Gene encoding human Ro-associated autoantigen Y5 RNA.

Ro ribonucleoproteins are composed of Y RNAs and the Ro 60 kDa protein. While the Ro 60 kDa protein is implicated in an RNA discard pathway that recognizes 3'-extended 5S rRNAs, the function of Y RNAs remains unknown [O'Brien,C.A. and Wolin,S.L. (1995) Genes Dev. 8,2891-2903]. Y5 RNA occupies a large fraction of Ro 60 kDa protein in human Ro RNPs, contains an atypical 3'-extension not found on other Y RNAs, and constitutes an RNA antigen in certain autoimmune patients [Boulanger et al. (1995) Clin. Exp. Immunol. 99, 29-36]. An overabundance of Y RNA retroposed pseudogenes has previously complicated the isolation of mammalian Y RNA genes. The source gene for Y5 RNA was isolated from human DNA as well as from Galago senegalis DNA. Authenticity of the hY5 RNA gene was demonstrated in vivo and its activity was compared with the hY4 RNA gene that also uses a type 3 promoter for RNA polymerase III. The hY5 RNA gene was subsequently found to reside within a few hundred thousand base pairs of other Y RNA genes and the linear order of the four human Y RNA genes on chromosome 7q36 was determined. Phylogenetic comparative analyses of promoter and RNA structure indicate that the Y5 RNA gene has been subjected to positive selection during primate evolution. Consistent with the proposal of O'Brien and Harley [O'Brian,C.A. and Wolin,S.L. (1992) Gene 116, 285-289], analysis of flanking sequences suggest that the hY5 RNA gene may have originated as a retroposon.     

Dynamics of arginase gene evolution in metazoans

In the present study, a comprehensive analysis of the arginase gene family in metazoans was performed. A total of 126 arginase genes have been identified in 44 species. Phylogenetic analyses indicate that arginase genes consist of four groups. Conservative and divergent gene structures are found among the groups. The syntenies also exist in distantly related genomes among multiple species. Adaptive evolution shows that, while purifying selection may have been the main force driving the evolution of the arginases, some of critical sites responsible for the functional divergence may have been under positive selection. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the arginase gene family and of the function and evolution of this family in metazoans.     

Molecular evolution of nitric oxide synthases in metazoans

Nitric oxide synthases (NOS), the enzymes responsible for the NO synthesis, are present in all eukaryotes. Three isoforms (neuronal, inducible and endothelial), encoded by different loci, have been described in vertebrates, although the endothelial isoform seems to be restricted to tetrapods. In invertebrates, a variety of NOS isoforms have been variably annotated as "inducible" or "neuronal", while others lack precise annotation. We have performed an exhaustive collection of the available NOS amino-acid sequences in order to perform a phylogenetic analysis. We hypothesized that the NOS isoforms reported in vertebrates derive from 1) different invertebrate NOS, 2) a single invertebrate ancestral gene, through an event related to the double whole genomic duplication that occurred at the origin of vertebrates, and 3) the endothelial form of NOS appeared late in the evolution of vertebrates, after the split of tetrapods and fishes. Our molecular evolution analysis strongly supports the second scenario, the three vertebrate NOS isoforms derived from a single ancestral invertebrate gene. Thus, the diverse NOS isoforms in invertebrates can be explained by events of gene duplication, but their characterization as "inducible" or "neuronal" should only be justified by physiological features, since they are evolutionarily unrelated to the homonym isoforms of vertebrates.     

On the origin and evolution of RNA editing in metazoans

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Molecular evolution of the moonlighting protein SMN in metazoans

The spinal muscular atrophy (SMA) associated protein survival of motor neuron (SMN) is known to be a moonlighting protein: having one primary, ancestral function (presumed to be involvement in U snRNP assembly) along with one or more secondary functions. One hypothesis for the evolution of moonlighting proteins is that regions of a structure under relatively weak negative selection could gain new functions without interfering with the primary function. To test this hypothesis, we investigated sequence conservation and dN/dS, which reflects the selection acting on a coding sequence, in SMN and a related protein, splicing factor 30 (SPF30), which is not currently known to be multifunctional. We found very different patterns of evolution in the two genes, with SPF30 characterized by strong sequence conservation and negative selection in most animal taxa investigated, and SMN with much lower sequence conservation, and much weaker negative selection at many sites. Evidence was found of positive selection acting on some sites in primate genes for SMN. SMN was also found to have been duplicated in a number of species, and with patterns that indicate reduced negative selection following some of these duplications. There were also several animal species lacking an SMN gene.     

