Course Of Metazoan Evolution Research Articles

DNA Instability in Neurons: Lifespan Clock and Driver of Evolution.

In the last ten years, the discovery of neuronal DNA postmitotic instability has changed the theoretical landscape in neuroscience and, more broadly, biology. In 2003, A. M. Olovnikov suggested that neuronal DNA is the "initial substrate of aging". Recent experimental data have significantly increased the likelihood of this hypothesis. How does neuronal DNA accumulate damage and in what genome regions? What factors contribute to this process and how are they associated with aging and lifespan? These questions will be discussed in the review. In the course of Metazoan evolution, the instability of neuronal DNA has been accompanied by searching for the pathways to reduce the biological cost of brain activity. Various processes and activities, such as sleep, evolutionary increase in the number of neurons in the vertebrate brain, adult neurogenesis, distribution of neuronal activity, somatic polyploidy, and RNA editing in cephalopods, can be reconsidered in the light of the trade-off between neuronal plasticity and DNA instability in neurons. This topic is of considerable importance for both fundamental neuroscience and translational medicine.

Deep conservation of the enhancer regulatory code in animals.

Interactions of transcription factors (TFs) with DNA regulatory sequences, known as enhancers, specify cell identity during animal development. Unlike TFs, the origin and evolution of enhancers has been difficult to trace. We drove zebrafish and mouse developmental transcription using enhancers from an evolutionarily distant marine sponge. Some of these sponge enhancers are located in highly conserved microsyntenic regions, including an Islet enhancer in the Islet-Scaper region. We found that Islet enhancers in humans and mice share a suite of TF binding motifs with sponges, and that they drive gene expression patterns similar to those of sponge and endogenous Islet enhancers in zebrafish. Our results suggest the existence of an ancient and conserved, yet flexible, genomic regulatory syntax that has been repeatedly co-opted into cell type-specific gene regulatory networks across the animal kingdom.

Enhancer function, from sponges to humans

Enhancer Genomics Identifying the function of enhancers, DNA regions that help to regulate gene expression and evolve rapidly, has been difficult. This area of research has been hampered by the difficultly in identifying functional conservation. Wong et al. now show that despite low sequence conservation, enhancer function is strongly conserved through the animal kingdom (see the Perspective by Harmston). Transgenic expression of sponge enhancers in zebrafish and mice demonstrates that these sequences can drive cell type–specific gene expression across species. These results suggest an unexpectedly deep level of conservation of gene regulation across the animal kingdom maintained over the course of metazoan evolution. Science , this issue p. [eaax8137][1]; see also p. [657][2] [1]: /lookup/doi/10.1126/science.aax8137 [2]: /lookup/doi/10.1126/science.abe9317

Trichinella spiralis: Adaptation and parasitism

Publication of the genome from the clade I organism, Trichinella spiralis, has provided us an avenue to address more holistic problems in parasitology; namely the processes of adaptation and the evolution of parasitism. Parasitism among nematodes has evolved in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and adaptation in nematodes; however, data is now coming available to investigate adaptation, host switching and parasitism at the genomic level. Herein we compare proteomic data from the clade I parasite, Trichinella spiralis with data from Brugia malayi (clade III), Meloidogyne hapla and Meloidogyne incognita (clade IV), and free-living nematodes belonging to the genera Caenorhabditis and Pristionchus (clade V). We explore changes in protein family birth/death and expansion/reduction over the course of metazoan evolution using Homo sapiens, Drosophila melanogaster and Saccharomyces cerevisiae as outgroups for the phylum Nematoda. We further examine relationships between these changes and the ability and/or result of nematodes adapting to their environments. Data are consistent with gene loss occurring in conjunction with nematode specialization resulting from parasitic worms acclimating to well-defined, environmental niches. We observed evidence for independent, lateral gene transfer events involving conserved genes that may have played a role in the evolution of nematode parasitism. In general, parasitic nematodes gained proteins through duplication and lateral gene transfer, and lost proteins through random mutation and deletions. Data suggest independent acquisition rather than ancestral inheritance among the Nematoda followed by selective gene loss over evolutionary time. Data also show that parasitism and adaptation affected a broad range of proteins, especially those involved in sensory perception, metabolism, and transcription/translation. New protein gains with functions related to regulating transcription and translation, and protein family expansions with functions related to morphology and body development have occurred in association with parasitism. Further gains occurred as a result of lateral gene transfer and in particular, with the cyanase protein family In contrast, reductions and/or losses have occurred in protein families with functions related to metabolic process and signal transduction. Taking advantage of the independent occurrences of parasitism in nematodes, which enabled us to distinguish changes associated with parasitism from species specific niche adaptation, our study provides valuable insights into nematode parasitism at a proteome level using T. spiralis as a benchmark for early adaptation to or acquisition of parasitism.

