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Reductive evolution of proteomes and protein structures

Wang, Minglei; Kurland, Charles LU and Caetano-Anolles, Gustavo (2011) In Proceedings of the National Academy of Sciences 108(29). p.11954-11958
Abstract
The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically... (More)
The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not. (Less)
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organization
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Contribution to journal
publication status
published
subject
keywords
protein domain, evolutionary constraint, intrinsic disorder
in
Proceedings of the National Academy of Sciences
volume
108
issue
29
pages
11954 - 11958
publisher
National Acad Sciences
external identifiers
  • wos:000292876900051
  • scopus:79961054837
ISSN
1091-6490
DOI
10.1073/pnas.1017361108
language
English
LU publication?
yes
id
d81e86f9-bd0c-4cab-a0b5-8fc2647e55bf (old id 2092857)
date added to LUP
2011-08-25 12:56:46
date last changed
2017-07-30 03:30:14
@article{d81e86f9-bd0c-4cab-a0b5-8fc2647e55bf,
  abstract     = {The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P &lt; 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.},
  author       = {Wang, Minglei and Kurland, Charles and Caetano-Anolles, Gustavo},
  issn         = {1091-6490},
  keyword      = {protein domain,evolutionary constraint,intrinsic disorder},
  language     = {eng},
  number       = {29},
  pages        = {11954--11958},
  publisher    = {National Acad Sciences},
  series       = {Proceedings of the National Academy of Sciences},
  title        = {Reductive evolution of proteomes and protein structures},
  url          = {http://dx.doi.org/10.1073/pnas.1017361108},
  volume       = {108},
  year         = {2011},
}