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McCulloch KJ, Babonis LS, Liu A, Daly CM, Martindale MQ, Koenig KM. Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia. EvoDevo 2023; 14:14. [PMID: 37735470 PMCID: PMC10512536 DOI: 10.1186/s13227-023-00218-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Opsins are the primary proteins responsible for light detection in animals. Cnidarians (jellyfish, sea anemones, corals) have diverse visual systems that have evolved in parallel with bilaterians (squid, flies, fish) for hundreds of millions of years. Medusozoans (e.g., jellyfish, hydroids) have evolved eyes multiple times, each time independently incorporating distinct opsin orthologs. Anthozoans (e.g., corals, sea anemones,) have diverse light-mediated behaviors and, despite being eyeless, exhibit more extensive opsin duplications than medusozoans. To better understand the evolution of photosensitivity in animals without eyes, we increased anthozoan representation in the phylogeny of animal opsins and investigated the large but poorly characterized opsin family in the sea anemone Nematostella vectensis. RESULTS We analyzed genomic and transcriptomic data from 16 species of cnidarians to generate a large opsin phylogeny (708 sequences) with the largest sampling of anthozoan sequences to date. We identified 29 opsins from N. vectensis (NvOpsins) with high confidence, using transcriptomic and genomic datasets. We found that lineage-specific opsin duplications are common across Cnidaria, with anthozoan lineages exhibiting among the highest numbers of opsins in animals. To establish putative photosensory function of NvOpsins, we identified canonically conserved protein domains and amino acid sequences essential for opsin function in other animal species. We show high sequence diversity among NvOpsins at sites important for photoreception and transduction, suggesting potentially diverse functions. We further examined the spatiotemporal expression of NvOpsins and found both dynamic expression of opsins during embryonic development and sexually dimorphic opsin expression in adults. CONCLUSIONS These data show that lineage-specific duplication and divergence has led to expansive diversity of opsins in eyeless cnidarians, suggesting opsins from these animals may exhibit novel biochemical functions. The variable expression patterns of opsins in N. vectensis suggest opsin gene duplications allowed for a radiation of unique sensory cell types with tissue- and stage-specific functions. This diffuse network of distinct sensory cell types could be an adaptive solution for varied sensory tasks experienced in distinct life history stages in Anthozoans.
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Affiliation(s)
- Kyle J McCulloch
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL, 32080, USA
| | - Alicia Liu
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA , 02138, , USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Christina M Daly
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA , 02138, , USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Mark Q Martindale
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL, 32080, USA
| | - Kristen M Koenig
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA , 02138, , USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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Research Advances in Heterotrimeric G-Protein α Subunits and Uncanonical G-Protein Coupled Receptors in Plants. Int J Mol Sci 2021; 22:ijms22168678. [PMID: 34445383 PMCID: PMC8395518 DOI: 10.3390/ijms22168678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022] Open
Abstract
As crucial signal transducers, G-proteins and G-protein-coupled receptors (GPCRs) have attracted increasing attention in the field of signal transduction. Research on G-proteins and GPCRs has mainly focused on animals, while research on plants is relatively rare. The mode of action of G-proteins is quite different from that in animals. The G-protein α (Gα) subunit is the most essential member of the G-protein signal cycle in animals and plants. The G-protein is activated when Gα releases GDP and binds to GTP, and the relationships with the GPCR and the downstream signal are also achieved by Gα coupling. It is important to study the role of Gα in the signaling pathway to explore the regulatory mechanism of G-proteins. The existence of a self-activated Gα in plants makes it unnecessary for the canonical GPCR to activate the G-protein by exchanging GDP with GTP. However, putative GPCRs have been found and proven to play important roles in G-protein signal transduction. The unique mode of action of G-proteins and the function of putative GPCRs in plants suggest that the same definition used in animal research cannot be used to study uncanonical GPCRs in plants. This review focuses on the different functions of the Gα and the mode of action between plants and animals as well as the functions of the uncanonical GPCR. This review employs a new perspective to define uncanonical GPCRs in plants and emphasizes the role of uncanonical GPCRs and Gα subunits in plant stress resistance and agricultural production.
