New insights into the phylogenetic distribution and evolutionary origins of the septins

Until recently, it had appeared that the septin family of proteins was restricted to the opisthokont eukaryotes (the fungi and animals and their close relatives the microsporidia and choanoflagellates). It has now become apparent that septins are also present in several other widely divergent eukaryotic lineages (chlorophyte algae, brown algae, and ciliates). This distribution and the details of the non-opisthokont septin sequences appear to require major revisions to hypotheses about the origins and early evolution of the septins.     

New insights into the evolution of metazoan tyrosinase gene family

Tyrosinases, widely distributed among animals, plants and fungi, are involved in the biosynthesis of melanin, a pigment that has been exploited, in the course of evolution, to serve different functions. We conducted a deep evolutionary analysis of tyrosinase family amongst metazoa, thanks to the availability of new sequenced genomes, assessing that tyrosinases (tyr) represent a distinctive feature of all the organisms included in our study and, interestingly, they show an independent expansion in most of the analyzed phyla. Tyrosinase-related proteins (tyrp), which derive from tyr but show distinct key residues in the catalytic domain, constitute an invention of chordate lineage. In addition we here reported a detailed study of the expression territories of the ascidian Ciona intestinalis tyr and tyrps. Furthermore, we put efforts in the identification of the regulatory sequences responsible for their expression in pigment cell lineage. Collectively, the results reported here enlarge our knowledge about the tyrosinase gene family as valuable resource for understanding the genetic components involved in pigment cells evolution and development.     

The origin of metazoan complexity: porifera as integrated animals

Sponges [Porifera] are the phylogenetically oldest metazoanphylum still extant today; they share the closest relationshipwith the hypothetical common metazoan ancestor, the Urmetazoa.During the past 8 years cDNAs coding for proteins involved incell-cell- and cell-tissue interaction have been cloned fromsponges, primarily from Suberites domuncula and Geodia cydoniumand their functions have been studied in vivo as well as invitro. Also, characteristic elements of the extracellular matrixhave been identified and cloned. Those data confirmed that allmetazoan phyla originate from one ancestor, the Urmetazoa. Theexistence of cell adhesion molecules allowed the emergence ofa colonial organism. However, for the next higher stage in evolution,individuation, two further innovations had to be formed: theimmune- and the apoptotic system. Major defense pathways/moleculesto prevent adverse effects against microbes/parasites have beenidentified in sponges. Furthermore, key molecules of the apoptoticpathway(s), e.g., the pro-apoptotic molecule comprising twodeath domains, the executing enzyme caspases, as well as theanti-apoptotic/cell survival proteins belonging to the Bcl-2family have been identified and cloned from sponges. Based onthese results—primarily obtained through a molecular biologicalapproach—it is concluded that cell-cell- and cell-matrixadhesion systems were required for the transition to a colonialstage of organization, while the development of an immune systemas well as of apoptotic processes were prerequisites for reachingthe integrated stage. As the latter stage already exists insponges, it is therefore likely that the hypothetical ancestor,the Urmetazoa, was also an "integrated colony."     

Biochemical identification of thymosin alpha-1: its phylogenetic distribution and evolutionary implications

1. Thymosin alpha-1, like reactivity, was found in several different species (insects, crab, protozoan, fungus and bacteria) by radioimmunoassay and immune fluorescence and as an extracellular product from the bacterial genus Mycobacterium. 2. Biochemically, thymosin alpha-1 has been isolated from combined crab visceral and nervous tissue by reverse phase HPLC. 3. The identification of thymosin alpha-1 in lower life forms suggests a more generalized exocrine origin in unicellular organisms prior to the development of the immune system or exocrine differentiation.     

The Notch signalling system: recent insights into the complexity of a conserved pathway

Notch signalling links the fate of one cell to that of an immediate neighbour and consequently controls differentiation, proliferation and apoptotic events in multiple metazoan tissues. Perturbations in this pathway activity have been linked to several human genetic disorders and cancers. Recent genome-scale studies in Drosophila melanogaster have revealed an extraordinarily complex network of genes that can affect Notch activity. This highly interconnected network contrasts our traditional view of the Notch pathway as a simple linear sequence of events. Although we now have an unprecedented insight into the way in which such a fundamental signalling mechanism is controlled by the genome, we are faced with serious challenges in analysing the underlying molecular mechanisms of Notch signal control.     

