Introduction to the symposium—Keeping Time During Evolution : Conservation and Innovation of the Circadian Clock

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative and Comparative Biology 53 (2013): 89-92, doi: 10.1093/icb/ict062.Diurnal and seasonal cues play critical and conserved roles in behavior, physiology, and reproduction in diverse animals. The circadian clock is a transcription-translation feedback loop that represents the molecular mechanism underlying many of these periodic processes, frequently through responses to light. Although much of the core regulatory machinery is deeply conserved among diverse animal lineages, there are also many examples of innovation in the way the clock either is constructed at the molecular-level or deployed in coordinating behavior and physiology. The nine papers contained within this issue address aspects of circadian signaling in diverse taxa, utilize wide-ranging approaches, and collectively provide thought-provoking discussion of future directions in circadian research.The symposium “Keeping Time During Animal Evolution: Conservation and Innovation of the Circadian Clock” was generously supported by the Society of Integrative and Comparative Biology and by Award 1239607 from the Integrative Organismal Systems Program at the National Science Foundation.2014-05-2

Nuclear receptor complement of the cnidarian Nematostella vectensis : phylogenetic relationships and developmental expression patterns

© 2009 Reitzel and Tarrant. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 9 (2009): 230, doi:10.1186/1471-2148-9-230.Nuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes. Sequenced genomes from an increasing number of bilaterians have provided a more complete picture of duplication and loss of nuclear receptors in protostomes and deuterostomes but have left open the question of which nuclear receptors were present in the cnidarian-bilaterian ancestor. In addition, nuclear receptor expression and function are largely uncharacterized within cnidarians, preventing determination of conserved and novel nuclear receptor functions in the context of animal evolution. Here we report the first complete set of nuclear receptors from a cnidarian, the starlet sea anemone Nematostella vectensis. Genomic searches using conserved DNA- and ligand-binding domains revealed seventeen nuclear receptors in N. vectensis. Phylogenetic analyses support N. vectensis orthologs of bilaterian nuclear receptors in four nuclear receptor subfamilies within nuclear receptor family 2 (COUP-TF, TLL, HNF4, TR2/4) and one putative ortholog of GCNF (nuclear receptor family 6). Other N. vectensis genes grouped well with nuclear receptor family 2 but represented lineage-specific duplications somewhere within the cnidarian lineage and were not clear orthologs of bilaterian genes. Three nuclear receptors were not well-supported within any particular nuclear receptor family. The seventeen nuclear receptors exhibited distinct developmental expression patterns, with expression of several nuclear receptors limited to a subset of developmental stages. N. vectensis contains a diverse complement of nuclear receptors including orthologs of several bilaterian nuclear receptors. Novel nuclear receptors in N. vectensis may be ancient genes lost from triploblastic lineages or may represent cnidarian-specific radiations. Nuclear receptors exhibited distinct developmental expression patterns, which are consistent with diverse regulatory roles for these genes. Understanding the evolutionary relationships and developmental expression of the N. vectensis nuclear receptor complement provides insight into the evolution of the nuclear receptor superfamily and a foundation for mechanistic characterization of cnidarian nuclear receptor function.We are grateful for financial support from the Woods Hole Oceanographic Institution (WHOI) through the Tropical Research Initiative, the Ocean Life Institute (AMT), the Academic Programs Office, and to the Beacon Institute for Rivers and Estuaries (AMR)

Circadian clocks in the cnidaria : environmental entrainment, molecular regulation, and organismal outputs

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative and Comparative Biology 53 (2013): 118-130, doi:10.1093/icb/ict024.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 role 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.This work was supported by the United States – Israel Binational Science Foundation award 2011187 (AMT and OL), the National Institutes of Health / National Institute of Child Health and Human Development award HD062178 (AMR), and generous funding from the University of North Carolina at Charlotte (AMR).2014-04-2

Light entrained rhythmic gene expression in the sea anemone Nematostella vectensis : the evolution of the animal circadian clock

