A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters

Scientific Reports
Chia-Tsen SunMing-Jing Hwang

Abstract

Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results c...Continue Reading

References

Jun 1, 1997·Current Opinion in Structural Biology·S E BrennerT J Hubbard
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Jun 22, 2000·Proceedings of the National Academy of Sciences of the United States of America·D J LairdI L Weissman
Apr 3, 2001·Nature Reviews. Genetics·D A Kimbrell, B Beutler
Jun 26, 2001·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·W E Müller
Sep 20, 2001·Genes & Development·N Silverman, T Maniatis
Mar 23, 2002·Cell·Nancy A Woychik, Michael Hampsey
Jun 7, 2002·Genome Biology·Shelley D Copley, Jasvinder K Dhillon
Jul 16, 2002·Bioinformatics·Jinfeng Liu, Burkhard Rost
Nov 6, 2002·Journal of Molecular Biology·Andrew HarrisonChristine Orengo
Feb 28, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jingtong HouSung-Hou Kim
Mar 1, 2003·Nature Genetics·Minoru Kanehisa, Peer Bork
Mar 6, 2003·Genome Research·J Kirk HarrisNorman R Pace
May 31, 2003·Nature Reviews. Genetics·Lynn MieselTodd A Black
Sep 2, 2003·Current Opinion in Structural Biology·William C Wimley
Dec 19, 2003·Nucleic Acids Research·Antonina AndreevaAlexey G Murzin
Jan 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·Song YangPhilip E Bourne
Jun 18, 2005·Bioinformatics·Henry F WinstanleyCharlotte M Deane
Jul 15, 2005·Molecular Biology and Evolution·Gang FangAntoine Danchin
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Oct 18, 2005·Molecular and Cellular Biology·Jeroen EssersWim Vermeulen
Mar 4, 2006·Science·Francesca D CiccarelliPeer Bork
Mar 3, 2007·Molecular Biology and Evolution·Kaoru Fukami-KobayashiKen Nishikawa
May 23, 2007·Proceedings of the National Academy of Sciences of the United States of America·Gustavo Caetano-AnollésJay E Mittenthal
May 9, 2008·Molecular Biology and Evolution·Natalya YutinEugene V Koonin
Mar 11, 2009·The Biochemical Journal·Cyrus Chothia, Julian Gough
May 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Christopher L DupontGustavo Caetano-Anollés
Jan 29, 2011·BMC Evolutionary Biology·Zlatko SmoleAnita Krisko
Jul 27, 2011·PloS One·Fran SupekTomislav Šmuc
Dec 12, 2012·Trends in Genetics : TIG·Carlos G Acevedo-RochaAntoine Danchin
Apr 5, 2013·PLoS Computational Biology·Syed Abbas Bukhari, Gustavo Caetano-Anollés
Nov 21, 2013·Nucleic Acids Research·UNKNOWN UniProt Consortium
Jan 5, 2014·Nature Reviews. Microbiology·Alistair B RussellJoseph D Mougous
Feb 7, 2014·PLoS Computational Biology·Arshan NasirGustavo Caetano-Anollés
Feb 21, 2014·The Journal of Biological Chemistry·Joseph D ChaoYossef Av-Gay

❮ Previous
Next ❯

Citations

Nov 20, 2020·Genome Biology and Evolution·Audrey DefossetOdile Lecompte

❮ Previous
Next ❯

Software Mentioned

Bacteria
InterPro
Bimax
REViGO
Generalized Association Plots ( GAP )
R
Plaid
Xmotifs
CATH
Gene Ontolog ( GO )

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.

© 2022 Meta ULC. All rights reserved