Evolution of CCL16 in Glires (Rodentia and Lagomorpha) shows an unusual random pseudogenization pattern

BMC Evolutionary Biology
Fabiana NevesPedro J Esteves

Abstract

The C-C motif chemokine ligand 16 (CCL16) is a potent pro-inflammatory chemokine and a chemoattractant for monocytes and lymphocytes. In normal plasma, it is present at high concentrations and elicits its effects on cells by interacting with cell surface chemokine receptors. In the European rabbit and in rodents such as mouse, rat and guinea pig, CCL16 was identified as a pseudogene, while in the thirteen-lined ground squirrel it appears to be potentially functional. To gain insight into the evolution of this gene in the superorder Glires (rodents and lagomorphs), we amplified the CCL16 gene from eleven Leporidae and seven Ochotonidae species. We compared our sequences with CCL16 sequences of twelve rodent species retrieved from public databases. The data show that for all leporid species studied CCL16 is a pseudogene. This is primarily due to mutations at the canonical Cys Cys motif, creating either premature stop codons, or disrupting amino acid replacements. In the Mexican cottontail, CCL16 is pseudogenized due to a frameshift deletion. Additionally, in the exon 1 (signal peptide), there are frameshift deletions present in all leporids studied. In contrast, in Ochotona species, CCL16 is potentially functional, except for an ...Continue Reading

References

Jul 5, 1991·Journal of Molecular Biology·S BrunakS Knudsen
Jan 23, 1999·American Journal of Human Genetics·M V Olson
May 11, 1999·DNA and Cell Biology·S FukudaH Nomiyama
Jun 24, 1999·Cytokine & Growth Factor Reviews·E Van CoillieG Opdenakker
Nov 5, 1999·Protein Science : a Publication of the Protein Society·M P CrumpB D Sykes
Apr 18, 2000·Gene·D C Shields
Apr 27, 2000·Immunology Today·L M Teran
Jun 6, 2003·The Journal of Allergy and Clinical Immunology·Santa Jeremy OnoMasako Toda
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jan 5, 2007·Genome Biology·Albert ZlotnikHisayuki Nomiyama
Sep 12, 2007·International Journal of Immunogenetics·P J EstevesW van der Loo
May 27, 2008·The Journal of Heredity·Andrey A PerelyginMargo A Brinton
Jun 28, 2008·Immunogenetics·Alison K SurridgePedro J Esteves
Apr 4, 2009·BMC Evolutionary Biology·Shani Blanga-KanfiDorothée Huchon
Jan 27, 2010·International Reviews of Immunology·Anupama Sahoo, Sin-Hyeog Im
Apr 9, 2010·Nature Reviews. Genetics·Hadas KerenGil Ast
May 4, 2010·Cytokine & Growth Factor Reviews·Hisayuki NomiyamaOsamu Yoshie
May 29, 2012·Immunity·Albert Zlotnik, Osamu Yoshie
Nov 14, 2012·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Hisayuki NomiyamaOsamu Yoshie
Aug 31, 2013·BioMed Research International·Kanako ShibataSumio Tanase
Oct 10, 2013·International Journal of Immunogenetics·A Lemos de MatosP J Esteves
Feb 1, 2015·Molecular Phylogenetics and Evolution·José Melo-FerreiraPedro J Esteves
Mar 6, 2015·Molecular Biology and Evolution·S Blair HedgesSudhir Kumar
Mar 31, 2015·Innate Immunity·Fabiana NevesPedro José Esteves
Apr 19, 2016·Nature Reviews. Genetics·Ricard Albalat, Cristian Cañestro
Jun 17, 2016·Journal of Molecular Evolution·Wessel van der LooPedro J Esteves
May 4, 2018·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura

❮ Previous
Next ❯

Citations

May 3, 2019·Immunogenetics·Mónica Lopes-MarquesL Filipe C Castro

❮ Previous
Next ❯

Datasets Mentioned

BETA
MK305131-MK305156

Methods Mentioned

BETA
PCR

Software Mentioned

NetGene2
BioEdit
Ensembl
MUltiple Sequence Comparison by Log - Expectation ( MUSCLE )
MEGAX

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.