The “street light syndrome”, or how protein taxonomy can bias experimental manipulations

Function and Evolution of Nuclear Receptors in Environmental-Dependent Postembryonic Development

Nuclear receptors (NRs) fulfill key roles in the coordination of postembryonal developmental transitions in animal species. They control the metamorphosis and sexual maturation in virtually all animals and by that the two main environmental-dependent developmental decision points. Sexual maturation and metamorphosis are controlled by steroid receptors and thyroid receptors, respectively in vertebrates, while both processes are orchestrated by the ecdysone receptor (EcR) in insects. The regulation of these processes depends on environmental factors like nutrition, temperature, or photoperiods and by that NRs form evolutionary conserved mediators of phenotypic plasticity. While the mechanism of action for metamorphosis and sexual maturation are well studied in model organisms, the evolution of these systems is not entirely understood and requires further investigation. We here review the current knowledge of NR involvement in metamorphosis and sexual maturation across the animal tree of life with special attention to environmental integration and evolution of the signaling mechanism. Furthermore, we compare commonalities and differences of the different signaling systems. Finally, we identify key gaps in our knowledge of NR evolution, which, if sufficiently investigated, would lead to an importantly improved understanding of the evolution of complex signaling systems, the evolution of life history decision points, and, ultimately, speciation events in the metazoan kingdom.

A critical evaluation of some of the recent so-called 'evidence' for the involvement of vertebrate-type sex steroids in the reproduction of mollusks

Many studies on the control of reproduction in mollusks have focused on hormones (and proteins associated with the production and signaling of those hormones) which were originally discovered in humans, in the belief that if they are also present in mollusks, they must have the same role. However, although human sex steroids can be found in mollusks, they are so readily absorbed that their presence is not necessarily evidence of endogenous synthesis. A homolog of the vertebrate nuclear estrogen receptor has been found in mollusks, but it does not bind to estrogens or indeed to any steroid at all. Antibodies against human aromatase show positive immunostaining in mollusks, yet the aromatase gene has not been found in the genome of any invertebrates (let alone mollusks). This review will deal with these and other examples of contradictory evidence for a role of human hormones in invertebrate reproduction.

Is there any value in measuring vertebrate steroids in invertebrates?

This brief review questions the belief that just because it is possible to measure vertebrate steroids (such as estradiol-17β, testosterone and progesterone) in the tissues of invertebrates, this necessarily means that they are endogenously derived or are hormones. There is a surprisingly large number of studies, mainly on mollusks, showing that they can readily absorb vertebrate steroids from the environment. They are also able to conjugate these steroids to fatty acids with great efficiency, and subsequently retain them for very long periods (with half-lives measured in weeks rather than days). This, plus the fact that key enzymes that are required for the biosynthesis of vertebrate steroids (e.g. aromatase) do not appear to be present in invertebrates, calls into doubt the claims in many studies on invertebrates that steroid concentrations are functionally linked to reproductive cycles or that invertebrates can be used as biomarker for vertebrate-type endocrine disrupters.

Gonadotropin-releasing hormone by any other name would smell as sweet

The goal of this article is to discuss the nomenclature of members of the gonadotropin-releasing hormone (GnRH) superfamily. This superfamily currently consists of 5 families: (1) vertebrate GnRH, (2) adipokinetic hormone, (3) corazonin, (4) adipokinetic hormone/corazonin-related peptide and (5) invertebrate GnRH (or GnRH/corazonin). The naming of some of these peptides, especially members of the invertebrate GnRH family, may not have reflected their true evolutionary origin, leading to some confusion and controversy. Using a few examples from the invertebrate GnRH family, this article proposes several peptide-naming criteria and discusses naming challenges and problem cases. It is recommended that the invertebrate GnRH family be renamed based on the naming criteria of (1) mature peptide structure, (2) prepropeptide phylogeny, and (3) receptor phylogeny. Following this approach, the names of the peptides should reflect their phylogeny, and if possible, delineate a monophyletic group.

Finding our way through phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Vitellogenin-like proteins among invertebrate species diversity: potential of proteomic mass spectrometry for biomarker development

Cost-effective methodologies along with cross-species applicability constitute key points for biomarker development in ecotoxicology. With the advent of cheaper affordable genomic techniques and high throughput sequencing, omics tools could facilitate the assessment of effects of environmental contaminants for all taxa biodiversity. We assessed the potential of absolute quantification of proteins using mass spectrometry to develop vitellogenin (Vg)-like protein assays for invertebrates. We used available sequences in public databases to rapidly identify Vg-proteotypic peptides in seven species from different main taxa of protostome invertebrates (mollusk bivalves, crustacean amphipods, branchiopods, copepods and isopods, and insect diptera). Functional validation was performed by comparing proteomic signals from reproductive female tissue samples and negative controls (male or juvenile tissues). In a second part, we demonstrate in gammarids, daphnids, drosophilids, and gastropods that the assay validated in Vg-sequenced species can be applied to Vg-unsequenced species thanks to the evolutionary conservation of Vg-proteotypic peptide motifs. Finally, we discuss the relevance of mass spectrometry for biomarker development (specific measurement, rapid development, transferability across species). Our study supplies an illustration of the promising strategy to address the challenge of biodiversity in ecotoxicology, which consists in employing omics tools from comparative and evolutionary perspectives.

