scholarly journals DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics

2018 ◽  
Vol 92 (18) ◽  
Author(s):  
Samantha James ◽  
Damien Donato ◽  
Jean-François Pouliquen ◽  
Manuel Ruiz-García ◽  
Anne Lavergne ◽  
...  
Keyword(s):  
Amino Acid ◽  
Host Range ◽  
Dna Polymerase ◽  
New World ◽  
Phylogenetic Analyses ◽  
Primate Species ◽  
New World Monkeys ◽  
Polymerase Gene ◽  
Evolutionary Processes ◽  
Genus Level

ABSTRACTOver the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to theCytomegalovirusgenus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCEInvestigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.

scholarly journals A novel form of oxytocin in New World monkeys

2011 ◽  
Vol 7 (4) ◽  
pp. 584-587 ◽  
Author(s):  
Alex G. Lee ◽  
David R. Cool ◽  
William C. Grunwald ◽  
Donald E. Neal ◽  
Christine L. Buckmaster ◽  
...  
Keyword(s):  
Amino Acid ◽  
Squirrel Monkey ◽  
Arginine Vasopressin ◽  
Functional Significance ◽  
New World ◽  
Amino Acid Position ◽  
Peptide Sequence ◽  
Saimiri Sciureus ◽  
New World Monkeys ◽  
Multiple Species

Oxytocin is widely believed to be present and structurally identical in all placental mammals. Here, we report that multiple species of New World monkeys possess a novel form of oxytocin, [P8] oxytocin. This mutation arises from a substitution of a leucine to a proline in amino acid position 8. Further analysis of this mutation in Saimiri sciureus (squirrel monkey) indicates that [P8] oxytocin is transcribed and translated properly. This mutation is specific to oxytocin, as the peptide sequence for arginine vasopressin, a structurally related nonapeptide, is unaltered. These findings dispel the notion that all placental mammals possess a ‘universal’ oxytocin sequence, and highlight the need for research on the functional significance of this novel nonapeptide in New World monkeys.

scholarly journals Evolutionary pattern in the OXT-OXTR system in primates: Coevolution and positive selection footprints

2014 ◽  
Vol 112 (1) ◽  
pp. 88-93 ◽  
Author(s):  
Pedro Vargas-Pinilla ◽  
Vanessa Rodrigues Paixão-Côrtes ◽  
Pamela Paré ◽  
Luciana Tovo-Rodrigues ◽  
Carlos Meton de Alencar Gadelha Vieira ◽  
...  
Keyword(s):  
Positive Selection ◽  
New World ◽  
World Monkey ◽  
Acid Sites ◽  
Cross Reactivity ◽  
Receptor Internalization ◽  
Primate Species ◽  
New World Monkeys ◽  
Evolutionary Pattern ◽  
Wide Range

Oxytocin is a nonapeptide involved in a wide range of physiologic and behavioral functions. Until recently, it was believed that an unmodified oxytocin sequence was present in all placental mammals. This study analyzed oxytocin (OXT) in 29 primate species and the oxytocin receptor (OXTR) in 21 of these species. We report here three novel OXT forms in the New World monkeys, as well as a more extensive distribution of a previously described variant (Leu8Pro). In structural terms, these OXTs share the same three low-energy conformations in solution during molecular dynamic simulations, with subtle differences in their side chains. A consistent signal of positive selection was detected in the Cebidae family, and OXT position 8 showed a statistically significant (P= 0.013) correlation with litter size. Several OXTR changes were identified, some of them promoting gain or loss of putative phosphorylation sites, with possible consequences for receptor internalization and desensitization. OXTR amino acid sites are under positive selection, and intramolecular and intermolecular coevolutionary processes with OXT were also detected. We suggest that some New World monkey OXT-OXTR forms can be correlated to male parental care through the increase of cross-reactivity with its correlated vasopressin system.

scholarly journals Isolation, Identification and Characterization of a Novel Megalocytivirus from Cultured Tilapia (Oreochromis spp.) from Southern California, USA

