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The Rise and Fall of TRP-N, an Ancient Family of Mechanogated Ion Channels, in Metazoa.

Schüler A, Schmitz G, Reft A, Özbek S, Thurm U, Bornberg-Bauer E - Genome Biol Evol (2015)

Bottom Line: In flies, the transient-receptor-potential N protein (TRP-N) was found to be a cilia-associated mechanoreceptor.We propose that these new candidate proteins help explain the sensory complexity of Cnidaria which has been previously observed but so far has lacked a molecular underpinning.Also, the ancient appearance of TRP-N supports a common origin of important components of the nervous systems in Ctenophores, Cnidaria, and Bilateria.

View Article: PubMed Central - PubMed

Affiliation: Institute for Evolution and Biodiversity, University of Muenster, Germany.

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Phylogeny of TRP protein families (A) and distributions of ankyrin domains in TRP proteins (B): Numbers at nodes indicate bootstrap supports and size of the polygons scales to the size of the families across all used genomes (see Materials and Methods for details). The bar plots in (B) show the distribution of ankyrin domains in proteins of the respective TRP families. “All” refers to all proteins, including all TRP proteins, from GenBank with at least one ankyrin domain. The bar plots are based on data from GenBank only and do not include our manually corrected gene models.
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evv091-F1: Phylogeny of TRP protein families (A) and distributions of ankyrin domains in TRP proteins (B): Numbers at nodes indicate bootstrap supports and size of the polygons scales to the size of the families across all used genomes (see Materials and Methods for details). The bar plots in (B) show the distribution of ankyrin domains in proteins of the respective TRP families. “All” refers to all proteins, including all TRP proteins, from GenBank with at least one ankyrin domain. The bar plots are based on data from GenBank only and do not include our manually corrected gene models.

Mentions: TRP-N has a long N-terminal ankyrin-repeat which comprises approximately 28 ankyrin domains. This repeat has been conjectured to be the gating spring which is involved in the transmission of mechanical force to the transmembrane domain (Howard and Bechstedt 2004; Liang et al. 2013). The ankyrin domains in this repeat presumably form a superhelix as they arrange into a complete turn which can be easily deformed mechanically. Ankyrin domains are widespread across proteins with very different functions and occur in 0.85% of all metazoan proteins. However, the average number of ankyrin domains across all ankyrin-containing proteins is only 4.8 (±4.5, median 3), and proteins with more than ten ankyrin domains are rare (Jernigan and Bordenstein 2014) (see also fig. 1). Note that determining the precise number of domains in a domain repeat is a difficult problem. The underlying reasons are inaccuracies arising during sequencing and assembly, and rapid evolutionary changes of sequences and number of domains, even at the population level. Finally, computational challenges are common, for example, in the frame capturing of the domains in a repeat (Schaper et al. 2012). Consequently, even the most accurate programs may fail to determine the number of domains in a repeat by a number of 1. We will, in the following work, always use the lower number of prediction, for example, 28 if there might be 28 or 29 domains in a repeat.Fig. 1.—


The Rise and Fall of TRP-N, an Ancient Family of Mechanogated Ion Channels, in Metazoa.

Schüler A, Schmitz G, Reft A, Özbek S, Thurm U, Bornberg-Bauer E - Genome Biol Evol (2015)

Phylogeny of TRP protein families (A) and distributions of ankyrin domains in TRP proteins (B): Numbers at nodes indicate bootstrap supports and size of the polygons scales to the size of the families across all used genomes (see Materials and Methods for details). The bar plots in (B) show the distribution of ankyrin domains in proteins of the respective TRP families. “All” refers to all proteins, including all TRP proteins, from GenBank with at least one ankyrin domain. The bar plots are based on data from GenBank only and do not include our manually corrected gene models.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4494053&req=5

evv091-F1: Phylogeny of TRP protein families (A) and distributions of ankyrin domains in TRP proteins (B): Numbers at nodes indicate bootstrap supports and size of the polygons scales to the size of the families across all used genomes (see Materials and Methods for details). The bar plots in (B) show the distribution of ankyrin domains in proteins of the respective TRP families. “All” refers to all proteins, including all TRP proteins, from GenBank with at least one ankyrin domain. The bar plots are based on data from GenBank only and do not include our manually corrected gene models.
Mentions: TRP-N has a long N-terminal ankyrin-repeat which comprises approximately 28 ankyrin domains. This repeat has been conjectured to be the gating spring which is involved in the transmission of mechanical force to the transmembrane domain (Howard and Bechstedt 2004; Liang et al. 2013). The ankyrin domains in this repeat presumably form a superhelix as they arrange into a complete turn which can be easily deformed mechanically. Ankyrin domains are widespread across proteins with very different functions and occur in 0.85% of all metazoan proteins. However, the average number of ankyrin domains across all ankyrin-containing proteins is only 4.8 (±4.5, median 3), and proteins with more than ten ankyrin domains are rare (Jernigan and Bordenstein 2014) (see also fig. 1). Note that determining the precise number of domains in a domain repeat is a difficult problem. The underlying reasons are inaccuracies arising during sequencing and assembly, and rapid evolutionary changes of sequences and number of domains, even at the population level. Finally, computational challenges are common, for example, in the frame capturing of the domains in a repeat (Schaper et al. 2012). Consequently, even the most accurate programs may fail to determine the number of domains in a repeat by a number of 1. We will, in the following work, always use the lower number of prediction, for example, 28 if there might be 28 or 29 domains in a repeat.Fig. 1.—

Bottom Line: In flies, the transient-receptor-potential N protein (TRP-N) was found to be a cilia-associated mechanoreceptor.We propose that these new candidate proteins help explain the sensory complexity of Cnidaria which has been previously observed but so far has lacked a molecular underpinning.Also, the ancient appearance of TRP-N supports a common origin of important components of the nervous systems in Ctenophores, Cnidaria, and Bilateria.

View Article: PubMed Central - PubMed

Affiliation: Institute for Evolution and Biodiversity, University of Muenster, Germany.

Show MeSH