Origins of specificity and promiscuity in metabolic networks

How enzymes have evolved to their present form is linked to the question of how pathways emerged and evolved into extant metabolic networks. To investigate this mechanism, we have explored the chemical diversity present in a largely unbiased data set of catalytic reactions processed by modern enzymes across the tree of life. In order to get a quantitative estimate of enzyme chemical diversity, we measure enzyme multispecificity or promiscuity using the reaction molecular signatures. Our main finding is that reactions that are catalyzed by a highly specific enzyme are shared by poorly divergent species, suggesting a later emergence of this function during evolution. In contrast, reactions that are catalyzed by highly promiscuous enzymes are more likely to appear uniformly distributed across species in the tree of life. From a functional point of view, promiscuous enzymes are mainly involved in amino acid and lipid metabolisms, which might be associated with the earliest form of biochemical reactions. In this way, results presented in this paper might assist us with the identification of primeval promiscuous catalytic functions contributing to life's minimal metabolism.

When orthologs diverge between human and mouse

Despite the common assumption that orthologs usually share the same function, there have been various reports of divergence between orthologs, even among species as close as mammals. The comparison of mouse and human is of special interest, because mouse is often used as a model organism to understand human biology. We review the literature on evidence for divergence between human and mouse orthologous genes, and discuss it in the context of biomedical research.

The evolution of the ligand/receptor couple: a long road from comparative endocrinology to comparative genomics

Comparative endocrinology considers the evolution of bioregulatory systems and the anatomical structures and molecules that constitute the neuroendocrine and endocrine systems. One aim of comparative endocrinology is to trace the origins of the main endocrine systems. The understanding of the evolution of the ligand/receptor couple is central to this objective. One classical approach to tackle this question is the characterization of receptors and ligands in various types of non-model organisms using as a starting point the knowledge accumulated on classical models such as mammals (mainly human and mouse) and arthropods (with Drosophila among other insects). In this review we discuss the potential caveats associated to this two-by-two comparison between a classical model and non-model organisms. We suggest that the use of an evolutionary approach involving comparisons of several organisms in a coherent framework permits reconstruction of the most probable scenarios. The use of the vast amount of genomic data now available, coupled to functional experiments, offers unprecedented possibilities to trace back the origins of the main ligand/receptor couples.

An amphioxus orthologue of the estrogen receptor that does not bind estradiol: insights into estrogen receptor evolution

Background

The origin of nuclear receptors (NRs) and the question whether the ancestral NR was a liganded or an unliganded transcription factor has been recently debated. To obtain insight into the evolution of the ligand binding ability of estrogen receptors (ER), we comparatively characterized the ER from the protochordate amphioxus (Branchiostoma floridae), and the ER from lamprey (Petromyzon marinus), a basal vertebrate.

Results

Extensive phylogenetic studies as well as signature analysis allowed us to confirm that the amphioxus ER (amphiER) and the lamprey ER (lampER) belong to the ER group. LampER behaves as a "classical" vertebrate ER, as it binds to specific DNA Estrogen Responsive Elements (EREs), and is activated by estradiol (E₂), the classical ER natural ligand. In contrast, we found that although amphiER binds EREs, it is unable to bind E₂ and to activate transcription in response to E₂. Among the 7 natural and synthetic ER ligands tested as well as a large repertoire of 14 cholesterol derivatives, only Bisphenol A (an endocrine disruptor with estrogenic activity) bound to amphiER, suggesting that a ligand binding pocket exists within the receptor. Parsimony analysis considering all available ER sequences suggest that the ancestral ER was not able to bind E₂ and that this ability evolved specifically in the vertebrate lineage. This result does not support a previous analysis based on ancestral sequence reconstruction that proposed the ancestral steroid receptor to bind estradiol. We show that biased taxonomic sampling can alter the calculation of ancestral sequence and that the previous result might stem from a high proportion of vertebrate ERs in the dataset used to compute the ancestral sequence.

Conclusion

Taken together, our results highlight the importance of comparative experimental approaches vs ancestral reconstructions for the evolutionary study of endocrine systems: comparative analysis of extant ERs suggests that the ancestral ER did not bind estradiol and that it gained the ability to be regulated by estradiol specifically in the vertebrate lineage, before lamprey split.