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3524
Author(s):  
Khalid Shahin ◽  
Kuttichantran Subramaniam ◽  
Alvin C. Camus ◽  
Zeinab Yazdi ◽  
Susan Yun ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Southern California ◽  
Phylogenetic Analyses ◽  
Head Kidney ◽  
Cell Culture Supernatant ◽  
Post Inoculation ◽  
Polymerase Gene ◽  
European Chub ◽  
Dna Polymerase Gene ◽  
Pcr Targeting

In spring 2019, diseased four-month-old tilapia (Oreochromis spp.) from an aquaculture farm in Southern California, USA were received for diagnostic evaluation with signs of lethargy, anorexia, abnormal swimming, and low-level mortalities. At necropsy, non-specific external lesions were noted including fin erosion, cutaneous melanosis, gill pallor, and coelomic distension. Internal changes included ascites, hepatomegaly, renomegaly, splenomegaly, and multifocal yellow-white nodules in the spleen and kidney. Cultures of spleen and kidney produced bacterial colonies identified as Francisella orientalis. Homogenized samples of gill, brain, liver, spleen, and kidney inoculated onto Mozambique tilapia brain cells (OmB) developed cytopathic effects, characterized by rounding of cells and detaching from the monolayer 6–10 days post-inoculation at 25 °C. Transmission electron microscopy revealed 115.4 ± 5.8 nm icosahedral virions with dense central cores in the cytoplasm of OmB cells. A consensus PCR, targeting the DNA polymerase gene of large double-stranded DNA viruses, performed on cell culture supernatant yielded a sequence consistent with an iridovirus. Phylogenetic analyses based on the concatenated full length major capsid protein and DNA polymerase gene sequences supported the tilapia virus as a novel species within the genus Megalocytivirus, most closely related to scale drop disease virus and European chub iridovirus. An intracoelomic injection challenge in Nile tilapia (O. niloticus) fingerlings resulted in 39% mortality after 16 days. Histopathology revealed necrosis of head kidney and splenic hematopoietic tissues.

scholarly journals Characterization of the DNA polymerase gene of varicella-zoster viruses resistant to acyclovir

2001 ◽  
Vol 82 (11) ◽  
pp. 2761-2765 ◽  
Author(s):  
Tomoko Kamiyama ◽  
Masahiko Kurokawa ◽  
Kimiyasu Shiraki
Keyword(s):  
Amino Acid ◽  
Dna Polymerase ◽  
Sequence Similarity ◽  
Polymerase Gene ◽  
Varicella Zoster ◽  
Dna Polymerase Gene ◽  
Simplex Virus ◽  
Polymerase Mutants ◽  
Hsv 1

The nucleotide changes of the DNA polymerase gene and the susceptibility of acyclovir (ACV)-resistant varicella-zoster virus (VZV) mutants to anti-herpetic drugs were determined and compared to those of herpes simplex virus type 1 (HSV-1) mutants. The seven ACV-resistant VZV mutants were classified into three groups, N779S, G805C and V855M, according to the sequences of their DNA polymerase genes. The amino acid substitutions N779S and G805C were identical in position to the N815S and G814C mutations in the HSV-1 DNA polymerase mutants, respectively, and the V855M amino acid substitution was similar to the HSV-1 V892M mutation. All three groups of VZV mutants were susceptible to ACV, phosphonoacetic acid, vidarabine and aphidicolin, at levels similar to those seen with the respective HSV-1 mutants, except for subtle differences that were due possibly to the non-conserved regions in their sequences. Although both the HSV-1 and the VZV DNA polymerase genes show 53% sequence similarity, both viruses essentially show a similar biochemical behaviour.

scholarly journals Identification of Postentry Restrictions to Mason-Pfizer Monkey Virus Infection in New World Monkey Cells

