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Complex fate of paralogs.

Szklarczyk R, Huynen MA, Snel B - BMC Evol. Biol. (2008)

Bottom Line: We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to bona fide structural growth.In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution.Such genes could provide the raw material for the evolution of new functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands. radek@cmbi.ru.nl

ABSTRACT

Background: Thanks to recent high coverage mass-spectrometry studies and reconstructed protein complexes, we are now in an unprecedented position to study the evolution of biological systems. Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein complexes.

Results: We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to bona fide structural growth. Inspection of paralogous proteins participating in two independent complexes shows that an ancient, pre-duplication protein functioned in both multi-protein assemblies and a gene duplication event allowed the respective copies to specialize and split their roles.

Conclusion: Variants with conditionally assembled, paralogous subunits likely have played a role in yeast's adaptation to anaerobic conditions. In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution. Such genes could provide the raw material for the evolution of new functions.

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A possible evolutionary scenario for incremental duplication of whole complexes. a) Ancestral three-subunit protein complex before duplications. b) Intra-complex duplication, gives rise to paralogous proteins, mutually exclusive as a part of the complex. Two module variants arise, with either A' or A" as one of subunits. c) Another intra-complex duplication makes possible assembly of up to four distinct module variants. d) Paralogs co-evolve to work together, specializing to accept only one of the interacting paralogs. This gives rise to more accentuated module variants, which now can be interpreted as separate complexes with a shared subunit. e) Eventually, all subunits may get duplicated, creating two independent protein complexes.
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Figure 5: A possible evolutionary scenario for incremental duplication of whole complexes. a) Ancestral three-subunit protein complex before duplications. b) Intra-complex duplication, gives rise to paralogous proteins, mutually exclusive as a part of the complex. Two module variants arise, with either A' or A" as one of subunits. c) Another intra-complex duplication makes possible assembly of up to four distinct module variants. d) Paralogs co-evolve to work together, specializing to accept only one of the interacting paralogs. This gives rise to more accentuated module variants, which now can be interpreted as separate complexes with a shared subunit. e) Eventually, all subunits may get duplicated, creating two independent protein complexes.

Mentions: Many parallel functional modules has been identified across all life kingdoms, including helicases and heat shock proteins in yeast [39]. Nevertheless, the absence of complete complex duplication at the WGD event (with a notable exception of CRPs) indicates that a stepwise duplication of modules [6], rather than whole-complex duplications, is a major mode of protein complex evolution in eukaryotes. Subunit-by-subunit module expansions amend the cellular machinery with the introduction of module variants. Subsequent duplications may give rise to bi-complex paralogs, which can be seen as intermediate phases on the evolutionary path leading to whole-complex duplication (see Figure 5). The process may be accompanied by attachment of additional subunits to one of the complexes or a differential loss of existing ones.


Complex fate of paralogs.

Szklarczyk R, Huynen MA, Snel B - BMC Evol. Biol. (2008)

A possible evolutionary scenario for incremental duplication of whole complexes. a) Ancestral three-subunit protein complex before duplications. b) Intra-complex duplication, gives rise to paralogous proteins, mutually exclusive as a part of the complex. Two module variants arise, with either A' or A" as one of subunits. c) Another intra-complex duplication makes possible assembly of up to four distinct module variants. d) Paralogs co-evolve to work together, specializing to accept only one of the interacting paralogs. This gives rise to more accentuated module variants, which now can be interpreted as separate complexes with a shared subunit. e) Eventually, all subunits may get duplicated, creating two independent protein complexes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2628386&req=5

Figure 5: A possible evolutionary scenario for incremental duplication of whole complexes. a) Ancestral three-subunit protein complex before duplications. b) Intra-complex duplication, gives rise to paralogous proteins, mutually exclusive as a part of the complex. Two module variants arise, with either A' or A" as one of subunits. c) Another intra-complex duplication makes possible assembly of up to four distinct module variants. d) Paralogs co-evolve to work together, specializing to accept only one of the interacting paralogs. This gives rise to more accentuated module variants, which now can be interpreted as separate complexes with a shared subunit. e) Eventually, all subunits may get duplicated, creating two independent protein complexes.
Mentions: Many parallel functional modules has been identified across all life kingdoms, including helicases and heat shock proteins in yeast [39]. Nevertheless, the absence of complete complex duplication at the WGD event (with a notable exception of CRPs) indicates that a stepwise duplication of modules [6], rather than whole-complex duplications, is a major mode of protein complex evolution in eukaryotes. Subunit-by-subunit module expansions amend the cellular machinery with the introduction of module variants. Subsequent duplications may give rise to bi-complex paralogs, which can be seen as intermediate phases on the evolutionary path leading to whole-complex duplication (see Figure 5). The process may be accompanied by attachment of additional subunits to one of the complexes or a differential loss of existing ones.

Bottom Line: We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to bona fide structural growth.In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution.Such genes could provide the raw material for the evolution of new functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands. radek@cmbi.ru.nl

ABSTRACT

Background: Thanks to recent high coverage mass-spectrometry studies and reconstructed protein complexes, we are now in an unprecedented position to study the evolution of biological systems. Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein complexes.

Results: We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to bona fide structural growth. Inspection of paralogous proteins participating in two independent complexes shows that an ancient, pre-duplication protein functioned in both multi-protein assemblies and a gene duplication event allowed the respective copies to specialize and split their roles.

Conclusion: Variants with conditionally assembled, paralogous subunits likely have played a role in yeast's adaptation to anaerobic conditions. In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution. Such genes could provide the raw material for the evolution of new functions.

Show MeSH