Phylogenetic and geographical analysis of a retrovirus during the early stages of endogenous adaptation and exogenous spread in a new host DOI
Bonnie L. Quigley, Faye Wedrowicz, Fiona Hogan

et al.

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(11), P. 2626 - 2640

Published: Nov. 21, 2020

Most retroviral endogenization and host adaptation happened in the distant past, with opportunity to study these processes as they occurred lost time. An exception exists discovery that koala retrovirus (KoRV) has recently begun its into (Phascolarctos cinereus) genome. What makes this remarkable is fact Northern Australian koalas appear be undergoing one KoRV subtype (KoRV-A), while all subtypes (KoRV-A-I) coexist exogenously, Southern carry an exogenous virus. To understand distribution relationship of variants koalas, proviral envelope gene receptor binding domain was assessed across koala's natural range. Examination subtype-specific copy numbers per cell found KoRV-A integration levels were consistent endogenous incorporation Australia (southeast Queensland northeast New South Wales) revealing lower (suggestive incorporation) southern regions Wales Victoria). Phylogeographical analysis indicated several major distributed uniformly country, non-KoRV-A appeared have undergone lineage diversification geographically distinct regions. Further revealed a shift variant proportions southeast Wales, suggesting geographical region where transitions from being predominantly koalas. Collectively, findings advance both our understanding general.

Language: Английский

Origins and evolutionary consequences of ancient endogenous retroviruses DOI
Welkin E. Johnson

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(6), P. 355 - 370

Published: April 8, 2019

Language: Английский

Citations

323
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation DOI Creative Commons
Daniel Fuentes, Tomek Swigut, Joanna Wysocka

et al.

eLife, Journal Year: 2018, Volume and Issue: 7

Published: Aug. 2, 2018

Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers integrations typical TEs, coupled with sequence divergence within families, have made systematic interrogation the regulatory contributions TEs challenging. Here, we employ CARGO, our recent method CRISPR gRNA multiplexing, to facilitate targeting LTR5HS, an ape-specific class HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout human genome. We combine CARGO activation or interference to, respectively, induce silence LTR5HS en masse, demonstrate this system robustly targets vast majority insertions. Remarkably, activation/silencing associated reciprocal up- down-regulation hundreds genes. These effects require presence retroviral sequences, but occur over long genomic distances, consistent a pervasive function as embryonic enhancers apes.

Language: Английский

Citations

180
Endogenous Retroviruses as Modulators of Innate Immunity DOI Creative Commons
Eric Russ, Sergey Iordanskiy

Pathogens, Journal Year: 2023, Volume and Issue: 12(2), P. 162 - 162

Published: Jan. 19, 2023

Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% the genome and over course evolution, HERV underwent positive selection accrued mutations rendered them non-infectious; thereby, could co-opt into constructive roles with important biological functions. In past two decades, help advances sequencing technology, increasingly considered to be components innate immune response. While typically silenced, expression HERVs can induced response traumatic, toxic, infection-related stress, leading buildup viral transcripts under certain circumstances, proteins, including functionally active reverse transcriptase envelopes. The activity context based on functional effect four major components: (1) LTRs, (2) HERV-derived RNAs, (3) RNA:DNA duplexes cDNA, (4) proteins ribonucleoprotein complexes. this review, we will discuss implications all contexts relation immunity their association various pathological disease states.

Language: Английский

Citations

41
The depths of virus exaptation DOI
Eugene V. Koonin, Mart Krupovìč

Current Opinion in Virology, Journal Year: 2018, Volume and Issue: 31, P. 1 - 8

Published: July 30, 2018

Language: Английский

Citations

73
Helping koalas battle disease – Recent advances inChlamydiaand koala retrovirus (KoRV) disease understanding and treatment in koalas DOI Creative Commons
Bonnie L. Quigley, Peter Timms

FEMS Microbiology Reviews, Journal Year: 2020, Volume and Issue: 44(5), P. 583 - 605

Published: June 15, 2020

The iconic Australian marsupial, the koala (Phascolarctos cinereus), has suffered dramatic population declines as a result of habitat loss and fragmentation, disease, vehicle collision mortality, dog attacks, bushfires climate change. In 2012, koalas were officially declared vulnerable by government listed threatened species. response, research into diseases affecting expanded rapidly. two major pathogens are Chlamydia pecorum, leading to chlamydial disease retrovirus (KoRV). last eight years, these their have received focused study regarding sources, genetics, prevalence, presentation transmission. This led vast improvements in pathogen detection treatment, including ongoing development vaccines for each management control strategy. review will summarize highlight important advances made understanding combating C. pecorum KoRV koalas, since they With complementary having also been from genome sequence our immune system, we primed make significant positive impact on health future.