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Leach WB, Reitzel AM. Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian. BMC Genomics 2020; 21:361. [PMID: 32410571 PMCID: PMC7222589 DOI: 10.1186/s12864-020-6766-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background Animals have specific molecular, physiological, and behavioral responses to light that are influenced by wavelength and intensity. Predictable environmental changes – predominantly solar and lunar cycles – drive endogenous daily oscillations by setting internal pacemakers, otherwise known as the circadian clock. Cnidarians have been a focal group to discern the evolution of light responsiveness due to their phylogenetic position as a sister phylum to bilaterians and broad range of light-responsive behaviors and physiology. Marine species that occupy a range of depths will experience different ranges of wavelengths and light intensities, which may result in variable phenotypic responses. Here, we utilize the eyeless sea anemone Nematostella vectensis, an estuarine anemone that typically resides in shallow water habitats, to compare behavioral and molecular responses when exposed to different light conditions. Results Quantitative measures of locomotion clearly showed that this species responds to light in the blue and green spectral range with a circadian activity profile, in contrast to a circatidal activity profile in the red spectral range and in constant darkness. Differences in average day/night locomotion was significant in each condition, with overall peak activity during the dark period. Comparative analyses of 96 transcriptomes from individuals sampled every 4 h in each lighting treatment revealed complex differences in gene expression between colors, including in many of the genes likely involved in the cnidarian circadian clock. Transcriptional profiling showed the majority of genes are differentially expressed when comparing mid-day with mid-night, and mostly in red light. Gene expression profiles were largely unique in each color, although animals in blue and green were overall more similar to each other than to red light. Conclusions Together, these analyses support the hypothesis that cnidarians are sensitive to red light, and this perception results in a rich transcriptional and divergent behavioral response. Future work determining the specific molecular mechanisms driving the circadian and potential circatidal rhythms measured here would be impactful to connect gene expression variation with behavioral variation in this eyeless species.
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Affiliation(s)
- Whitney B Leach
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Woodward Hall, Room 381A, Charlotte, NC, 28223, USA.
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Woodward Hall, Room 381A, Charlotte, NC, 28223, USA
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Taubner I, Hu MY, Eisenhauer A, Bleich M. Electrophysiological evidence for light-activated cation transport in calcifying corals. Proc Biol Sci 2019; 286:20182444. [PMID: 30963934 PMCID: PMC6408601 DOI: 10.1098/rspb.2018.2444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Light has been demonstrated to enhance calcification rates in hermatypic coral species. To date, it remains unresolved whether calcifying epithelia change their ion transport activity during illumination, and whether such a process is mediated by the endosymbiotic algae or can be controlled by the coral host itself. Using a modified Ussing chamber in combination with H+ sensitive microelectrode measurements, the present work demonstrates that light triggers the generation of a skeleton positive potential of up to 0.9 mV in the hermatypic coral Stylophora pistillata. This potential is generated by a net flux of cations towards the skeleton and reaches its maximum at blue (450 nm) light. The effects of pharmacological inhibitors targeting photosynthesis 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and anion transport 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS) were investigated by pH microelectrode measurements in coral tissues demonstrating a rapid decrease in tissue pH under illumination. However, these inhibitors showed no effect on the electrophysiological light response of the coral host. By contrast, metabolic inhibition by cyanide and deoxyglucose reversibly inhibited the light-induced cation flux towards the skeleton. These results suggest that ion transport across coral epithelia is directly triggered by blue light, independent of photosynthetic activity of algal endosymbionts. Measurements of this very specific and quantifiable physiological response can provide parameters to identify photoreception mechanisms and will help to broaden our understanding of the mechanistic link between light stimulation and epithelial ion transport, potentially relevant for calcification in hermatypic corals.