Exploring metazoan evolution through dynamic and holistic changes in protein families and domains

BackgroundProteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new proteins and protein families. Processes that affect proteome evolution drive species diversity and adaptation. Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species.ResultsIn studying members of the three major metazoan groups, the vertebrates, arthropods, and nematodes, we found that the number of protein families increased at the majority of lineages over the course of metazoan evolution where the magnitude of these increases was greatest at the lineages leading to mammals. In contrast, the number of protein domains decreased at most lineages and at all terminal lineages. This resulted in a weak correlation between protein family birth and domain birth; however, the correlation between domain birth and domain member duplication was quite strong. These data suggest that domain birth and protein family birth occur via different mechanisms, and that domain shuffling plays a role in the formation of protein families. The ratio of protein family birth to protein domain birth (domain shuffling index) suggests that shuffling had a more demonstrable effect on protein families in nematodes and arthropods than in vertebrates. Through the contrast of high and low domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, we propose a link between protein redundancy and evolutionary changes controlled by domain shuffling; however, the speed of adaptation among the different lineages was relatively invariant. Evaluating the functions of protein families that appeared or disappeared at the last common ancestors (LCAs) of the three metazoan clades supports a correlation with organism adaptation. Furthermore, bursts of new protein families and domains in the LCAs of metazoans and vertebrates are consistent with whole genome duplications.ConclusionMetazoan speciation and adaptation were explored by birth/death and duplication/deletion events among protein families and domains. Our results provide insights into protein evolution and its bearing on metazoan evolution.

Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions.

OVO-like proteins (OVOL) are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies that describe OVOL proteins from an evolutionary perspective. Using comparative genomic analysis, we traced three different OVOL genes (OVOL1-3) in vertebrates. One gene, OVOL3, was duplicated during a whole-genome-duplication event in fish, but only the copy (OVOL3b) was retained. From early-branching metazoa to humans, we found that a core domain, comprising a tetrad of C2H2 zinc fingers, is conserved. By domain comparison of the OVOL proteins, we found that they evolved in different metazoan lineages by attaching intrinsically-disordered (ID) segments of N/C-terminal extensions of 100 to 1000 amino acids to this conserved core. These ID regions originated independently across different animal lineages giving rise to different types of OVOL genes over the course of metazoan evolution. We illustrated the molecular evolution of metazoan OVOL genes over a period of 700 million years (MY). This study both extends our current understanding of the structure/function relationship of metazoan OVOL genes, and assembles a good platform for further characterization of OVOL genes from diverged organisms.

The “Eyes absent” (eya) Gene in the Eye‐Bearing Hydrozoan Jellyfish Cladonema radiatum: Conservation of the Retinal Determination Network

Eyes absent (Eya) is a member of the Retinal Determination Gene Network (RDGN), a set of genes responsible for eye specification in Drosophila. Eya is a dual function protein, working as a transcription factor in the nucleus and as a tyrosine phosphatase in the cytoplasm. It had been shown that Pax and Six family genes, main components of the RDGN, are present in the hydrozoan Cladonema radiatum and that they are expressed in the eye. However, nothing had been known about the Eya family in hydrozoan jellyfish. Here we report the presence of an Eya homologue (CrEya) in Cladonema. Real-time PCR analysis and in situ hybridization showed that CrEya is expressed in the eye. Furthermore, the comprehensive survey of eukaryote genomes revealed that the acquisition of the N-terminal transactivation domain, including the EYA Domain 2 and its adjacent sequence shared by all eumetazoans, happened early in evolution, before the separation of Cnidaria and Bilateria. Our results uncover the evolution of the two domains and show a conservation of the expression pattern of the Eya gene between Cnidaria and Bilateria, which, together with previous data, supports the hypothesis of the monophyletic origin of metazoans eyes. We additionally show that CrEya is also expressed in the oocytes, where two other members of the RDGN, CrPaxB, and Six4/5-Cr, are known to be expressed. These data suggest that several members of the RDGN have begun to be localized also into the different context of egg development early in the course of metazoan evolution.

