative to the RV-A+B, but conserved, internal RV-C residues affect the shape and charge of the VP1 hydrophobic pocket that confers antiviral drug susceptibility. When predictions of the model were tested in organ cultures or ALI systems with recombinant C15 virus, there was a resistance to capsid-binding drugs, including pleconaril, BTA-188, WIN56291, WIN52035 and WIN52084. Unique to all RV-C, the model predicts conserved amino acids within the pocket and capsid surface pore leading to the pocket may correlate with this activity.

The leader (L) and 2A proteins of cardioviruses are the primary antihost agents produced during infection. For encephalomyocarditis virus (EMCV), the prototype of the genus Cardiovirus, these proteins interact independently with key cellular partners to bring about inhibition of active nucleocytoplasmic trafficking and cap-dependent translation, respectively. L and 2A also bind each other and require this cooperation to achieve their effects during infection.