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Affiliation(s)
- Isabelle Taubner
- Christian-Albrechts-Universität, Institute of Physiology, Kiel, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Marian Y. Hu
- Christian-Albrechts-Universität, Institute of Physiology, Kiel, Germany
| | | | - Markus Bleich
- Christian-Albrechts-Universität, Institute of Physiology, Kiel, Germany
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Traylor-Knowles N. In Situ Hybridization Techniques for Paraffin-Embedded Adult Coral Samples. J Vis Exp 2018. [PMID: 30222153 DOI: 10.3791/57853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Corals are important ocean invertebrates that are critical for overall ocean health as well as human health. However, due to human impacts such as rising ocean temperatures and ocean acidification, corals are increasingly under threat. To tackle these challenges, advances in cell and molecular biology have proven to be crucial for diagnosing the health of corals. Modifying some of the techniques commonly used in human medicine could greatly improve researchers' ability to treat and save corals. To address this, a protocol for in situ hybridization used primarily in human medicine and evolutionary developmental biology has been adapted for use in adult corals under stress. The purpose of this method is to visualize the spatial expression of an RNA probe in adult coral tissue that has been embedded in paraffin and sectioned onto glass slides. This method focuses on removal of the paraffin and rehydration of the sample, pretreatment of the sample to ensure permeability of the sample, pre-hybridization incubation, hybridization of the RNA probe, and visualization of the RNA probe. This is a powerful method when using non-model organisms to discover where specific genes are expressed, and the protocol can be easily adapted for other non-model organisms. However, the method is limited in that it is primarily qualitative, because expression intensity can vary depending on the amount of time used during the visualization step and the concentration of the probe. Furthermore, patience is required, as this protocol can take up to 5 days (and in many cases, longer) depending on the probe being used. Finally, non-specific background staining is common, but this limitation can be overcome.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami, Rosenstiel School of Marine and Atmospheric Sciences;
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Jones R, Ricardo GF, Negri AP. Effects of sediments on the reproductive cycle of corals. MARINE POLLUTION BULLETIN 2015; 100:13-33. [PMID: 26384866 DOI: 10.1016/j.marpolbul.2015.08.021] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/29/2015] [Accepted: 08/02/2015] [Indexed: 05/07/2023]
Abstract
Dredging, river plumes and natural resuspension events can release sediments into the water column where they exert a range of effects on underlying communities. In this review we examine possible cause-effect pathways whereby light reduction, elevated suspended sediments and sediment deposition could affect the reproductive cycle and early life histories of corals. The majority of reported or likely effects (30+) were negative, including a suite of previously unrecognized effects on gametes. The length of each phase of the life-cycle was also examined together with analysis of water quality conditions that can occur during a dredging project over equivalent durations, providing a range of environmentally relevant exposure scenarios for future testing. The review emphasizes the need to: (a) accurately quantify exposure conditions, (b) identify the mechanism of any effects in future studies, and (c) recognize the close interlinking of proximate factors which could confound interpretation of studies.
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Affiliation(s)
- R Jones
- Australian Institute of Marine Science (AIMS), Perth, Australia; Western Australian Marine Science Institution (WAMSI), Perth, Australia; Oceans Institute, University of Western Australia, Perth, Australia.
| | - G F Ricardo
- Australian Institute of Marine Science (AIMS), Perth, Australia; Western Australian Marine Science Institution (WAMSI), Perth, Australia; Centre of Microscopy, Charaterisation and Analysis, The University of Western Australia, Perth, Australia.
| | - A P Negri
- Australian Institute of Marine Science (AIMS), Perth, Australia; Western Australian Marine Science Institution (WAMSI), Perth, Australia.