The diversity of ontogeny in animals with asexual reproduction and plasticity of early development

Diversity of blastogenesis and embryogenesis in animals with different reproductive strategy and different variants of the isolation of germ lineage cells, defined in the literature as preformation, epigenesis, and somatic embryogenesis, is discussed. In the course of somatic embryogenesis (or, more precisely, blastogenesis), the oozooid that has developed from the egg is naturally cloned and forms numerous genetically and morphologically identical clonal individuals or modular units of a colony. This cloning results in amplification of the parent genotype; the subsequent sexual reproduction provides for genetic recombination, and the emergence of a huge number of larvae with dispersal function provides for reproductive success. In invertebrates that reproduce asexually, no isolation of the germ cell lineage takes place; the population of stem cell capable of realizing the complete developmental program, which includes gametogenesis and blastogenesis, is represented by a diaspora of cells dispersed in the organism and possessing evolutionarily conservative features of morphofunctional organization typical to cells of the germ lineage. The plasticity of early animal embryogenesis is revealed in experiments with embryonic cells cultivated in vitro. Asexual reproduction emerged repeatedly in the course of metazoan evolution; blastogenesis in animals of different taxa is more variable and less conservative than embryogenesis, but the installation of blastogenesis into the process of early embryogenesis undermines the conservatism of embryonic development.

Patterns of internal gene duplication in the course of metazoan evolution

Internal duplication can enhance the function of a gene or provide raw material for the emergence of a new function in a gene. Therefore, it is interesting to see whether the frequency of internal duplication has increased during metazoan evolution. The growing number of sequenced eukaryotic genomes provides an excellent opportunity to study the change in the pattern of internal duplication in the course of metazoan evolution. We studied repeated segments in proteins in the proteomes of 11 eukaryotes. We found that the frequency of internal duplication in Caenorhabditis elegans and Drosophila melanogaster (two protostomes) is higher than that in fungi but lower than that in chordates. Moreover, the frequencies of internal duplication for the chordates studied are largely similar. We classified orthologous proteins of chordates into three antiquity groups and found that more recently derived proteins in the metazoan lineage have higher repetitiveness than older ones. Our analysis suggests that lineage-specific internal duplication in protein evolution increases with organismal complexity before the emergence of chordates but not so afterward. Proteins with repeated regions might have been preferred before the protostome–chordate split. This finding supports the suggestion that exon-shuffling occurred more frequently after the first multicellular organism appeared and might have contributed to the metazoan radiation.

Direct cell–cell communication: a new approach derived from recent data on the nature and self-organisation of ultradian (circahoralian) intracellular rhythms

Recent data concerning ultradian (circahoralian) intracellular rhythms are used to assess the biochemical mechanisms of direct cell-cell communication. New results and theoretical considerations suggest a fractal nature of ultradian rhythms and their self-organisation. The fundamental and innate nature of these rhythms relates to their self-similarity at different levels of cell and tissue organisation. They can be detected in cell-free systems as well as in cells and organs in vivo. Such rhythms are a means of finding an optimal state of cell function rather than achieving a state of absolute stability. As a consequence, oscillations, being irregular and numerous by the set of periods, are resilient to functional overload and injury. Recent data on the maintenance of their fractal structure and, especially on the selection of optimal periods are discussed. The positive role of chaotic dynamics is stressed. The ultradian rhythm of protein synthesis in hepatocytes in vitro was used as a marker of direct cell-cell communication. The system demonstrates cell cooperation and synchronisation throughout the cell population, and suggests that the ultradian rhythms are self-organised. These observations also led to the detection of mechanisms of direct cell-cell communication in which extracellular factors have an essential role. Experimental evidence indicated the involvement of gangliosides and/or catecholamines in this large-scale synchronisation of protein synthesis. The response of all, or a major part, of the cell population is important; after the initial trigger effect, a periodic pattern is retained for some time. The influence of Ca2+-dependent protein kinases on protein phosphorylation can be a final step in the phase modulation of rhythms during cell-cell synchronisation. The intercellular medium plays an important role in self-synchronisation of ultradian rhythms between individual cells. Low cooperative activity of hepatocytes of old rats resulted from altered composition of the intercellular medium rather than direct effects of animal and cellular ageing. Similarly, in the whole body, changes in levels of gangliosides and catecholamines in the blood serum, a natural intercellular medium, can be critical events in age-dependent changes of the serum and accordingly cell-cell synchronisation. Hepatocytes of old rats exhibit some of the properties of young cells following an increase in blood serum ganglioside level, as well as, in in vitro conditions, after the addition of gangliosides to the culture medium. Together with data on ultradian functional and metabolic rhythms, all the material reviewed here allows us to propose a mechanism of direct cell-cell cooperation via the medium in which the cells exist, that supplements the nervous and hormonal central regulation of organ functions. Ultradian intracellular rhythms may thus provide a finer framework within which the integrated dynamics of respiration, heart rate, brain activity, and even behavioural patterns, are brought to an optimal functional pattern. Innate and direct cell-cell cooperation may have been employed as a means of intercellular regulation during the course of metazoan evolution, that preceded nervous regulation and is presently retained in mammals.