Contingent predictability in evolution: key traits and diversification

Key innovations have often been invoked to explain the exceptional diversification of particular groups. However, there are few convincing examples of traits that are repeatedly and consistently associated with increased diversification. The paucity of such cases may reflect the contingent nature of the diversifying effect of key traits. These contingencies can be viewed as statistical interactions between the trait and at least three kinds of factors: (1) other taxa, (2) other traits of the group itself, and (3) the physical environment. I describe tentative examples in each of these categories: (1) a dampening of the diversification of clades with image-forming eyes by groups that earlier evolved such eyes, (2) an effect of growth form (woody or herbaceous) on the diversifying effect of biotic seed dispersal in angiosperms, and (3) an effect of atmospheric CO(2) level on the diversifying effect of C(4) photosynthesis in monocots. These examples suggest the need for more complex analyses of the relationship between possible key traits and diversification. They also suggest that radiations may be predictable given certain circumstances, thus supporting a view of evolution as both predictable and contingent. Ironically, a certain degree of predictability may be critical to arguments for evolutionary contingency.     

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12 766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.     

The evolution of protein domains and the organizational complexities of metazoans

There is an increasingly heated debate on the very existence of a 'universe of exons' and on the types of genomes that existed after the RNA world. What has been lost in the excitement are the biological issues that relate to the rapid emergence of phenotypic novelties. These issues can be examined by integrating data on protein domains and genomic evolution with the geochemical and palaeontological records.     

The evolution and diversification of sleep

The evolutionary origins of sleep and its sub-states, rapid eye movement (REM) and non-REM (NREM) sleep, found in mammals and birds, remain a mystery. Although the discovery of a single type of sleep in jellyfish suggests that sleep evolved much earlier than previously thought, it is unclear when and why sleep diversified into multiple types of sleep. Intriguingly, multiple types of sleep have recently been found in animals ranging from non-avian reptiles to arthropods to cephalopods. Although there are similarities between these states and those found in mammals and birds, notable differences also exist. The diversity in the way sleep is expressed confounds attempts to trace the evolution of sleep states, but also serves as a rich resource for exploring the functions of sleep.     

Rotifers: exquisite metazoans

Rotifers comprise a modestly sized phylum (1,850 species) oftiny (ca. 50–2,000 µm), bilaterally symmetrical,eutelic metazoans, traditionally grouped within the pseudocoelomatesor Aschelminthes. These saccate to cylindrically shaped protostomespossess three prominent regions (corona, trunk, foot). Theyare distinguished by a ciliated, anterior corona (used in locomotionand food gathering) and a pharynx equipped with a complex setof jaws. Unfortunately, these generalizations grossly oversimplifya rich and fascinating diversity. Chief among the charms ofthe study of rotifers are their ecological importance, easeof culture (including chemostat technology), and the fact thatmuch remains unknown about this exquisite phylum.     

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.     

Polyploidy: its consequences and enabling role in plant diversification and evolution

BackgroundMost, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility.ScopeWorld-wide interest in how green plants have evolved under different conditions – whether in small, isolated populations, or globally – suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids.ConclusionChromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy – generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.     

The evolution and diversification of oakleaf butterflies

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Formation and evolution ofTombusvirusdefective interfering RNAs

Defective interfering (DI) RNAs associated with members of the genusTombusvirusare among the most extensively characterized. These molecules, which represent replicable deletion mutants of viral genomes, are able to accumulate to high levels in viral infections and have the effect of suppressing virus accumulation and attenuating virus-induced symptoms in host plants. Numerous studies have led to a greater understanding of how these molecules are formed and what factors influence their accumulation. Here an overview is provided of what is currently known about the structure, formation and evolution of this important class of sub-viral replicon.     

Functional roles of non-coding Y RNAs

Non-coding RNAs are involved in a multitude of cellular processes but the biochemical function of many small non-coding RNAs remains unclear. The family of small non-coding Y RNAs is conserved in vertebrates and related RNAs are present in some prokaryotic species. Y RNAs are also homologous to the newly identified family of non-coding stem-bulge RNAs (sbRNAs) in nematodes, for which potential physiological functions are only now emerging. Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates and, when bound to the Ro60 protein, they are involved in RNA stability and cellular responses to stress in several eukaryotic and prokaryotic species. Additionally, short fragments of Y RNAs have recently been identified as abundant components in the blood and tissues of humans and other mammals, with potential diagnostic value. While the number of functional roles of Y RNAs is growing, it is becoming increasingly clear that the conserved structural domains of Y RNAs are essential for distinct cellular functions. Here, we review the biochemical functions associated with these structural RNA domains, as well as the functional conservation of Y RNAs in different species. The existing biochemical and structural evidence supports a domain model for these small non-coding RNAs that has direct implications for the modular evolution of functional non-coding RNAs.