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Reitzel AM, Tarrant AM, Levy O. Circadian clocks in the cnidaria: environmental entrainment, molecular regulation, and organismal outputs. Integr Comp Biol 2013; 53:118-30. [PMID: 23620252 DOI: 10.1093/icb/ict024] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The circadian clock is a molecular network that translates predictable environmental signals, such as light levels, into organismal responses, including behavior and physiology. Regular oscillations of the molecular components of the clock enable individuals to anticipate regularly fluctuating environmental conditions. Cnidarians play important roles in benthic and pelagic marine environments and also occupy a key evolutionary position as the likely sister group to the bilaterians. Together, these attributes make members of this phylum attractive as models for testing hypotheses on roles for circadian clocks in regulating behavior, physiology, and reproduction as well as those regarding the deep evolutionary conservation of circadian regulatory pathways in animal evolution. Here, we review and synthesize the field of cnidarian circadian biology by discussing the diverse effects of daily light cycles on cnidarians, summarizing the molecular evidence for the conservation of a bilaterian-like circadian clock in anthozoan cnidarians, and presenting new empirical data supporting the presence of a conserved feed-forward loop in the starlet sea anemone, Nematostella vectensis. Furthermore, we discuss critical gaps in our current knowledge about the cnidarian clock, including the functions directly regulated by the clock and the precise molecular interactions that drive the oscillating gene-expression patterns. We conclude that the field of cnidarian circadian biology is moving rapidly toward linking molecular mechanisms with physiology and behavior.
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Affiliation(s)
- Adam M Reitzel
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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Shoguchi E, Tanaka M, Shinzato C, Kawashima T, Satoh N. A genome-wide survey of photoreceptor and circadian genes in the coral, Acropora digitifera. Gene 2012; 515:426-31. [PMID: 23266624 DOI: 10.1016/j.gene.2012.12.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/29/2012] [Accepted: 12/06/2012] [Indexed: 12/30/2022]
Abstract
Corals exhibit circadian behaviors, but little is known about the molecular mechanisms underlying the regulation of these behaviors. We surveyed the recently decoded genome of the coral, Acropora digitifera, for photoreceptor and circadian genes, using molecular phylogenetic analyses. Our search for photoreceptor genes yielded seven opsin and three cryptochrome genes. Two genes from each family likely underwent tandem duplication in the coral lineage. We also found the following A. digitifera orthologs to Drosophila and mammalian circadian clock genes: four clock, one bmal/cycle, three pdp1-like, one creb/atf, one sgg/zw3, two ck2alpha, one dco (csnk1d/cnsk1e), one slim/BTRC, and one grinl. No vrille, rev-ervα/nr1d1, bhlh2, vpac2, adcyap1, or adcyaplr1 orthologs were found. Intriguingly, in spite of an extensive survey, we also failed to find homologs of period and timeless, although we did find one timeout gene. In addition, the coral genes were compared to orthologous genes in the sea anemone, Nematostella vectensis. Thus, the coral and sea anemone genomes share a similar repertoire of circadian clock genes, although A. digitifera contains more clock genes and fewer photoreceptor genes than N. vectensis. This suggests that the circadian clock system was established in a common ancestor of corals and sea anemones, and was diversified by tandem gene duplications and the loss of paralogous genes in each lineage. It will be interesting to determine how the coral circadian clock functions without period.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan.
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Hilton JD, Brady AK, Spaho SA, Vize PD. Photoreception and signal transduction in corals: proteomic and behavioral evidence for cytoplasmic calcium as a mediator of light responsivity. THE BIOLOGICAL BULLETIN 2012; 223:291-299. [PMID: 23264475 DOI: 10.1086/bblv223n3p291] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Little is known about how corals sense and respond to light. In this report the proteome of coral is explored using 2D protein electrophoresis in two species, Montastraea cavernosa and Acropora millepora. Multiple protein species have major shifts in abundance in both species when sampled in daylight compared to corals sampled late in the night. These changes were observed both in larvae lacking zooxanthellae and in adult tissue containing zooxanthellae, including both Pacific and Caribbean corals. When larvae kept in the dark were treated with either thapsigargin or ionomycin, compounds that raise the level of cytoplasmic calcium, the night pattern of proteins shifted to the day pattern. This implies that photoreceptors responding to light elevate calcium levels and that calcium acts as the second messenger relaying light responses in corals. Corals spawn at night, and spawning can be delayed by exposure to light or pushed forward by early artificial sunsets. In a series of behavioral experiments, treatment of corals with ionomycin or thapsigargin was found to delay broadcast spawning in M. franksi, demonstrating that pharmacologically altering cytoplasmic calcium levels generates the same response as light exposure. Together these results show that the photo-responsive cells of corals detect and respond to light by altering cytoplasmic calcium levels, similarly to the transduction pathways in complex invertebrate eyes. The primacy of cytoplasmic calcium levels in light responsivity has broad implications for coral reproduction, including predicting how different species spawn at different times after sunset and how reproductive isolation is achieved during coral speciation.
