The evolution of protein domain families

Buljan, Marija; Bateman, Alex

doi:10.1042/bst0370751

Cited by 113 publications

(107 citation statements)

References 31 publications

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“…Our initial interest in SOGA was based on conserved domains, which predicted that SOGA could participate in the regulation of autophagy. 36 The results presented here indicate that the regulation and function of SOGA can explain how adiponectin enhances insulin inhibition of autophagy while activating AMPK.…”

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confidence: 85%

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Adiponectin Lowers Glucose Production by Increasing SOGA

Asmar

Alderman

et al. 2010

The American Journal of Pathology

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Adiponectin is a hormone that lowers glucose production by increasing liver insulin sensitivity. Insulin blocks the generation of biochemical intermediates for glucose production by inhibiting autophagy. However, autophagy is stimulated by an essential mediator of adiponectin action, AMPK. This deadlock led to our hypothesis that adiponectin inhibits autophagy through a novel mediator. Mass spectrometry revealed a novel protein that we call suppressor of glucose by autophagy (SOGA) in adiponectin-treated hepatoma cells. Adiponectin increased SOGA in hepatocytes, and siRNA knockdown of SOGA blocked adiponectin inhibition of glucose production. Furthermore , knockdown of SOGA increased late autophagosome and lysosome staining and the secretion of valine , an amino acid that cannot be synthesized or metabolized by liver cells , suggesting that SOGA inhibits autophagy. SOGA decreased in response to AICAR , an activator of AMPK , and LY294002, an inhibitor of the insulin signaling intermediate , PI3K. AICAR reduction of SOGA was blocked by adiponectin; however , adiponectin did not increase SOGA during PI3K inhibition, suggesting that adiponectin increases SOGA through the insulin signaling pathway. SOGA contains an internal signal peptide that enables the secretion of a circulating fragment of SOGA, providing a surrogate marker for intracellular SOGA levels. Circulating SOGA increased in parallel with adiponectin and insulin activity in both humans and mice. These results suggest that adiponectinmediated increases in SOGA contribute to the inhibition of glucose production.

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confidence: 85%

“…36 Both Atg16 and Rab5 contribute to the early stages of autophagy. 43 Although Atg16 is an essential component of the autophagic machinery, adenoviral overexpression of Atg16 inhibits autophagy in mammalian cells.…”

Section: Discussionmentioning

confidence: 99%

Adiponectin Lowers Glucose Production by Increasing SOGA

Asmar

Alderman

et al. 2010

The American Journal of Pathology

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“…Most observed additions and removals of protein domains following gene duplication occur at protein termini (21). Thus, the addition of an N-terminal helix to an ancestral tail tube protein to make a "gpFII" protein, or addition of an N-terminal helix and loop structure to make a "gpU" protein are both feasible mechanisms by which these proteins may have evolved new functions.…”

Section: C-terminal Truncations Of Both Gpfii and Gpv Results In Dominmentioning

confidence: 99%

Phages have adapted the same protein fold to fulfill multiple functions in virion assembly

Cardarelli¹,

Pell

Neudecker

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Evolutionary relationships may exist among very diverse groups of proteins even though they perform different functions and display little sequence similarity. The tailed bacteriophages present a uniquely amenable system for identifying such groups because of their huge diversity yet conserved genome structures. In this work, we used structural, functional, and genomic context comparisons to conclude that the head–tail connector protein and tail tube protein of bacteriophage λ diverged from a common ancestral protein. Further comparisons of tertiary and quaternary structures indicate that the baseplate hub and tail terminator proteins of bacteriophage may also be part of this same family. We propose that all of these proteins evolved from a single ancestral tail tube protein fold, and that gene duplication followed by differentiation led to the specialized roles of these proteins seen in bacteriophages today. Although this type of evolutionary mechanism has been proposed for other systems, our work provides an evolutionary mechanism for a group of proteins with different functions that bear no sequence similarity. Our data also indicate that the addition of a structural element at the N terminus of the λ head–tail connector protein endows it with a distinctive protein interaction capability compared with many of its putative homologues.

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“…Within these families, there are notable examples of some of the mechanisms driving divergence between duplicate copies. Duplication can lead to loss or gain of domains, often at the ends (N-terminus or C-terminus) of the protein [95]. In addition, duplicate genes can diverge in sequence to acquire novel binding motifs either within the SH2 domain or elsewhere within the protein (discussed in detail in §7).…”

Section: Diversification Of Sh2 Domain Proteins Through Gene Duplicationmentioning

confidence: 99%

Evolution of SH2 domains and phosphotyrosine signalling networks

Liu

Nash

2012

Phil. Trans. R. Soc. B

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Src homology 2 (SH2) domains mediate selective protein-protein interactions with tyrosine phosphorylated proteins, and in doing so define specificity of phosphotyrosine (pTyr) signalling networks. SH2 domains and protein-tyrosine phosphatases expand alongside protein-tyrosine kinases (PTKs) to coordinate cellular and organismal complexity in the evolution of the unikont branch of the eukaryotes. Examination of conserved families of PTKs and SH2 domain proteins provides fiduciary marks that trace the evolutionary landscape for the development of complex cellular systems in the proto-metazoan and metazoan lineages. The evolutionary provenance of conserved SH2 and PTK families reveals the mechanisms by which diversity is achieved through adaptations in tissue-specific gene transcription, altered ligand binding, insertions of linear motifs and the gain or loss of domains following gene duplication. We discuss mechanisms by which pTyr-mediated signalling networks evolve through the development of novel and expanded families of SH2 domain proteins and the elaboration of connections between pTyr-signalling proteins. These changes underlie the variety of general and specific signalling networks that give rise to tissue-specific functions and increasingly complex developmental programmes. Examination of SH2 domains from an evolutionary perspective provides insight into the process by which evolutionary expansion and modification of molecular protein interaction domain proteins permits the development of novel protein-interaction networks and accommodates adaptation of signalling networks.

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The evolution of protein domain families

Cited by 113 publications

References 31 publications

Adiponectin Lowers Glucose Production by Increasing SOGA

Adiponectin Lowers Glucose Production by Increasing SOGA

Phages have adapted the same protein fold to fulfill multiple functions in virion assembly

Evolution of SH2 domains and phosphotyrosine signalling networks

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