Evolutionary diversification of the multimeric states of proteins

Lynch, Michael

doi:10.1073/pnas.1310980110

Cited by 84 publications

(88 citation statements)

References 46 publications

(56 reference statements)

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“…Possible answers might come from elucidating why many soluble proteins are found in oligomeric states. This fundamental question has been addressed in several reviews that discuss plausible hypotheses, many of which may also be applicable to membrane protein nanoclusters (Ali and Imperiali, 2005;Hashimoto et al, 2011;Lynch, 2013). One important feature of soluble, oligomeric proteins is that they present the possibility of allosteric regulation; thus membrane protein nanoclusters might also be subject to this type of regulation.…”

Section: Why Nanoclusters?mentioning

confidence: 99%

Nanoclustering as a dominant feature of plasma membrane organization

García-Parajo

Cambi

Torreño-Pina

et al. 2014

Journal of Cell Science

257

254

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Early studies have revealed that some mammalian plasma membrane proteins exist in small nanoclusters. The advent of super-resolution microscopy has corroborated and extended this picture, and led to the suggestion that many, if not most, membrane proteins are clustered at the plasma membrane at nanoscale lengths. In this Commentary, we present selected examples of glycosylphosphatidyl-anchored proteins, Ras family members and several immune receptors that provide evidence for nanoclustering. We advocate the view that nanoclustering is an important part of the hierarchical organization of proteins in the plasma membrane. According to this emerging picture, nanoclusters can be organized on the mesoscale to form microdomains that are capable of supporting cell adhesion, pathogen binding and immune cell-cell recognition amongst other functions. Yet, a number of outstanding issues concerning nanoclusters remain open, including the details of their molecular composition, biogenesis, size, stability, function and regulation. Notions about these details are put forth and suggestions are made about nanocluster function and why this general feature of protein nanoclustering appears to be so prevalent.

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Section: Why Nanoclusters?mentioning

confidence: 99%

Nanoclustering as a dominant feature of plasma membrane organization

García-Parajo

Cambi

Torreño-Pina

et al. 2014

Journal of Cell Science

257

254

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“…1). The relative probability of each state can then be obtained by multiplying all of the coefficients on the arrows pointing up to the class with the product of all of the coefficients pointing down (5). After a number of simplifying steps, the solution reduces toP…”

Section: Significancementioning

confidence: 99%

“…For example, transcription-factor binding-site motifs often vary dramatically among orthologous genes in different species and even among similarly regulated genes within the same species (1)(2)(3). The binding interfaces of multimeric proteins can vary substantially among species, sometimes with no overlap at all (4,5). The key amino acid sequences involved in intermolecular cross-talk in signal-transduction systems can evolve at high rates (6,7), and growing evidence suggests that the locations of sites involved in posttranslational modification in individual proteins are under much weaker selective constraints than their absolute numbers (8).…”

