Modular evolution

Garb, J. E., and Hayashi, C. Y. (2005). Modular evolution of egg case silk genes across orb-weaving spider superfamilies. PNAS 102, 11379-11384. 

Kappock, T.J., Ealick, S.E., Stubbe, J. (2000) Modular evolution of the purine biosynthetic pathway. Curr. Opin. Chem. Biol. 4, 567-572. 

Fredrich, T. and Weiss, H. (1997). Modular evolution of the respiratory NADH ubiquinone oxidoreductase and the origin of its modules. J. Theor. Biol. 187 529-540. 

Hayashi C. and Lewis R., Molecular architecture and evolution of a modular spider silk protein gene. Science, 287, 1477, 2000. 

Hwang DM, Dempsey A, Tan KT, Liew CC. 1996. A modular domain of NifU, a nitrogen fixation cluster protein, is highly conserved in evolution. J Mol Evol 43 536 0. 

The evolution of proteins in a modular fashion by fusion of segments of genes, each coding for a module of a compact structural unit of polypeptide, is thus a credible and attractive hypothesis for explaining the rapid generation of enzyme diversity. 

Structure analysis of several proteases involved in blood coagulation and fibrinolysis reveals a diverse, sometimes repetitive, assembly of discrete protein modules (Fig. 9.4) [56]. While these modules represent independent structural units with individual folding pathways, their concerted action contributes to function and specificity in the final protein product. On the genetic level, these individual modules are encoded in separate exons. Over the course of modular protein evolution, new genes are created by duplication, deletion, and rearrangement of these exons. Mechanistically, the exon shuffling actually takes place in the intervening intron sequences (intronic recombination - for further details see [10]). 

The significance of exon shuffling to protein evolution, in particular in respect to the development of multicellularity, is signified by a short inventory of processes involving proteins created by modular assembly. Exon shuffling facilitates the construction of proteins involved in regulation of blood coagulation, fibrinolysis, and complement activation, plus most constituents of the extracellular matrix, cell adhesion proteins, and receptor proteins [10, 57]. 

Fig. 9.4. Schematic illustration of modular protein evolution, exemplified on proteases, involved in blood coagulation and fibrinolysis. Varying type and number of modules, fused onto a common protease unit, generates a family of highly specific hydrolytic enzymes. (Adapted from [56])...

Advances in molecular biology and high-throughput screening, as well as the projected flexibility and diversity of modular assembly in natural protein evolution has inspired the development of various techniques to implement combinatorial domain recombination, better known as exon shuffling, in vitro. 

Moss SJ, Martin CJ, Wilkinson B (2004) Loss of Co-Linearity by Modular Polyketide Synthases a Mechanism for the Evolution of Chemical Diversity. Nat Prod Rep 21 575... 

Scrutton, N. S., 1994, a/p barrel evolution and the modular assembly of enzymes emerging trends in the flavin dehydrogenase/oxidase family, BioEssays 16 1159122. 

Oligomeric states of similarly folded subunits can be very disparate in architecture through evolution and have implications in terms of functions as it has been well exemplified with the hemoglobin family (Royer et al. 2005). The gain of modularity expected by switching from a single domain to multidomains proteins and then to supramolecular assemblies, the fact that components of stable complexes are more conserved than transient ones as well as the fact that essential proteins tend to be subunit of complexes have been discussed from the point of view of evolution (Pereira-Leal et al. 2006 Bomberg-Bauer et al. 2005). 

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