Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Subscribe

Sci. Signal., 24 November 2009
Vol. 2, Issue 98, p. ra76
[DOI: 10.1126/scisignal.2000546]

RESEARCH ARTICLES

Eukaryotic Protein Domains as Functional Units of Cellular Evolution

Jing Jin1*, Xueying Xie2{dagger}{ddagger}, Chen Chen1{ddagger}, Jin Gyoon Park1, Chris Stark1§, D. Andrew James1, Marina Olhovsky1, Rune Linding1, Yongyi Mao2*, and Tony Pawson1,3*

1 Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.
2 School of Information Technology and Engineering (SITE), University of Ottawa, Ottawa, Ontario, Canada K1N 6N5.
3 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.

{dagger} Present address: Key Laboratory of Child Development and Learning Science, Ministry of Education, 2 Sipai Lou, Nanjing 210096, China.

{ddagger} These authors contributed equally to this work.

§ Present address: University Health Network Microarray Centre, 101 College Street, Toronto, Ontario, Canada M5G 1L7.

Present address: Cellular and Molecular Logic Team, The Institute of Cancer Research, London SW3 6JB, UK.

Abstract: Modular protein domains are functional units that can be modified through the acquisition of new intrinsic activities or by the formation of novel domain combinations, thereby contributing to the evolution of proteins with new biological properties. Here, we assign proteins to groups with related domain compositions and functional properties, termed "domain clubs," which we use to compare multiple eukaryotic proteomes. This analysis shows that different domain types can take distinct evolutionary trajectories, which correlate with the conservation, gain, expansion, or decay of particular biological processes. Evolutionary jumps are associated with a domain that coordinately acquires a new intrinsic function and enters new domain clubs, thereby providing the modified domain with access to a new cellular microenvironment. We also coordinately analyzed the covalent and noncovalent interactions of different domain types to assess the molecular compartment occupied by each domain. This reveals that specific subsets of domains demarcate particular cellular processes, such as growth factor signaling, chromatin remodeling, apoptotic and inflammatory responses, or vesicular trafficking. We suggest that domains, and the proteins in which they reside, are selected during evolution through reciprocal interactions with protein domains in their local microenvironment. Based on this scheme, we propose a mechanism by which Tudor domains may have evolved to support different modes of epigenetic regulation and suggest a role for the germline group of mammalian Tudor domains in Piwi-regulated RNA biology.

* To whom correspondence should be addressed. E-mail: pawson{at}lunenfeld.ca (T.P.); yymao{at}site.uottawa.ca (Y.M.); jjin{at}lunenfeld.ca (J.J.)

Citation: J. Jin, X. Xie, C. Chen, J. G. Park, C. Stark, D. A. James, M. Olhovsky, R. Linding, Y. Mao, T. Pawson, Eukaryotic Protein Domains as Functional Units of Cellular Evolution. Sci. Signal. 2, ra76 (2009).

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
SH3 interactome conserves general function over specific form.
X. Xin, D. Gfeller, J. Cheng, R. Tonikian, L. Sun, A. Guo, L. Lopez, A. Pavlenco, A. Akintobi, Y. Zhang, et al. (2014)
Mol Syst Biol 9, 652
   Abstract »    Full Text »    PDF »
Modular evolution of phosphorylation-based signalling systems.
J. Jin and T. Pawson (2012)
Phil Trans R Soc B 367, 2540-2555
   Abstract »    Full Text »    PDF »
Evolution of SH2 domains and phosphotyrosine signalling networks.
B. A. Liu and P. D. Nash (2012)
Phil Trans R Soc B 367, 2556-2573
   Abstract »    Full Text »    PDF »
NHERF1 acts as a molecular switch to program metastatic behavior and organotropism via its PDZ domains.
R. A. Cardone, M. R. Greco, M. Capulli, E. J. Weinman, G. Busco, A. Bellizzi, V. Casavola, E. Antelmi, B. Ambruosi, M. E. Dell'Aquila, et al. (2012)
Mol. Biol. Cell 23, 2028-2040
   Abstract »    Full Text »    PDF »
The SH2 Domain-Containing Proteins in 21 Species Establish the Provenance and Scope of Phosphotyrosine Signaling in Eukaryotes.
B. A. Liu, E. Shah, K. Jablonowski, A. Stergachis, B. Engelmann, and P. D. Nash (2011)
Science Signaling 4, ra83
   Abstract »    Full Text »    PDF »
Tandem BRCT Domains: DNA's Praetorian Guard.
R. D. Mesquita, N. T. Woods, E. S. Seabra-Junior, and A. N. A. Monteiro (2010)
Genes & Cancer 1, 1140-1146
   Abstract »    Full Text »    PDF »
Domain Recombination: A Workhorse for Evolutionary Innovation.
G. Apic and R. B. Russell (2010)
Science Signaling 3, pe30
   Abstract »    Full Text »    PDF »
LOTUS, a new domain associated with small RNA pathways in the germline.
I. Callebaut and J. P. Mornon (2010)
Bioinformatics 26, 1140-1144
   Abstract »    Full Text »    PDF »
Science Signaling Podcast: 24 November 2009.
T. Pawson and A. M. VanHook (2009)
Science Signaling 2, pc21
   Abstract »    Full Text »

To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882