2008 ◽  
Vol 82 (22) ◽  
pp. 11140-11151 ◽  
Author(s):  
William E. Diehl ◽  
Elizabeth Stansell ◽  
Shari M. Kaiser ◽  
Michael Emerman ◽  
Eric Hunter
Keyword(s):  
Cell Lines ◽  
New World ◽  
Rhesus Macaques ◽  
World Monkey ◽  
Resistant Cell Line ◽  
Spider Monkey ◽  
Primate Species ◽  
New World Monkeys ◽  
Old World ◽  
New World Monkey

ABSTRACT TRIM5α has been shown to be a major postentry determinant of the host range for gammaretroviruses and lentiviruses and, more recently, spumaviruses. However, the restrictive potential of TRIM5α against other retroviruses has been largely unexplored. We sought to determine whether or not Mason-Pfizer monkey virus (M-PMV), a prototype betaretrovirus isolated from rhesus macaques, was sensitive to restriction by TRIM5α. Cell lines from both Old World and New World primate species were screened for their susceptibility to infection by vesicular stomatitis virus G protein pseudotyped M-PMV. All of the cell lines tested that were established from Old World primates were found to be susceptible to M-PMV infection. However, fibroblasts established from three New World monkey species specifically resisted infection by this virus. Exogenously expressing TRIM5α from either tamarin or squirrel monkeys in permissive cell lines resulted in a block to M-PMV infection. Restriction in the resistant cell line of spider monkey origin was determined to occur at a postentry stage. However, spider monkey TRIM5α expression in permissive cells failed to restrict M-PMV infection, and interference with endogenous TRIM5α in the spider monkey fibroblasts failed to relieve the block to infectivity. Our results demonstrate that TRIM5α specificity extends to betaretroviruses and suggest that New World monkeys have evolved additional mechanisms to restrict the infection of at least one primate betaretrovirus.

Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of Anticarsia gemmatalis nucleopolyhedrovirus

2005 ◽  
Vol 110 (1-2) ◽  
pp. 99-109 ◽  
Author(s):  
Caren Cristina Dalmolin ◽  
Felipe R. da Silva ◽  
Luciane V. Mello ◽  
Daniel J. Rigden ◽  
Maria Elita B. Castro
Keyword(s):  
Nucleotide Sequence ◽  
Dna Polymerase ◽  
Phylogenetic Analyses ◽  
Anticarsia Gemmatalis ◽  
Polymerase Gene ◽  
Dna Polymerase Gene

scholarly journals Phaeoviral Infections Are Present in Macrocystis, Ecklonia and Undaria (Laminariales) and Are Influenced by Wave Exposure in Ectocarpales

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 410 ◽  
Author(s):  
Dean McKeown ◽  
Joanna Schroeder ◽  
Kim Stevens ◽  
Akira Peters ◽  
Claudio Sáez ◽  
...  
Keyword(s):  
South America ◽  
Host Range ◽  
Dna Polymerase ◽  
Major Capsid Protein ◽  
Undaria Pinnatifida ◽  
Phylogenetic Analyses ◽  
Brown Macroalgae ◽  
Common Multiple ◽  
Ecklonia Maxima ◽  
Natural Hosts

Two sister orders of the brown macroalgae (class Phaeophyceae), the morphologically complex Laminariales (commonly referred to as kelp) and the morphologically simple Ectocarpales are natural hosts for the dsDNA phaeoviruses (family Phycodnaviridae) that persist as proviruses in the genomes of their hosts. We have previously shown that the major capsid protein (MCP) and DNA polymerase concatenated gene phylogeny splits phaeoviruses into two subgroups, A and B (both infecting Ectocarpales), while MCP-based phylogeny suggests that the kelp phaeoviruses form a distinct third subgroup C. Here we used MCP to better understand the host range of phaeoviruses by screening a further 96 and 909 samples representing 11 and 3 species of kelp and Ectocarpales, respectively. Sporophyte kelp samples were collected from their various natural coastal habitats spanning five continents: Africa, Asia, Australia, Europe, and South America. Our phylogenetic analyses showed that while most of the kelp phaeoviruses, including one from Macrocystispyrifera, belonged to the previously designated subgroup C, new lineages of Phaeovirus in 3 kelp species, Ecklonia maxima, Ecklonia radiata, Undaria pinnatifida, grouped instead with subgroup A. In addition, we observed a prevalence of 26% and 63% in kelp and Ectocarpales, respectively. Although not common, multiple phaeoviral infections per individual were observed, with the Ectocarpales having both intra- and inter-subgroup phaeoviral infections. Only intra-subgroup phaeoviral infections were observed in kelp. Furthermore, prevalence of phaeoviral infections within the Ectocarpales is also linked to their exposure to waves. We conclude that phaeoviral infection is a widely occurring phenomenon in both lineages, and that phaeoviruses have diversified with their hosts at least since the divergence of the Laminariales and Ectocarpales.