Same Difference: Sea Urchins or Starfish

DEVELOPMENT Evolutionary forces are known to work on the gene at many levels, from sequence to organization. In the sea urchin, there have been extensive efforts to map the network responsible for endoderm formation. Despite their differences—including the ability of sea urchin larvae to form a skeleton during embryogenesis—endoderm formation shows similarities between sea urchins and starfish. Hinman et al. studied the conservation and changes in embryonic gene regulatory networks during the course of metazoan evolution. They compared the expression patterns of genes involved in endoderm formation in embryo development and the effects of perturbing expression profiles. A crucial feedback loop involving three transcription factors was found to be almost identical in both of these evolutionarily distant species. — BJ Proc. Natl. Acad. Sci. U.S.A. 100, 13356 (2003).

Developmental rescue of Drosophila cephalic defects by the human Otx genes.

The molecular mechanisms of head development are a central question in vertebrate and invertebrate developmental biology. The anteriorly expressed homeobox gene otd in Drosophila and its homolog Otx in mouse are required for the early development of the most anterior part of the body, suggesting that a fundamental genetic program of cephalic development might be conserved between vertebrates and invertebrates. We have examined this hypothesis by introducing the human Otx genes into flies. By inducing expression of the human Otx homologs with a heat shock promoter, we found that both Otx1 and Otx2 functionally complement the cephalic defects of a fly otd mutant through specific activation and inactivation of downstream genes. Combined with previous morphological studies, these results are consistent with the view that a common molecular ground plan of cephalization was invented before the diversification of the protostome and the deuterostome in the course of metazoan evolution.

Cell adhesion in sponges: potentiation by a cell surface 68 kDa proteoglycan-binding protein.

Constitutive, stable intercellular adhesion is one of the distinguishing properties of metazoans, of which the sponges (Phylum Porifera) are the most primitive representatives. In sponges, intercellular adhesion is mediated by the large proteoglycan-like cell agglutinating molecule 'aggregation factor', which binds to cell surfaces via an oligosaccharide moiety. Previous studies indicated that this aggregation factor binds to two proteins associated with the surface of sponge cells. One of these, a 68 kDa peripheral membrane protein, was isolated by affinity chromatography on aggregation factor conjugated to Sepharose. This monomeric 68 kDa glycoprotein plays a key role in sponge cell adhesion since it potently inhibits the binding of aggregation factor to cell surfaces and completely prevents aggregation factor-mediated cell adhesion. The 68 kDa aggregation factor ligand binds with high affinity to both aggregation factor (KD = 2 x 10(-9) M) and cell surfaces (KD = 6 x 10(-8) M) providing evidence that it serves as an intramolecular bridge between the aggregation factor molecule and a cell surface receptor. Therefore, this early metazoan protein may represent one of the earliest extracellular matrix adhesion proteins to have arisen in the course of metazoan evolution.

PARENTAL CARE COMES OF AGE

Parental care has evolved numerous times during the course of metazoan evolution and represents an important issue in evolutionary biology because of its effect on fitness. Moreover, because the nature and extent of care allocated have a direct influence on each parent's opportunity to mate, analyses of parental care are axiomatic to the study of the evolution of breeding systems. In The Evolution of Parental Care, Tim Clutton-Brock provides an extensive review and critique of the field that will have a major impact on biological research for many years. Five questions about the origins and evolution of parental care are set out in the introduction. First, what are the principal costs and benefits of parental care? Second, why does it vary so widely between species? Third, why do species differ in the extent to which each sex provides care? Fourth, is parental care adjusted to variations in its costs to parents and benefits to offspring? And fifth, how do parents divide expenditure between sons and daughters? Using these questions to structure the existing data set, Clutton-Brock first addresses interspecific differences in forms of parental care and then discusses the adaptive significance of intraspecific patterns of care. As the reader is taken through the data, however, it becomes apparent that fundamental questions about parental care remain unanswered. Consequently, much of the book can be summarized as an exhaustively researched cautionary tale warning that without better measures of the costs and benefits, theories will continue to be forced to rely on dubious assumptions (p. 263). It is, however, more than a cautionary tale. It is a masterfully organized book that applies extensive empirical evidence (there are 1,390 references) to current theory, and in so doing not only defines the state of the art, but uncovers huge holes in both the theoretical and empirical canvasses. We are woefully ignorant not only about costs and benefits, but also about the most basic features of parental care in far too many taxa; and many hypotheses contain fatal defects. These holes, Clutton-Brock argues, cripple any serious attempt to provide a coherent picture of the origins and evolution of parental care. Because many facets of parental care are only partially understood and there is much research to be done, the timing of this book is ideal.