Home LiteratureArticle Details
PMID: 19494908 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Chaperonin overexpression promotes genetic variation and enzyme evolution.

Nature ·Vol. 459 ·No. 7247 ·2009-06-04 ·Pages 668-73

Tokuriki N, Tawfik DS

Abstract

Most protein mutations, and mutations that alter protein functions in particular, undermine stability and are therefore deleterious. Chaperones, or heat-shock proteins, are often implicated in buffering mutations, and could thus facilitate the acquisition of neutral genetic diversity and the rate of adaptation. We examined the ability of the Escherichia coli GroEL/GroES chaperonins to buffer destabilizing and adaptive mutations. Here we show that mutational drifts performed in vitro with four different enzymes indicated that GroEL/GroES overexpression doubled the number of accumulating mutations, and promoted the folding of enzyme variants carrying mutations in the protein core and/or mutations with higher destabilizing effects (destabilization energies of >3.5 kcal mol(-)(1), on average, versus approximately 1 kcal mol(-)(1) in the absence of GroEL/GroES). The divergence of modified enzymatic specificity occurred much faster under GroEL/GroES overexpression, in terms of the number of adapted variants (>or=2-fold) and their improved specificity and activity (>or=10-fold). These results indicate that protein stability is a major constraint in protein evolution, and buffering mechanisms such as chaperonins are key in alleviating this constraint.