scholarly journals Possible changes in fidelity of DNA polymerase δ in ancestral mammals

2020 ◽  
Author(s):  
Kazutaka Katoh ◽  
Naoyuki Iwabe ◽  
Takashi Miyata
Keyword(s):  
Amino Acid ◽  
Dna Polymerase ◽  
Phylogenetic Analyses ◽  
Amino Acid Level ◽  
Amino Acid Substitutions ◽  
Dna Polymerase Δ ◽  
Time Period ◽  
Mammalian Lineage ◽  
Exonuclease Domain

AbstractDNA polymerase δ (polδ) is one of the major DNA polymerases that replicate chromosomal genomes in eukaryotes. Given the essential role of this protein, its phylogenetic tree was expected to reflect the relationship between taxa, like many other essential proteins. However, the tree of the catalytic subunit of polδ showed an unexpectedly strong heterogeneity among vertebrate lineages in evolutionary rate at the amino acid level, suggesting unusual amino acid substitutions specifically in the ancestral mammalian lineage. Structural and phylogenetic analyses were used to pinpoint where and when these amino acid substitutions occurred: around the 3′-5′ exonuclease domain in later mammal ancestry, after the split between monotremes and therians. The 3′-5′ exonuclease domain of this protein is known to have an impact on the fidelity of replication. Based on these observations, we explored the possibility that the amino acid substitutions we identified in polδ affected the mutation rate of entire chromosomal genomes in this time period.

scholarly journals Isolation and phylogeny of endogenous retrovirus sequences belonging to the HERV-W family in primates

1999 ◽  
Vol 80 (10) ◽  
pp. 2613-2619 ◽  
Author(s):  
Heui-Soo Kim ◽  
Osamu Takenaka ◽  
Timothy J. Crow
Keyword(s):  
Multiple Sclerosis ◽  
New World ◽  
Parallel Evolution ◽  
Endogenous Retrovirus ◽  
Primate Species ◽  
Human Endogenous Retrovirus ◽  
New World Monkeys ◽  
Old World Monkeys ◽  
Gene Sequences ◽  
Old World

An investigation was undertaken of primate pol gene sequences from a novel endogenous retrovirus family, ERV-W, related to a new human endogenous retrovirus family (HERV-W) that includes multiple sclerosis-associated retrovirus (MSRV) sequences identified in particles recovered from monocyte cultures from patients with multiple sclerosis. The pol gene sequences of the ERV-W family were detected in hominoids and Old World monkeys, but not in New World monkeys, whereas ERV-W long terminal repeat-like elements were detected in all primates (hominoids, Old World monkeys and New World monkeys). Thirty-two pol gene sequences from hominoids and Old World monkeys showed a high degree of sequence identity to MSRV and other HERV-W sequences. Phylogenetic analysis indicated close relationships of pol gene sequences across primate species. The analysis suggests that the ERV-W family has evolved independently but in constrained patterns (‘parallel evolution’) in different primate species, including man. The ratio of synonymous to non- synonymous substitutions indicated that negative selective pressure is acting on CHW1-1 from chimpanzee, HBW6-6 from baboon and HWX5 from man, sequences that have no disruption by point mutation or insertions/deletions. Therefore, these pol gene sequences could be associated with an active provirus in primates. The findings indicate that the ERV-W family has continued to evolve in the course of the primate radiation and may include members with a capacity to influence gene function and possibly cause disease.

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