Effective estimation of the minimum number of amino acid residues required for functional divergence between duplicate genes

Molecular Phylogenetics and Evolution
Jingqi ZhouXun Gu

Abstract

One of hot research foci has always been predicting amino acid residues underlying functional divergence after gene duplication, as those predicted sites can be used as candidates for further functional experimentations. It is important and interesting to know how many sites, on average, may have been responsible for the functional divergence between duplicate genes. In this article, we studied two basic types of functional divergence (type-I and type-II) in depth in order to give an accurate estimation of functional divergence-related sites. Type-I divergences result from altered functional constraints (i.e., different evolutionary rates) between duplicate genes, whereas type-II divergences refer to residues that are conserved by functional constraints but exhibit different physicochemical properties (e.g., charge or hydrophobicity) between duplicates. An effective site number (NE) strategy was applied in our study, which implements a stepwise regression model to calculate the minimum number of residues responsible for functional divergence without choosing preset threshold. We found that NE-determined cut-off value varies among different duplicate pairs, suggesting that empirical cutoff value is not suitable for every case. U...Continue Reading

References

Jan 1, 1991·Methods in Enzymology·T Hunter
Jan 1, 1971·Journal of Molecular Evolution·W M Fitch
Dec 24, 1997·Genomics·W R PearsonW Miller
Dec 22, 1999·Molecular Biology and Evolution·X Gu
May 4, 2000·Protein Science : a Publication of the Protein Society·D R CaffreyD C Shields
Oct 7, 2000·Journal of Molecular Biology·S S Hannenhalli, R B Russell
Nov 10, 2000·Science·M Lynch, J S Conery
Feb 22, 2001·Science·J C VenterX Zhu
Feb 24, 2001·Proceedings of the National Academy of Sciences of the United States of America·E A GaucherS A Benner
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Mar 29, 2001·Journal of Bacteriology·J L SeffernickL P Wackett
Dec 6, 2001·Proceedings of the National Academy of Sciences of the United States of America·B Knudsen, M M Miyamoto
Dec 26, 2001·Molecular Biology and Evolution·P LopezH Philippe
Jun 19, 2002·Trends in Biochemical Sciences·Eric A GaucherSteven A Benner
Dec 10, 2002·Science·G ManningS Sudarsanam
Feb 19, 2003·Journal of Molecular Biology·Antonio del SolAlfonso Valencia
Apr 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Lewyn LiLeonid A Mirny
Jul 26, 2003·IUBMB Life·Hervé PhilippeJulien Meunier
Jan 24, 2004·Protein Science : a Publication of the Protein Society·Olga V KalininaAleksandra B Rakhmaninova
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Feb 4, 2005·Molecular Biology and Evolution·Ziheng YangRasmus Nielsen
Aug 13, 2005·Bioinformatics·Tobias SingThomas Lengauer
Sep 15, 2005·Bioinformatics·Richard J Edwards, Denis C Shields
Mar 30, 2006·BMC Bioinformatics·Vicente ArnauIgnacio Marín
May 5, 2006·Molecular Biology and Evolution·Saraswathi AbhimanErik L L Sonnhammer
Jul 6, 2006·Trends in Ecology & Evolution·Adam Eyre-Walker
Oct 24, 2006·Molecular Biology and Evolution·Huai-Chun WangAndrew J Roger
Dec 5, 2006·Oncogene·L ArceM L Waterman
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Nov 19, 2008·Nature Reviews. Genetics·Gavin C Conant, Kenneth H Wolfe
Jul 21, 2009·Biochemical Society Transactions·Romain A Studer, Marc Robinson-Rechavi
Jun 17, 2010·Molecular Biology and Evolution·Romain A Studer, Marc Robinson-Rechavi
Jul 17, 2010·Algorithms for Molecular Biology : AMB·Pavel V MazinOlga V Kalinina
Aug 1, 2012·Molecular Phylogenetics and Evolution·Jay F StorzFederico G Hoffmann
Sep 11, 2012·Cell·Shane NephJohn A Stamatoyannopoulos

❮ Previous
Next ❯

Citations

Dec 22, 2019·International Journal of Molecular Sciences·Dmitry KarasevVladimir Poroikov
Aug 11, 2020·BMC Evolutionary Biology·Samuel H A von der Dunk, Berend Snel

❮ Previous
Next ❯

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.