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Affiliation(s)
- J Daniel Hilton
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
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Hoyle CH. Evolution of neuronal signalling: Transmitters and receptors. Auton Neurosci 2011; 165:28-53. [DOI: 10.1016/j.autneu.2010.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 05/09/2010] [Accepted: 05/18/2010] [Indexed: 11/16/2022]
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Brady AK, Snyder KA, Vize PD. Circadian cycles of gene expression in the coral, Acropora millepora. PLoS One 2011; 6:e25072. [PMID: 21949855 PMCID: PMC3176305 DOI: 10.1371/journal.pone.0025072] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 08/25/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Circadian rhythms regulate many physiological, behavioral and reproductive processes. These rhythms are often controlled by light, and daily cycles of solar illumination entrain many clock regulated processes. In scleractinian corals a number of different processes and behaviors are associated with specific periods of solar illumination or non-illumination--for example, skeletal deposition, feeding and both brooding and broadcast spawning. METHODOLOGY/PRINCIPAL FINDINGS We have undertaken an analysis of diurnal expression of the whole transcriptome and more focused studies on a number of candidate circadian genes in the coral Acropora millepora using deep RNA sequencing and quantitative PCR. Many examples of diurnal cycles of RNA abundance were identified, some of which are light responsive and damped quickly under constant darkness, for example, cryptochrome 1 and timeless, but others that continue to cycle in a robust manner when kept in constant darkness, for example, clock, cryptochrome 2, cycle and eyes absent, indicating that their transcription is regulated by an endogenous clock entrained to the light-dark cycle. Many other biological processes that varied between day and night were also identified by a clustering analysis of gene ontology annotations. CONCLUSIONS/SIGNIFICANCE Corals exhibit diurnal patterns of gene expression that may participate in the regulation of circadian biological processes. Rhythmic cycles of gene expression occur under constant darkness in both populations of coral larvae that lack zooxanthellae and in individual adult tissue containing zooxanthellae, indicating that transcription is under the control of a biological clock. In addition to genes potentially involved in regulating circadian processes, many other pathways were found to display diel cycles of transcription.
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Affiliation(s)
- Aisling K. Brady
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kevin A. Snyder
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Peter D. Vize
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Pelé J, Abdi H, Moreau M, Thybert D, Chabbert M. Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors. PLoS One 2011; 6:e19094. [PMID: 21544207 PMCID: PMC3081337 DOI: 10.1371/journal.pone.0019094] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 03/16/2011] [Indexed: 11/21/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) constitute the largest family of transmembrane receptors in the human genome. Understanding the mechanisms which drove the evolution of such a large family would help understand the specificity of each GPCR sub-family with applications to drug design. To gain evolutionary information on class A GPCRs, we explored their sequence space by metric multidimensional scaling analysis (MDS). Three-dimensional mapping of human sequences shows a non-uniform distribution of GPCRs, organized in clusters that lay along four privileged directions. To interpret these directions, we projected supplementary sequences from different species onto the human space used as a reference. With this technique, we can easily monitor the evolutionary drift of several GPCR sub-families from cnidarians to humans. Results support a model of radiative evolution of class A GPCRs from a central node formed by peptide receptors. The privileged directions obtained from the MDS analysis are interpretable in terms of three main evolutionary pathways related to specific sequence determinants. The first pathway was initiated by a deletion in transmembrane helix 2 (TM2) and led to three sub-families by divergent evolution. The second pathway corresponds to the differentiation of the amine receptors. The third pathway corresponds to parallel evolution of several sub-families in relation with a covarion process involving proline residues in TM2 and TM5. As exemplified with GPCRs, the MDS projection technique is an important tool to compare orthologous sequence sets and to help decipher the mutational events that drove the evolution of protein families.