Language: Английский

Citations

56
A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence-specific immunity against subviral parasites DOI Creative Commons
Zachary K. Barth, Maria Nguyen, Kimberley D. Seed

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: July 7, 2021

Mobile genetic elements, elements that can move horizontally between genomes, have profound effects on their host's fitness. The phage-inducible chromosomal island-like element (PLE) is a mobile integrates into the chromosome of Vibrio cholerae and parasitizes bacteriophage ICP1 to cells. This parasitism by PLE such it abolishes production progeny provides defensive boon host cell population. In response severe imposed PLE, has acquired an adaptive CRISPR-Cas system targets genome during infection. However, isolates naturally lack are still able overcome certain variants, mechanism this immunity against thus far remained unknown. Here, we show encode endonuclease in same locus, with subset PLEs. Further analysis shows chimeric origin, incorporating DNA-binding domain highly similar some replication origin-binding proteins. similarity allows bind cleave origins replication. appears exert considerable selective pressure PLEs may drive module swapping origin restructuring as mechanisms escape. work demonstrates new defense systems arise through shuffling greater understanding evolutionary forces driving modularity temporal succession elements.

Language: Английский

Citations

47
The Battle between Retroviruses and APOBEC3 Genes: Its Past and Present DOI Creative Commons

Keiya Uriu,

Yusuke Kosugi,

Jumpei Ito

et al.

Viruses, Journal Year: 2021, Volume and Issue: 13(1), P. 124 - 124

Published: Jan. 17, 2021

The APOBEC3 family of proteins in mammals consists cellular cytosine deaminases and well-known restriction factors against retroviruses, including lentiviruses. genes are highly amplified diversified mammals, suggesting that their evolution diversification have been driven by conflicts with ancient viruses. At present, lentiviruses, HIV, the causative agent AIDS, known to encode a viral protein called Vif overcome antiviral effects hosts. Recent studies revealed acquisition an anti-APOBEC3 ability lentiviruses is key step achieving successful cross-species transmission. Here, we summarize current knowledge interplay between mammalian infections introduce scenario coevolution

Language: Английский

Citations

43
A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan–Myanmar Border of China DOI Creative Commons
Muddassar Hameed, Abdul Wahaab, Tongling Shan

et al.

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 11

Published: Feb. 8, 2021

Metagenomic analysis of mosquito-borne and mosquito-specific viruses is useful to understand the viral diversity for surveillance pathogens medical veterinary importance. Yunnan province located at southwest China has rich abundance mosquitoes. Arbovirus not conducted regularly in this particularly animal farms, which have public health as well Here, we analyzed 10 pools mosquitoes belonging Culex tritaeniorhyncus , Aedes aegypti Anopheles sinensis Armigeres subalbatus species, collected from different farms by using metagenomic next-generation sequencing technique. The generated data reveal that community matched reads was highly diverse varied among contained more than 19 taxonomic families, specific vertebrates, invertebrates, fungi, plants, protozoa, bacteria. Additionally, a large number were related are non-classified. included parvoviruses, anelloviruses, circoviruses, flaviviruses, rhabdoviruses, seadornaviruses, might be taken viremic hosts during blood feeding. Notably, presence with Japanese encephalitis virus, Getah porcine parvoviruses geographic sites suggested potential circulation these their vertebrate hosts. Overall, study provides comprehensive knowledge populations present China, source diseases humans domestic animals.

Language: Английский

Citations

43
Interplay between endogenous and exogenous human retroviruses DOI
Eleni Kyriakou, Gkikas Magiorkinis

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 31(9), P. 933 - 946

Published: April 4, 2023

Language: Английский

Citations

19
Unique Structure and Distinctive Properties of the Ancient and Ubiquitous Gamma-Type Envelope Glycoprotein DOI Creative Commons
Victoria Hogan, Welkin E. Johnson

Viruses, Journal Year: 2023, Volume and Issue: 15(2), P. 274 - 274

Published: Jan. 18, 2023

After the onset of AIDS pandemic, HIV-1 (genus Lentivirus) became predominant model for studying retrovirus Env glycoproteins and their role in entry. However, HIV is an inadequate understanding entry viruses Alpharetrovirus, Gammaretrovirus Deltaretrovirus genera. For example, oncogenic system such as Rous sarcoma virus (RSV, Alpharetrovirus), murine leukemia (MLV, Gammaretrovirus) human T-cell (HTLV-I HTLV-II, Deltaretrovirus) encode Envs that are structurally functionally distinct from Env. We refer to these Gamma-type Envs. probably most widespread retroviral nature. They found exogenous endogenous retroviruses representing a broad spectrum vertebrate hosts including amphibians, birds, reptiles, mammals fish. In form, gamma-type have been evolutionarily coopted numerous times, notably placental syncytins (e.g., SYNC1 SYNC2). Remarkably, also outside Retroviridae. Gp2 proteins filoviruses Ebolavirus) snake arenaviruses genus Reptarenavirus homologs, products ancient recombination events involving different Baltimore classes. Distinctive hallmarks include labile disulfide bond linking surface transmembrane subunits, multi-stage attachment fusion mechanism, highly conserved (but poorly understood) “immunosuppressive domain”, activation by viral protease during virion maturation. Here, we synthesize work diverse systems illustrate distinctive properties highlight avenues further exploration structure function.

Language: Английский

Citations

17