scholarly journals Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
Author(s):  
Elena A. Ritschard ◽  
Robert R. Fitak ◽  
Oleg Simakov ◽  
Sönke Johnsen
Keyword(s):  
Signal Transduction ◽  
Positive Selection ◽  
G Protein ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Signatures ◽  
History Of ◽  
G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

scholarly journals The complex evolution of the HSP70 gene family

2020 ◽  
Author(s):  
Er-meng Yu ◽  
Tatsuki Yoshinaga ◽  
Frank L. Jalufka ◽  
Hashimul Ehsan ◽  
David B. Mark Welch ◽  
...  
Keyword(s):  
Heat Shock ◽  
Evolutionary History ◽  
Brachionus Plicatilis ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Evolutionary Genetics ◽  
Purifying Selection ◽  
Hsp70 Family ◽  
History Of ◽  
Species Specific

AbstractThe 70-kDa heat shock protein (HSP70) family contains several isoforms localized in different subcellular compartments. The cytosolic isoforms have been classified into stress-inducible HSP70s and constitutive heat shock cognates (HSC70s), but occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons have been a source of confusion in the evolution of the metazoan HSP70 family. Here we provide novel insights into the evolutionary history of this important molecular chaperone. We first cloned two HSP70 genes from the rotifer Brachionus plicatilis, an emerging model in evolutionary genetics, and confirmed their stress inducibility. Subsequent phylogenetic analyses of 100 full-length HSP70 family member genes revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage contains a relatively small number of Lophotrochozoan and Ecdysozoan genes, none of which have been shown to be constitutively expressed. The second included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and in the second there are well-supported phylum-specific clades for Rotifera, Nematoda, and Chordata. Some genes in this lineage have likely independently acquired stress inducibility, which may explain the sporadic distribution of genes designated as “HSP70” or “HSC70” in previous analyses. Consistent with the history of diversification within each group, stress-inducible members of the second lineage show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family independent from their expression patterns, encouraging the development of new nomenclature based on evolutionary history.

scholarly journals Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates

2019 ◽  
Vol 12 (1) ◽  
pp. 3615-3634 ◽  
Author(s):  
Guangshuai Liu ◽  
Huanxin Zhang ◽  
Chao Zhao ◽  
Honghai Zhang
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Receptor Gene ◽  
Purifying Selection ◽  
Protein Architecture ◽  
Wide Range ◽  
History Of ◽  
Membrane Bound

Abstract Adaptation to a wide range of pathogenic environments is a major aspect of the ecological adaptations of vertebrates during evolution. Toll-like receptors (TLRs) are ancient membrane-bound sensors in animals and are best known for their roles in detecting and defense against invading pathogenic microorganisms. To understand the evolutionary history of the vertebrate TLR gene family, we first traced the origin of single-cysteine cluster TLRs that share the same protein architecture with vertebrate TLRs in early-branching animals and then analyzed all members of the TLR family in over 200 species covering all major vertebrate clades. Our results indicate that although the emergence of single-cysteine cluster TLRs predates the separation of bilaterians and cnidarians, most vertebrate TLR members originated shortly after vertebrate emergence. Phylogenetic analyses divided 1,726 vertebrate TLRs into 8 subfamilies, and TLR3 may represent the most ancient subfamily that emerged before the branching of deuterostomes. Our analysis reveals that purifying selection predominated in the evolution of all vertebrate TLRs, with mean dN/dS (ω) values ranging from 0.082 for TLR21 in birds to 0.434 for TLR11 in mammals. However, we did observe patterns of positive selection acting on specific codons (527 of 60,294 codons across all vertebrate TLRs, 8.7‰), which are significantly concentrated in ligand-binding extracellular domains and suggest host–pathogen coevolutionary interactions. Additionally, we found stronger positive selection acting on nonviral compared with viral TLRs, indicating the more essential nonredundant function of viral TLRs in host immunity. Taken together, our findings provide comprehensive insight into the complex evolutionary processes of the vertebrate TLR gene family, involving gene duplication, pseudogenization, purification, and positive selection.

scholarly journals Every Detail Matters. That Is, How the Interaction between Gα Proteins and Membrane Affects Their Function

Membranes ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 222
Author(s):  
Agnieszka Polit ◽  
Paweł Mystek ◽  
Ewa Błasiak
Keyword(s):  
Signal Transduction ◽  
G Protein ◽  
G Proteins ◽  
Lipid Membranes ◽  
Signaling Proteins ◽  
Heterotrimeric G Proteins ◽  
Membrane Attachment ◽  
The Individual ◽  
Multicellular Organisms ◽  
G Protein Coupled

