Comparative conservation analysis of the human mitotic phosphoproteome

Bioinformatics
Rainer MalikRoman Körner

Abstract

A key challenge in phosphoproteomic studies is to distinguish functionally relevant phosphorylation sites from potentially 'silent' phosphorylation. Considering that relevant phosphorylation sites are expected to be better conserved during evolution than overall Serine, Threonine and Tyrosine (S/ T/ Y) residues, we asked whether this can be directly demonstrated through statistic analysis, using a large experimental dataset. Analyzing phosphoproteomic data derived from the human mitotic spindle apparatus, we found that 95.2% of 1744 phosphorylation sites are conserved in at least one of six other vertebrate species. Using a new score, termed conservation Z-score (CZ-score), we demonstrate that phosphorylation sites are significantly better conserved than other S/T/Y sites, a conclusion validated from several kinase consensus motifs. Most importantly, phosphorylation sites with experimentally verified biological functions were significantly better conserved than other phosphorylation sites, indicating that analysis utilizing evolutionary conservation may constitute a powerful basis for the development of improved phosphorylation site predictors. malik@biochem.mpg.de Supplementary data are available at Bioinformatics online.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Oct 1, 1988·Biomedical & Environmental Mass Spectrometry·K Biemann
Apr 1, 1986·Analytical Biochemistry·L Andersson, J Porath
Dec 12, 1996·Biochimica Et Biophysica Acta·L A Pinna, M Ruzzene
Dec 10, 1998·Nucleic Acids Research·A KreegipuuS Brunak
Dec 23, 1999·Current Opinion in Structural Biology·J A EndicottJ A Tucker
Nov 20, 2001·Chemical Reviews·R Aebersold, D R Goodlett
Aug 2, 2002·The Journal of Biological Chemistry·Hui ZhangMichael J Comb
Dec 10, 2002·Science·G ManningS Sudarsanam
Mar 14, 2003·Nature·Ruedi Aebersold, Matthias Mann
May 10, 2003·The Journal of Biological Chemistry·Hiroyuki NakajimaEisuke Nishida
Aug 20, 2003·Molecular Biology of the Cell·Reiko HondaErich A Nigg
Jan 9, 2004·Cell Cycle·Matthew P Stokes, W Matthew Michael
Aug 11, 2004·Proceedings of the National Academy of Sciences of the United States of America·Sean A BeausoleilSteven P Gygi
Dec 8, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hilary S BoothJill E Gready
Dec 14, 2004·Nature Biotechnology·John RushMichael J Comb
Apr 29, 2005·Molecular & Cellular Proteomics : MCP·Martin R LarsenThomas J D Jørgensen
Jun 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jaehong ParkLeonardo Brizuela
Jun 14, 2005·Trends in Biochemical Sciences·Tony Pawson, John D Scott
Aug 9, 2005·The Biochemical Journal·Stefano FerrariLorenzo A Pinna
Sep 21, 2005·Biochimica Et Biophysica Acta·Bostjan KobeRoss I Brinkworth
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Yelena V BudovskayaPaul K Herman
Mar 28, 2006·Proceedings of the National Academy of Sciences of the United States of America·Marjaana NousiainenRoman Körner
Feb 9, 2007·Proceedings of the National Academy of Sciences of the United States of America·Henrik MolinaAkhilesh Pandey
Feb 24, 2007·Nature Reviews. Molecular Cell Biology·Greg B G MoorheadAnnegret Ulke-Lemée
Oct 17, 2007·Molecular & Cellular Proteomics : MCP·Boris MacekMatthias Mann

❮ Previous
Next ❯

Citations

Jun 15, 2011·Journal of Chemical Information and Modeling·Kalidas Yeturu, Nagasuma Chandra
Feb 9, 2013·Journal of Chemical Information and Modeling·Mathias M von BehrenMatthias Rarey
Sep 25, 2008·Nature Reviews. Molecular Cell Biology·Helfrid HocheggerTim Hunt
Dec 17, 2011·The Journal of Biological Chemistry·Elena L RudashevskayaMichael G Palmgren
Apr 7, 2010·Molecular Biology and Evolution·Alex N Nguyen Ba, Alan M Moses
Oct 20, 2010·Molecular Biology and Evolution·Zhen WangYixue Li
Aug 15, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Emmanuel D LevyChristian R Landry
Nov 10, 2011·Science Signaling·Björn HegemannJan-Michael Peters
Feb 11, 2011·Biology Direct·Yerbol Z KurmangaliyevMikhail S Gelfand
Jan 28, 2014·PLoS Genetics·Luca FreschiChristian R Landry
Nov 26, 2009·Expert Review of Proteomics·Viveka Mayya, David K Han
Sep 8, 2010·Trends in Genetics : TIG·Alan M Moses, Christian R Landry
Apr 8, 2009·Trends in Genetics : TIG·Christian R LandryStephen W Michnick
Aug 29, 2009·The FEBS Journal·Amelie SteinPatrick Aloy
Nov 13, 2010·EMBO Reports·Teresa SardonPatrick Aloy
Jul 19, 2012·Molecular Systems Biology·Pablo MinguezPeer Bork
Oct 22, 2013·Journal of Molecular and Cellular Cardiology·Ziyou CuiAldrin V Gomes
Oct 15, 2013·Journal of Molecular and Cellular Cardiology·Ivan A Katrukha, Nikolai B Gusev
Nov 15, 2013·Biochimica Et Biophysica Acta·Georgios N TsaousisStavros J Hamodrakas
Oct 18, 2014·Frontiers in Genetics·Antonio PalmeriManuela Helmer-Citterich
May 17, 2014·Molecular & Cellular Proteomics : MCP·Antonio PalmeriPier Federico Gherardini
Mar 14, 2012·Reproductive Sciences·G Nicholas Europe-FinnerMagdalena Karolczak-Bayatti
Jun 22, 2018·Annual Review of Biochemistry·David L Brautigan, Shirish Shenolikar
Sep 5, 2014·American Journal of Physiology. Cell Physiology·Andrew PhilpSimon Schenk
Feb 13, 2020·Cell Cycle·Luke J Fulcher, Gopal P Sapkota

❮ 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.