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Affiliation(s)
- Julien Pelé
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - Hervé Abdi
- School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Matthieu Moreau
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - David Thybert
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - Marie Chabbert
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
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Anctil M. Chemical transmission in the sea anemone Nematostella vectensis: A genomic perspective. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2009; 4:268-289. [PMID: 20403752 DOI: 10.1016/j.cbd.2009.07.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 06/30/2009] [Accepted: 07/07/2009] [Indexed: 12/30/2022]
Abstract
The sequencing of the starlet sea anemone (Nematostella vectensis) genome provides opportunities to investigate the function and evolution of genes associated with chemical neurotransmission and hormonal signaling. This is of particular interest because sea anemones are anthozoans, the phylogenetically basal cnidarians least changed from the common ancestors of cnidarians and bilaterian animals, and because cnidarians are considered the most basal metazoans possessing a nervous system. This analysis of the genome has yielded 20 orthologues of enzymes and nicotinic receptors associated with cholinergic function, an even larger number of genes encoding enzymes, receptors and transporters for glutamatergic (28) and GABAergic (34) transmission, and two orthologues of purinergic receptors. Numerous genes encoding enzymes (14), receptors (60) and transporters (5) for aminergic transmission were identified, along with four adenosine-like receptors and one nitric oxide synthase. Diverse neuropeptide and hormone families are also represented, mostly with genes encoding prepropeptides and receptors related to varying closeness to RFamide (17) and tachykinin (14), but also galanin (8), gonadotropin-releasing hormones and vasopressin/oxytocin (5), melanocortins (11), insulin-like peptides (5), glycoprotein hormones (7), and uniquely cnidarian peptide families (44). Surprisingly, no muscarinic acetylcholine receptors were identified and a large number of melatonin-related, but not serotonin, orthologues were found. Phylogenetic tree construction and inspection of multiple sequence alignments reveal how evolutionarily and functionally distant chemical transmitter-related proteins are from those of higher metazoans.
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Affiliation(s)
- Michel Anctil
- Département de sciences biologiques and Centre de recherches en sciences neurologiques, Université de Montréal, Case postale 6128, Succursale Centre-Ville, Montréal, Québec, Canada H3C 3J7.
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Vize PD. Transcriptome analysis of the circadian regulatory network in the coral Acropora millepora. THE BIOLOGICAL BULLETIN 2009; 216:131-137. [PMID: 19366924 DOI: 10.1086/bblv216n2p131] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Entrained circadian rhythms control many biological processes. These cyclical systems are synchronized by environmental signals but continue to free run for a considerable time when the synchronizing stimuli are removed. In scleractinian corals that reproduce by broadcast spawning, timing processes are essential in ensuring successful fertilization. It is not known whether spawn timing is regulated directly by environmental signals or if it is entrained and regulated by circadian or circalunar rhythms. The genetic components of circadian systems have been studied in considerable detail in microbes, plants, and animals. To identify potential participants in regulating scleractinian circadian systems, we have undertaken a bioinformatic analysis of the transcriptome of larvae of the coral Acropora millepora. Acropora contigs assembled from more than 600,000 sequencing reads from larval mRNA were searched via NCBI BLAST for matches to 24 key insect and mammalian circadian genes. Matches were found to all queried genes, with 22 of 24 of these matches having strong confidence levels. An Acropora match to the nonvisual photoreceptor melanopsin was also identified. The high level of conservation of circadian gene networks implies that the regulatory interactions between pathway members are also likely to be conserved and to regulate entrained processes in corals.
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Affiliation(s)
- Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N1N4, Canada.