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confidence: 99%

Evolutionary meandering of intermolecular interactions along the drift barrier

Lynch¹,

Hagner

2014

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

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Many cellular functions depend on highly specific intermolecular interactions, for example transcription factors and their DNA binding sites, microRNAs and their RNA binding sites, the interfaces between heterodimeric protein molecules, the stems in RNA molecules, and kinases and their response regulators in signaltransduction systems. Despite the need for complementarity between interacting partners, such pairwise systems seem to be capable of high levels of evolutionary divergence, even when subject to strong selection. Such behavior is a consequence of the diminishing advantages of increasing binding affinity between partners, the multiplicity of evolutionary pathways between selectively equivalent alternatives, and the stochastic nature of evolutionary processes. Because mutation pressure toward reduced affinity conflicts with selective pressure for greater interaction, situations can arise in which the expected distribution of the degree of matching between interacting partners is bimodal, even in the face of constant selection. Although biomolecules with larger numbers of interacting partners are subject to increased levels of evolutionary conservation, their more numerous partners need not converge on a single sequence motif or be increasingly constrained in more complex systems. These results suggest that most phylogenetic differences in the sequences of binding interfaces are not the result of adaptive fine tuning but a simple consequence of random genetic drift. cellular evolution | molecular interaction | transcription | random genetic drift | coevolution M uch of biology relies on the specificity of intermolecular interactions-the regulation of gene expression, the transmission of information via signal transduction, the assembly of monomeric subunits into multimers, vesicle sorting in eukaryotic cells, toxin-antitoxin systems in microbes, mating-type recognition, and many other cellular features. Although the basic structural features of such fitness-related traits would seem to be under strong purifying selection, molecular specificity often seems to be highly flexible in evolutionary time. For example, transcription-factor binding-site motifs often vary dramatically among orthologous genes in different species and even among similarly regulated genes within the same species (1-3). The binding interfaces of multimeric proteins can vary substantially among species, sometimes with no overlap at all (4, 5). The key amino acid sequences involved in intermolecular cross-talk in signal-transduction systems can evolve at high rates (6, 7), and growing evidence suggests that the locations of sites involved in posttranslational modification in individual proteins are under much weaker selective constraints than their absolute numbers (8). Although it is often argued that subtle differences in the motifs involved in intermolecular interactions are molded by the demands of natural selection, seldom has any direct evidence ever been provided in support of such arguments.The theory provided below makes the case...

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“…Over the years, this has been confirmed by various researchers and gene duplication is now considered to be of great importance for evolution in general. Whole-genome duplications (WGDs) in particular are acknowledged as foremost players in evolution, resulting in expanded biological complexity (Lynch and Conery, 2000;Otto and Whitton, 2000;Wendel, 2000;Van de Peer et al, 2009;Lynch, 2013). Following a WGD event, retained duplicated genes often undergo sub-or neofunctionalization due to increased genetic redundancy (Fawcett et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Evolution and structural diversification ofNictaba-like lectin genes in food crops with a focus on soybean (Glycine max)

Holle¹,

Rougé²,

Damme³

2017

Ann Bot

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Background and Aims The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba-like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored. Furthermore, this study included domain organization analysis, searching for orthologous genes in the legume family and transcript profiling of the Nictaba-like lectin genes in soybean.Methods Using a combination of BLASTp, InterPro analysis and hidden Markov models, the genomes of Medicago truncatula, Cicer arietinum, Lotus japonicus, Glycine max, Cajanus cajan, Phaseolus vulgaris, Theobroma cacao, Solanum lycopersicum, Solanum tuberosum, Coffea canephora, Oryza sativa, Zea mays, Sorghum bicolor, Musa acuminata and Elaeis guineensis were searched for Nictaba-like genes. Phylogenetic analysis was performed using RAxML and additional protein domains in the Nictaba-like sequences were identified using InterPro. Expression analysis of the soybean Nictaba-like genes was investigated using microarray data.Key Results Nictaba-like genes were identified in all studied species and analysis of the duplication events demonstrated that both tandem and segmental duplication contributed to the expansion of the Nictaba gene family in angiosperms. The single-domain Nictaba protein and the multi-domain F-box Nictaba architectures are ubiquitous among all analysed species and microarray analysis revealed differential expression patterns for all soybean Nictaba-like genes.Conclusions Taken together, the comparative genomics data contributes to our understanding of the Nictaba-like gene family in species for which the occurrence of Nictaba domains had not yet been investigated. Given the ubiquitous nature of these genes, they have probably acquired new functions over time and are expected to take on various roles in plant development and defence.

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Evolutionary diversification of the multimeric states of proteins

Cited by 84 publications

References 46 publications

Nanoclustering as a dominant feature of plasma membrane organization

Nanoclustering as a dominant feature of plasma membrane organization

Evolutionary meandering of intermolecular interactions along the drift barrier

Evolution and structural diversification ofNictaba-like lectin genes in food crops with a focus on soybean (Glycine max)

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