In highly organized multicellular organisms such as humans, the functions of an individual cell are dependent on signal transduction through G protein-coupled receptors (GPCRs) and subsequently heterotrimeric G proteins. As most of the elements belonging to the signal transduction system are bound to lipid membranes, researchers are showing increasing interest in studying the accompanying protein–lipid interactions, which have been demonstrated to not only provide the environment but also regulate proper and efficient signal transduction. The mode of interaction between the cell membrane and G proteins is well known. Despite this, the recognition mechanisms at the molecular level and how the individual G protein-membrane attachment signals are interrelated in the process of the complex control of membrane targeting of G proteins remain unelucidated. This review focuses on the mechanisms by which mammalian Gα subunits of G proteins interact with lipids and the factors responsible for the specificity of membrane association. We summarize recent data on how these signaling proteins are precisely targeted to a specific site in the membrane region by introducing well-defined modifications as well as through the presence of polybasic regions within these proteins and interactions with other components of the heterocomplex.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

Caffeine does not inhibit substance P-evoked intracellular Ca2+ mobilization in rat salivary acinar cells

1999 ◽  
Vol 276 (4) ◽  
pp. C915-C922 ◽  
Author(s):  
J. T. Seo ◽  
H. Sugiya ◽  
S. I. Lee ◽  
M. C. Steward ◽  
A. C. Elliott
Keyword(s):  
Signal Transduction ◽  
Substance P ◽  
G Protein ◽  
Acinar Cells ◽  
Inhibitory Effect ◽  
Structural Motif ◽  
Stimulus Response ◽  
Inhibit Substance ◽  
Prior Application ◽  
G Protein Coupled

We used the Ca2+-sensitive fluorescent dye fura 2, together with measurements of intracellulard- myo-inositol 1,4,5-trisphosphate [Ins(1,4,5) P 3], to assess the inhibitory effects of caffeine on signal transduction via G protein-coupled receptor pathways in isolated rat mandibular salivary acinar cells. ACh, norepinephrine (NE), and substance P (SP) all evoked substantial increases in the intracellular free Ca2+ concentration ([Ca2+]i). Responses to ACh and NE were markedly inhibited by prior application of 20 mM caffeine. The inhibitory effect of caffeine was not reproduced by phosphodiesterase inhibition with IBMX or addition of cell-permeant dibutyryl cAMP. In contrast to the ACh and NE responses, the [Ca2+]iresponse to SP was unaffected by caffeine. Despite this, SP and ACh appeared to mobilize Ca2+ from a common intracellular pool. Measurements of agonist-induced changes in Ins(1,4,5) P 3levels confirmed that caffeine inhibited the stimulus-response coupling pathway at a point before Ins(1,4,5) P 3generation. Caffeine did not, however, inhibit [Ca2+]iresponses evoked by direct activation of G proteins with 40 mM F−. These data show that caffeine inhibits G protein-coupled signal transduction in these cells at some element that is common to the muscarinic and α-adrenergic signaling pathways but is not shared by the SP signaling pathway. We suggest that this element might be a specific structural motif on the G protein-coupled muscarinic and α-adrenergic receptors.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals The Vertical and Horizontal Pathways in the Monkey Retina Are Modulated by Typical and Atypical Cannabinoid Receptors

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3160
Author(s):  
Joseph Bouskila ◽  
Maxime Bleau ◽  
Catarina Micaelo-Fernandes ◽  
Jean-François Bouchard ◽  
Maurice Ptito
Keyword(s):  
G Protein ◽  
Visual Information ◽  
Cannabinoid Receptors ◽  
Transient Receptor Potential ◽  
Expression Patterns ◽  
Retinal Function ◽  
Age Related Macular Degeneration ◽  
Transient Receptor Potential Vanilloid ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

The endocannabinoid (eCB) system has been found in all visual parts of the central ner-vous system and plays a role in the processing of visual information in many species, including monkeys and humans. Using anatomical methods, cannabinoid receptors are present in the monkey retina, particularly in the vertical glutamatergic pathway, and also in the horizontal GABAergic pathway. Modulating the eCB system regulates normal retinal function as demonstrated by electrophysiological recordings. The characterization of the expression patterns of all types of cannabinoid receptors in the retina is progressing, and further research is needed to elucidate their exact role in processing visual information. Typical cannabinoid receptors include G-protein coupled receptor CB1R and CB2R, and atypical cannabinoid receptors include the G-protein coupled receptor 55 (GPR55) and the ion channel transient receptor potential vanilloid 1 (TRPV1). This review focuses on the expression and localization studies carried out in monkeys, but some data on other animal species and humans will also be reported. Furthermore, the role of the endogenous cannabinoid receptors in retinal function will also be presented using intraocular injections of known modulators (agonists and antagonists) on electroretinographic patterns in monkeys. The effects of the natural bioactive lipid lysophosphatidylglucoside and synthetic FAAH inhibitor URB597 on retinal function, will also be described. Finally, the potential of typical and atypical cannabinoid receptor acti-vity regulation in retinal diseases, such as age-related macular degeneration, diabetic retinopathy, glaucoma, and retinitis pigmentosa will be briefly explored.

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