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e12805, doi:10.1371/journal.pone.0012805.Circadian rhythms in behavior and physiology are the observable phenotypes from cycles in expression of, interactions between, and degradation of the underlying molecular components. In bilaterian animals, the core molecular components include Timeless-Timeout, photoreceptive cryptochromes, and several members of the basic-loop-helix-Per-ARNT-Sim (bHLH-PAS) family. While many of core circadian genes are conserved throughout the Bilateria, their specific roles vary among species. Here, we identify and experimentally study the rhythmic gene expression of conserved circadian clock members in a sea anemone in order to characterize this gene network in a member of the phylum Cnidaria and to infer critical components of the clockwork used in the last common ancestor of cnidarians and bilaterians. We identified homologs of circadian regulatory genes in the sea anemone Nematostella vectensis, including a gene most similar to Timeout, three cryptochromes, and several key bHLH-PAS transcription factors. We then maintained N. vectensis either in complete darkness or in a 12 hour light: 12 hour dark cycle in three different light treatments (blue only, full spectrum, blue-depleted). Gene expression varied in response to light cycle and light treatment, with a particularly strong pattern observed for NvClock. The cryptochromes more closely related to the light-sensitive clade of cryptochromes were upregulated in light treatments that included blue wavelengths. With co-immunoprecipitation, we determined that heterodimerization between CLOCK and CYCLE is conserved within N. vectensis. Additionally, we identified E-box motifs, DNA sequences recognized by the CLOCK:CYCLE heterodimer, upstream of genes showing rhythmic expression. This study reveals conserved molecular and functional components of the circadian clock that were in place at the divergence of the Cnidaria and Bilateria, suggesting the animal circadian clockwork is more ancient than previous data suggest. Characterizing circadian regulation in a cnidarian provides insight into the early origins of animal circadian rhythms and molecular regulation of environmentally cued behaviors.The project described was supported by Award Number F32HD062178 to AMR from the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the Tropical Research Initiative of the Woods Hole Oceanographic Institution

Asexual Reproduction of Marine Invertebrate Embryos and Larvae

The life histories of marine invertebrates are incredibly diverse and provide a wealth of opportunities to develop and test hypotheses about how and why modes of reproduction, development, and behavior evolve within and among lineages. With respect to the evolution of reproductive and developmental mode, phylogenetic, adaptive, and functional hypotheses presented over the past century have predominantly focused on the evolution of reproductive traits (e.g., free spawning, brooding, encapsulation; nutritional mode of larvae (e.g., planktotrophy and lecithotrophy; and developmental form (e.g., larval morphology; direct and indirect development. Frequently, but not exclusively, these hypotheses have been tied to changes in per-offspring investment and influential models of per-offspring investment often serve as a framework for studies of the evolution of developmental modes. Phylogenetic assessment of the evolution of character states within lineages has revealed frequent shifts among life histories traits.https://scholarworks.wm.edu/asbookchapters/1011/thumbnail.jp

Heat shock protein expression during stress and diapause in the marine copepod Calanus finmarchicus

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Insect Physiology 57 (2011): 665-675, doi:10.1016/j.jinsphys.2011.03.007.Calanoid copepods, such as Calanus finmarchicus, are a key component of marine food webs. C. finmarchicus undergoes a facultative diapause during juvenile development, which profoundly affects their seasonal distribution and availability to their predators. The current ignorance of how copepod diapause is regulated limits understanding of copepod population dynamics, distribution, and ecosystem interactions. Heat shock proteins (Hsps) are a superfamily of molecular chaperones characteristically upregulated in response to stress conditions and frequently associated with diapause in other taxa. In this study, 8 heat shock proteins were identified in C. finmarchicus C5 copepodids (Hsp21, Hsp22, p26, Hsp90, and 4 forms of Hsp70), and expression of these transcripts was characterized in response to handling stress and in association with diapause. Hsp21, Hsp22, and Hsp70A (cytosolic subfamily) were induced by handling stress. Expression of Hsp70A was also elevated in shallow active copepodids relative to deep diapausing copepodids, which may reflect induction of this gene by varied stressors in active animals. In contrast, expression of Hsp22 was elevated in deep diapausing animals; Hsp22 may play a role both in short-term stress responses and in protecting proteins from degradation during diapause. Expression of most of the Hsps examined did not vary in response to diapause, perhaps because the diapause of C. finmarchicus is not associated with the extreme environmental conditions (e.g., freezing, desiccation) experienced by many other taxa, such as overwintering insects or Artemia cysts.Funding for AMA was provided by the WHOI Summer Student Fellowship Program and an EPA STAR fellowship

Daily cycle in oxygen consumption by the sea anemone Nematostella vectensis Stephenson

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Open (2016): 1-4, doi:10.1242/bio.013474.In bilaterian animals, the circadian clock is intimately involved in regulating energetic metabolism. Although cnidarians exhibit diel behavioral rhythms including cycles in locomotor activity, tentacle extension and spawning, daily cycles in cnidarian metabolism have not been described. To explore a possible circadian metabolic cycle, we maintained the anemone Nematostella vectensis in a 12 h light/dark cycle, a reversed light cycle, or in constant darkness. Oxygen consumption rates were measured at intervals using an optical oxygen meter. Respiration rates responded to entrainment with higher rates during light periods. During a second experiment with higher temporal resolution, respiration rates peaked late in the light period. The diel pattern could be detected after six days in constant darkness. Together, our results suggest that respiration rates in Nematostella exhibit a daily cycle that may be under circadian control and that the cycle in respiration rate is not driven by the previously described nocturnal increase in locomotor activity in this species.Funding was provided by the US–Israel Binational Science Foundation [Grant 201187]. I.T.J. was supported by the WHOI Summer Student Fellow program, which is partially funded by the National Science Foundation Research Experience for Undergraduates program. A.M.R. was supported by National Institutes of Heath [R15GM114740]

