Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS)

Himmel, Nathaniel J.; Gray, Thomas R.; Cox, Daniel N.

doi:10.1093/molbev/msaa065

Cited by 28 publications

(45 citation statements)

References 59 publications

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“…R. Soc. B 287: 20201309 extend to non-arthropod protostomes nor non-protostome invertebrates [2,3,20,21], and thus here, only vertebrate paralogues and a broad protostome clade are shown (electronic supplementary material, figure S3B). The proposed α-β distinction is phylogenetically well supported in the literature cited above, but has not been explicitly named.…”

Section: (B) Trpc: Canonicalmentioning

confidence: 99%

“…A third putative subfamily, TRPMc (formerly called TRPMm), has been found in some arthropods and possibly cnidarians; however, its presence and position are inconsistent and phylogenetically unstable [2,20,21].…”

Section: (B) Trpc: Canonicalmentioning

confidence: 99%

“…There is no evidence of TRPN in placozoans, comb jellies, or choanoflagellates, leading to the suggestion that TRPN emerged in a common cnidarian-bilaterian ancestor after animals emerged [3,17]. However, the most closely related TRP family is typically thought to be TRPC, and choanoflagellates are thought to have a TRPC [2,3,17]; this would suggest that TRPC and TRPN split before animals emerged, and that TRPN was lost in the taxa indicated above.…”

Section: (D) Trpml: Mucolipinmentioning

confidence: 99%

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Transient receptor potential channels: current perspectives on evolution, structure, function and nomenclature

Himmel

Cox

2020

Proc. R. Soc. B.

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The transient receptor potential superfamily of ion channels (TRP channels) is widely recognized for the roles its members play in sensory nervous systems. However, the incredible diversity within the TRP superfamily, and the wide range of sensory capacities found therein, has also allowed TRP channels to function beyond sensing an organism's external environment, and TRP channels have thus become broadly critical to (at least) animal life. TRP channels were originally discovered in Drosophila and have since been broadly studied in animals; however, thanks to a boom in genomic and transcriptomic data, we now know that TRP channels are present in the genomes of a variety of creatures, including green algae, fungi, choanoflagellates and a number of other eukaryotes. As a result, the organization of the TRP superfamily has changed radically from its original description. Moreover, modern comprehensive phylogenetic analyses have brought to light the vertebrate-centricity of much of the TRP literature; much of the nomenclature has been grounded in vertebrate TRP subfamilies, resulting in a glossing over of TRP channels in other taxa. Here, we provide a comprehensive review of the function, structure and evolutionary history of TRP channels, and put forth a more complete set of non-vertebrate-centric TRP family, subfamily and other subgroup nomenclature.

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Section: (B) Trpc: Canonicalmentioning

confidence: 99%

Section: (B) Trpc: Canonicalmentioning

confidence: 99%

Section: (D) Trpml: Mucolipinmentioning

confidence: 99%

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Transient receptor potential channels: current perspectives on evolution, structure, function and nomenclature

Himmel

Cox

2020

Proc. R. Soc. B.

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“…The amount of sequences and their phylogenetic distribution allows performing robust inferences regarding how gene family members are related to each other and a description of the processes associated with the evolution of these gene families (Nei and Rooney 2005) . The available genomes also open an opportunity to discover new gene family members that are not currently described mainly because they are not present in model species and/or to the absence of appropriate evolutionary analyses (Wichmann et al 2016;Céspedes et al 2017;Himmel et al 2020) . It is important to know the number of gene lineages that belong to a given gene family, as well as the variation in the repertoire of genes between species.…”

Section: Introductionmentioning

confidence: 99%

How many sirtuin genes are out there? evolution of sirtuin genes in vertebrates with a description of a new family member*

Opazo

Zavala

Vandewege

et al. 2020

Preprint

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Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

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“…Their structure includes a SLOG domain, a TRP domain, and a nudix-Hydrolase domain. (adapted from [99,107]). (I) TRPP channels.…”

Section: Trp Superfamilymentioning

confidence: 99%

Biophysics and Modeling of Mechanotransduction in Neurons: A Review

2021

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Mechanosensing is a key feature through which organisms can receive inputs from the environment and convert them into specific functional and behavioral outputs. Mechanosensation occurs in many cells and tissues, regulating a plethora of molecular processes based on the distribution of forces and stresses both at the cell membrane and at the intracellular organelles levels, through complex interactions between cells’ microstructures, cytoskeleton, and extracellular matrix. Although several primary and secondary mechanisms have been shown to contribute to mechanosensation, a fundamental pathway in simple organisms and mammals involves the presence of specialized sensory neurons and the presence of different types of mechanosensitive ion channels on the neuronal cell membrane. In this contribution, we present a review of the main ion channels which have been proven to be significantly involved in mechanotransduction in neurons. Further, we discuss recent studies focused on the biological mechanisms and modeling of mechanosensitive ion channels’ gating, and on mechanotransduction modeling at different scales and levels of details.

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Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS)

Cited by 28 publications

References 59 publications

Transient receptor potential channels: current perspectives on evolution, structure, function and nomenclature

Transient receptor potential channels: current perspectives on evolution, structure, function and nomenclature

How many sirtuin genes are out there? evolution of sirtuin genes in vertebrates with a description of a new family member*

Biophysics and Modeling of Mechanotransduction in Neurons: A Review

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