MeSH Terms
Chaperonin 10/genetics,metabolism Chaperonin 60/genetics,metabolism Chaperonins/metabolism Escherichia coli/genetics,metabolism Esterases/metabolism Evolution, Molecular Gene Expression Genetic Variation Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism Humans Mutation Protein Stability Pseudomonas/enzymology Substrate Specificity
Chemicals
Chaperonin 10 Chaperonin 60 Glyceraldehyde-3-Phosphate Dehydrogenases Esterases Chaperonins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Tokuriki Nobuhiko
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
Tawfik Dan S
References (44)
44 references, click to expand
  1. Directed evolution of mammalian paraoxonases PON1 and PON3 for bacterial expression and catalytic specialization.
    Proc Natl Acad Sci U S A. 2004 Jan 13;101(2):482-7 PMID: 14695884
  2. Protein stability imposes limits on organism complexity and speed of molecular evolution.
    Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16152-7 PMID: 17913881
  3. The FoldX web server: an online force field.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8 PMID: 15980494
  4. Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation.
    Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3076-81 PMID: 18287048
  5. Directed evolution of phosphotriesterase from Pseudomonas diminuta for heterologous expression in Escherichia coli results in stabilization of the metal-free state.
    Protein Eng Des Sel. 2005 Jan;18(1):51-8 PMID: 15790580
  6. How protein stability and new functions trade off.
    PLoS Comput Biol. 2008 Feb 29;4(2):e1000002 PMID: 18463696
  7. Loss of protein structure stability as a major causative factor in monogenic disease.
    J Mol Biol. 2005 Oct 21;353(2):459-73 PMID: 16169011
  8. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.
    J Mol Biol. 2002 Jul 5;320(2):369-87 PMID: 12079393
  9. Intense neutral drifts yield robust and evolvable consensus proteins.
    J Mol Biol. 2008 Jun 20;379(5):1029-44 PMID: 18495157
  10. Hsp90 as a capacitor of phenotypic variation.
    Nature. 2002 Jun 6;417(6889):618-24 PMID: 12050657
  11. The stability effects of protein mutations appear to be universally distributed.
    J Mol Biol. 2007 Jun 22;369(5):1318-32 PMID: 17482644
  12. Endosymbiotic bacteria: groEL buffers against deleterious mutations.
    Nature. 2002 May 23;417(6887):398 PMID: 12024205
  13. GroEL and the maintenance of bacterial endosymbiosis.
    Trends Genet. 2004 Sep;20(9):413-6 PMID: 15313549
  14. Demonstration by genetic suppression of interaction of GroE products with many proteins.
    Nature. 1989 Nov 23;342(6248):451-3 PMID: 2573840
  15. Under cover: causes, effects and implications of Hsp90-mediated genetic capacitance.
    Bioessays. 2004 Apr;26(4):348-62 PMID: 15057933
  16. Continuity in evolution: on the nature of transitions.
    Science. 1998 May 29;280(5368):1451-5 PMID: 9603737
  17. Predicting the tolerance of proteins to random amino acid substitution.
    Biophys J. 2005 Dec;89(6):3714-20 PMID: 16150971
  18. Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL.
    Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15800-5 PMID: 17043235
  19. A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities.
    Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13497-502 PMID: 18757760
  20. Why molecular chaperones buffer mutational damage: a case study with a yeast Hsp40/70 system.
    Genetics. 2006 Oct;174(2):937-44 PMID: 16849597
  21. Evolution of evolvability.
    Ann N Y Acad Sci. 1999 May 18;870:146-55 PMID: 10415480
  22. Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other Escherichia coli proteins.
    Bioinformatics. 2007 Dec 15;23(24):3276-9 PMID: 18006553
  23. Missense meanderings in sequence space: a biophysical view of protein evolution.
    Nat Rev Genet. 2005 Sep;6(9):678-87 PMID: 16074985
  24. Between genotype and phenotype: protein chaperones and evolvability.
    Nat Rev Genet. 2003 Apr;4(4):263-74 PMID: 12671657
  25. Evolutionary potential of hidden genetic variation.
    Trends Ecol Evol. 2008 Jan;23(1):33-7 PMID: 18079017
  26. The selection of acceptable protein mutations.
    Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10080-5 PMID: 17540730
  27. Hsp90 as a capacitor for morphological evolution.
    Nature. 1998 Nov 26;396(6709):336-42 PMID: 9845070
  28. Transient kinetic analysis of adenosine 5'-triphosphate binding-induced conformational changes in the allosteric chaperonin GroEL.
    Biochemistry. 1998 May 19;37(20):7083-8 PMID: 9585518
  29. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research.
    DNA Res. 2005;12(5):291-9 PMID: 16769691
  30. Genomic buffering mitigates the effects of deleterious mutations in bacteria.
    Nat Genet. 2005 Dec;37(12):1376-9 PMID: 16273106
  31. Chaperone-assisted protein folding.
    Curr Opin Struct Biol. 1997 Feb;7(1):41-52 PMID: 9032064
  32. Chaperone coexpression plasmids: differential and synergistic roles of DnaK-DnaJ-GrpE and GroEL-GroES in assisting folding of an allergen of Japanese cedar pollen, Cryj2, in Escherichia coli.
    Appl Environ Microbiol. 1998 May;64(5):1694-9 PMID: 9572938
  33. Hsp90 potentiates the rapid evolution of new traits: drug resistance in diverse fungi.
    Science. 2005 Sep 30;309(5744):2185-9 PMID: 16195452
  34. GroEL reversibly binds to, and causes rapid inactivation of, human carbonic anhydrase II at high temperatures.
    Biochim Biophys Acta. 1996 Dec 5;1298(2):191-8 PMID: 8980645
  35. Role of mutator alleles in adaptive evolution.
    Nature. 1997 Jun 12;387(6634):700-2 PMID: 9192893
  36. The HSP90 chaperone complex, an emerging force in plant development and phenotypic plasticity.
    Curr Opin Plant Biol. 2005 Feb;8(1):86-92 PMID: 15653405
  37. Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli.
    Cell. 2005 Jul 29;122(2):209-20 PMID: 16051146
  38. Shared promiscuous activities and evolutionary features in various members of the amidohydrolase superfamily.
    Biochemistry. 2005 Sep 27;44(38):12728-36 PMID: 16171387
  39. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.
    J Mol Biol. 2002 Jun 28;320(1):85-95 PMID: 12079336
  40. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein.
    Nature. 2006 Dec 14;444(7121):929-32 PMID: 17122770
  41. Simultaneous purification of hexokinase, class-I fructose-bisphosphate aldolase, triosephosphate isomerase and phosphoglycerate kinase from Trypanosoma brucei.
    Eur J Biochem. 1984 Nov 2;144(3):475-83 PMID: 6489338
  42. Directed evolution of the promiscuous esterase activity of carbonic anhydrase II.
    Biochemistry. 2005 Apr 12;44(14):5444-52 PMID: 15807537
  43. Chaperonin-mediated protein folding.
    Annu Rev Biophys Biomol Struct. 2001;30:245-69 PMID: 11340060
  44. Latent evolutionary potentials under the neutral mutational drift of an enzyme.
    HFSP J. 2007 May;1(1):67-78 PMID: 19404461
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2009-06-04
Pages
668-73
Language
English
Region
England
NLM ID
0410462
Subset
IM
Grants
PHS HHS · W81XWH-07-2-0020 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]