Transcriptomic Analysis of Four Cerianthid (Cnidaria, Ceriantharia) Venoms

This work is licensed under a Creative Commons Attribution 4.0 International License.Tube anemones, or cerianthids, are a phylogenetically informative group of cnidarians with complex life histories, including a pelagic larval stage and tube-dwelling adult stage, both known to utilize venom in stinging-cell rich tentacles. Cnidarians are an entirely venomous group that utilize their proteinaceous-dominated toxins to capture prey and defend against predators, in addition to several other ecological functions, including intraspecific interactions. At present there are no studies describing the venom for any species within cerianthids. Given their unique development, ecology, and distinct phylogenetic-placement within Cnidaria, our objective is to evaluate the venom-like gene diversity of four species of cerianthids from newly collected transcriptomic data. We identified 525 venom-like genes between all four species. The venom-gene profile for each species was dominated by enzymatic protein and peptide families, which is consistent with previous findings in other cnidarian venoms. However, we found few toxins that are typical of sea anemones and corals, and furthermore, three of the four species express toxin-like genes closely related to potent pore-forming toxins in box jellyfish. Our study is the first to provide a survey of the putative venom composition of cerianthids and contributes to our general understanding of the diversity of cnidarian toxins.São Paulo Research Foundation FAPESP 2015/24408-42017/50028-0 (SPRINT)2019/03552-0CNPq (PROTAX) 440539/2015-3CNPq (Research Productivity Scholarship)301293/2019-

Solar Damage To the Solitary Ascidian, Corella Inflata

The ascidian Corella inflata (Chordata, Ascidiacea) is common in many areas of Puget Sound, Washington, USA. However, it occurs only in habitats where it is protected from direct sunlight. Previous experiments with artificial lights showed that UV irradiation kills all life stages of this animal. The effects of natural sunlight exposure (measuring survival of adults, juveniles, larvae, and embryos) were compared. We partitioned the light spectrum to separate the effects of UVB, UVA, and visible light (PAR). Natural sunlight severely damaged C. inflata. Adults and juveniles died after 2-5 d. Exposed embryos failed to develop normally and larvae did not settle. As expected, UVB had significant effects, but pronounced effects were also seen when the animals were exposed to longer wavelengths alone (UVA and PAR). Thus, the distribution of C. inflata may be determined largely by exposure to light. Understanding the basic ecology of this species requires consideration of its vulnerability to sunlight damage and the effects of UVB, UVA, and PAR

Genomic survey of candidate stress-response genes in the estuarine anemone Nematostella vectensis

Author Posting. © Marine Biological Laboratory, 2008. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 214 (2008): 233-254.Salt marshes are challenging habitats due to natural variability in key environmental parameters including temperature, salinity, ultraviolet light, oxygen, sulfides, and reactive oxygen species. Compounding this natural variation, salt marshes are often heavily impacted by anthropogenic insults including eutrophication, toxic contamination, and coastal development that alter tidal and freshwater inputs. Commensurate with this environmental variability, estuarine animals generally exhibit broader physiological tolerances than freshwater, marine, or terrestrial species. One factor that determines an organism's physiological tolerance is its ability to upregulate "stress-response genes" in reaction to particular stressors. Comparative studies on diverse organisms have identified a number of evolutionarily conserved genes involved in responding to abiotic and biotic stressors. We used homology-based scans to survey the sequenced genome of Nematostella vectensis, the starlet sea anemone, an estuarine specialist, to identify genes involved in the response to three kinds of insult—physiochemical insults, pathogens, and injury. Many components of the stress-response networks identified in triploblastic animals have clear orthologs in the sea anemone, meaning that they must predate the cnidarian-triploblast split (e.g., xenobiotic receptors, biotransformative genes, ATP-dependent transporters, and genes involved in responding to reactive oxygen species, toxic metals, osmotic shock, thermal stress, pathogen exposure, and wounding). However, in some instances, stress-response genes known from triploblasts appear to be absent from the Nematostella genome (e.g., many metal-complexing genes). This is the first comprehensive examination of the genomic stress-response repertoire of an estuarine animal and a member of the phylum Cnidaria. The molecular markers of stress response identified in Nematostella may prove useful in monitoring estuary health and evaluating coastal conservation efforts. These data may also inform conservation efforts on other cnidarians, such as the reef-building corals.AMR was supported by a Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by The Beacon Institute for Rivers and Estuaries, and the J. Seward Johnson Fund. NTK was supported by a graduate research training grant from the National Institutes of Health. This research was also supported by NSF grant FP-91656101-0 to JCS and JRF, EPA grant F5E11155 to AMR and JRF, and a grant from the Conservation International Marine Management Area Science Program to JRF