Evolution of the rodent Trim5 cluster is marked by divergent paralogous expansions and independent acquisitions of TrimCyp fusions

Scientific Reports
Guney BosoChristine A Kozak

Abstract

Evolution of cellular innate immune genes in response to viral threats represents a rich area of study for understanding complex events that shape mammalian genomes. One of these genes, TRIM5, is a retroviral restriction factor that mediates a post-entry block to infection. Previous studies on the genomic cluster that contains TRIM5 identified different patterns of gene amplification and the independent birth of CypA gene fusions in various primate species. However, the evolution of Trim5 in the largest order of mammals, Rodentia, remains poorly characterized. Here, we present an expansive phylogenetic and genomic analysis of the Trim5 cluster in rodents. Our findings reveal substantial evolutionary changes including gene amplifications, rearrangements, loss and fusion. We describe the first independent evolution of TrimCyp fusion genes in rodents. We show that the TrimCyp gene found in some Peromyscus species was acquired about 2 million years ago. When ectopically expressed, the P. maniculatus TRIMCyp shows anti-retroviral activity that is reversed by cyclosporine, but it does not activate Nf-κB or AP-1 promoters, unlike the primate TRIMCyps. These results describe a complex pattern of differential gene amplification in the T...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 2, 2001·The EMBO Journal·A ReymondA Ballabio
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jul 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Melvyn W YapJonathan P Stoye
Aug 25, 2004·Proceedings of the National Academy of Sciences of the United States of America·Sébastien NisoleMelvyn W Yap
Nov 16, 2005·Annual Review of Genetics·Masatoshi Nei, Alejandro P Rooney
Mar 17, 2006·Proceedings of the National Academy of Sciences of the United States of America·Matthew StremlauJoseph Sodroski
May 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Zhihai SiJoseph Sodroski
Dec 28, 2007·PLoS Pathogens·Sara L SawyerHarmit S Malik
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Greg BrennanShiu-Lok Hu
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Cesar A VirgenTheodora Hatziioannou
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Sam J WilsonGreg J Towers
Apr 5, 2008·PLoS Pathogens·Ruchi M NewmanWelkin Johnson
Aug 5, 2008·BMC Evolutionary Biology·Marco SardielloGermana Meroni
Jan 17, 2009·Virology·Semih U TareenMichael Emerman
Dec 3, 2009·Genome Research·Sara HaydenEmma C Teeling
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Dec 29, 2010·Proceedings of the National Academy of Sciences of the United States of America·Barbie K Ganser-PornillosMark Yeager
Apr 23, 2011·Nature·Thomas PertelJeremy Luban
Feb 22, 2012·Nature Immunology·Nan Yan, Zhijian J Chen
Sep 15, 2012·Nature Reviews. Immunology·Nisha K Duggal, Michael Emerman
Dec 21, 2012·Retrovirology·Yong-Hui ZhengKenzo Tokunaga
Jan 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ray Malfavon-BorjaHarmit Singh Malik
Dec 18, 2013·Journal of Molecular Biology·Ricardo RajsbaumGijs A Versteeg
Mar 29, 2014·BMC Evolutionary Biology·Ignacio Marín
Aug 16, 2014·Developmental Cell·Michael A MandellVojo Deretic
Mar 6, 2015·Molecular Biology and Evolution·S Blair HedgesSudhir Kumar
Jul 17, 2015·Journal of Virology·Lara ManganaroViviana Simon
Nov 2, 2017·Nucleic Acids Research·Cynthia L SmithUNKNOWN Mouse Genome Database Group

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
transfection
PCRs
electrophoresis

Software Mentioned

BLAST
TrimCyp
Geneious
MUSCLE
RAxML
GraphPad Prism

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Ray Malfavon-BorjaHarmit S Malik
Proceedings of the National Academy of Sciences of the United States of America
Greg BrennanShiu-Lok Hu
© 2021 Meta ULC. All rights reserved