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Shinzato C, Iguchi A, Hayward DC, Technau U, Ball EE, Miller DJ. Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa. BMC Evol Biol 2008; 8:311. [PMID: 19014479 PMCID: PMC2613919 DOI: 10.1186/1471-2148-8-311] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 11/12/2008] [Indexed: 12/22/2022] Open
Abstract
Background Sox genes encode transcription factors that function in a wide range of developmental processes across the animal kingdom. To better understand both the evolution of the Sox family and the roles of these genes in cnidarians, we are studying the Sox gene complement of the coral, Acropora millepora (Class Anthozoa). Results Based on overall domain structures and HMG box sequences, the Acropora Sox genes considered here clearly fall into four of the five major Sox classes. AmSoxC is expressed in the ectoderm during development, in cells whose morphology is consistent with their assignment as sensory neurons. The expression pattern of the Nematostella ortholog of this gene is broadly similar to that of AmSoxC, but there are subtle differences – for example, expression begins significantly earlier in Acropora than in Nematostella. During gastrulation, AmSoxBb and AmSoxB1 transcripts are detected only in the presumptive ectoderm while AmSoxE1 transcription is restricted to the presumptive endoderm, suggesting that these Sox genes might play roles in germ layer specification. A third type B Sox gene, AmSoxBa, and a Sox F gene AmSoxF also have complex and specific expression patterns during early development. Each of these genes has a clear Nematostella ortholog, but in several cases the expression pattern observed in Acropora differs significantly from that reported in Nematostella. Conclusion These differences in expression patterns between Acropora and Nematostella largely reflect fundamental differences in developmental processes, underscoring the diversity of mechanisms within the anthozoan Sub-Class Hexacorallia (Zoantharia).
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Affiliation(s)
- Chuya Shinzato
- ARC Centre of Excellence for Coral Reef Studies and Comparative Genomics Centre, James Cook University, Townsville, Queensland 4811, Australia.
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Gookin TE, Kim J, Assmann SM. Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling. Genome Biol 2008; 9:R120. [PMID: 18671868 PMCID: PMC2530877 DOI: 10.1186/gb-2008-9-7-r120] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 04/19/2008] [Accepted: 07/31/2008] [Indexed: 11/10/2022] Open
Abstract
Computational prediction and in vivo protein coupling experiments identify candidate plant G-protein coupled receptors in Arabidopsis, rice and poplar. Background The classic paradigm of heterotrimeric G-protein signaling describes a heptahelical, membrane-spanning G-protein coupled receptor that physically interacts with an intracellular Gα subunit of the G-protein heterotrimer to transduce signals. G-protein coupled receptors comprise the largest protein superfamily in metazoa and are physiologically important as they sense highly diverse stimuli and play key roles in human disease. The heterotrimeric G-protein signaling mechanism is conserved across metazoa, and also readily identifiable in plants, but the low sequence conservation of G-protein coupled receptors hampers the identification of novel ones. Using diverse computational methods, we performed whole-proteome analyses of the three dominant model plant species, the herbaceous dicot Arabidopsis thaliana (mouse-eared cress), the monocot Oryza sativa (rice), and the woody dicot Populus trichocarpa (poplar), to identify plant protein sequences most likely to be GPCRs. Results Our stringent bioinformatic pipeline allowed the high confidence identification of candidate G-protein coupled receptors within the Arabidopsis, Oryza, and Populus proteomes. We extended these computational results through actual wet-bench experiments where we tested over half of our highest ranking Arabidopsis candidate G-protein coupled receptors for the ability to physically couple with GPA1, the sole Gα in Arabidopsis. We found that seven out of eight tested candidate G-protein coupled receptors do in fact interact with GPA1. We show through G-protein coupled receptor classification and molecular evolutionary analyses that both individual G-protein coupled receptor candidates and candidate G-protein coupled receptor families are conserved across plant species and that, in some cases, this conservation extends to metazoans. Conclusion Our computational and wet-bench results provide the first step toward understanding the diversity, conservation, and functional roles of plant candidate G-protein coupled receptors.
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Affiliation(s)
- Timothy E Gookin
- Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA.
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