New insights into p53 functions through its target microRNAs

The tumor suppressor p53 pathway, whose alterations are highly associated with all types of human cancers, plays an essential role in preventingtumor development and progression mostly through its downstream target genes. Over the last decade, a growing list of p53 microRNA （miRNA） targets has been identified as additional downstream players of this pathway. Further studies ofthese miRNAs have revealed their more complicated regulations and functions in executing and/or regulating p53 activity. Here, we review the p53 miRNA targets identified thus far, and discuss how they fine-tune p53 stress responses, mediate the crosstalk between p53 and other signaling pathways, and expand the role of p53 in other human diseases in addition to cancers.     

The evolutionary trajectory of mitochondrial carrier family during metazoan evolution

Background  

Exploring metabolic evolution is a way to understand metabolic complexity. The substrate transport of mitochondrial carrier family (MCF) influences direct metabolic activities, making it possible to understand indirectly metabolic evolution from the evolution of substrate transport of MCF. However, the evolutionary study of substrate transport of MCF does not mean that all the concrete structures of mitochondrial carriers (MCs) must first be gained.     

New insights into the evolutionary history of photoreceptor cells

Although the common descent of all life has been widely accepted since Darwin's time, new research occasionally provides us with arresting reminders of the unity of evolutionary history. Recent papers by Arendt et al. and Panda et al. provide one such reminder. They illustrate that the two classes of animal photoreceptors, ciliary and rhabdomeric photoreceptors, are likely to share an ancient common ancestor and have been evolving in parallel since their duplication over 600 million years ago.     

Nested genes and increasing organizational complexity of metazoan genomes

The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.     

Gene flow between vicariant tree species: insights into savanna-forest evolutionary relationships

Studying the genetic structure of vicariant species (i.e., closely related species that occupy ecologically distinct yet adjacent habitats) can shed light on the evolution and divergence of species with different ecological requirements. A previous phylogeographic study identified chloroplast DNA haplotype sharing between two vicariant tree species, one from forest (Hymenaea courbaril) and one from savanna (H. stigonocarpa) habitats. These species co-occur in the Brazilian Cerrado, a biome that encompasses forest patches and riverine forests within a savanna matrix. In order to investigate the evolutionary processes involved in the genetic divergence of these trees, we used nuclear microsatellite markers, statistical methods including approximate Bayesian computation (ABC), and leaf morphology to analyze neighboring and distant populations. Bayesian analysis revealed admixture between the species. ABC analysis supported the scenarios with the occurrence of gene flow between species during the Last Glacial Maximum or from the Holocene to the present, when compared to alternative scenarios of no gene flow or constant gene flow since divergence. However, putative hybrids did not exhibit intermediate leaflet morphology, which could be related to distinct selective pressures maintaining species integrity even in the face of gene flow. Our results suggest that despite morphological differences between savanna and forest species, interspecific barriers to gene flow might not be fully developed between vicariant tree species and that interspecific hybridization in trees from Cerrado biome may be an underdiagnosed process.     

TB domain proteins: evolutionary insights into the multifaceted roles of fibrillins and LTBPs

Fibrillins and LTBPs [latent TGFβ (transforming growth factor β)-binding proteins] perform vital and complex roles in the extracellular matrix and are relevant to a wide range of human diseases. These proteins share a signature 'eight cysteine' or 'TB (TGFβ-binding protein-like)' domain that is found nowhere else in the human proteome, and which has been shown to mediate a variety of protein-protein interactions. These include covalent binding of the TGFβ propeptide, and RGD-directed interactions with a repertoire of integrins. TB domains are found interspersed with long arrays of EGF (epidermal growth factor)-like domains, which occur more widely in extracellular proteins, and also mediate binding to a large number of proteins and proteoglycans. In the present paper, newly available protein sequence information from a variety of sources is reviewed and related to published findings on the structure and function of fibrillins and LTBPs. These sequences give valuable insight into the evolution of TB domain proteins and suggest that the fibrillin domain organization emerged first, over 600 million years ago, prior to the divergence of Cnidaria and Bilateria, after which it has remained remarkably unchanged. Comparison of sequence features and domain organization in such a diverse group of organisms also provides important insights into how fibrillins and LTBPs might perform their roles in the extracellular matrix.     

The urbilaterian brain: developmental insights into the evolutionary origin of the brain in insects and vertebrates

Classical phylogenetic, neuroanatomical and neuroembryological studies propose an independent evolutionary origin of the brains of insects and vertebrates. Contrasting with this, data from three sets of molecular and genetic analyses indicate that the developmental program of brains of insects and vertebrates might be highly conserved and suggest a monophyletic origin of the brain of protostomes and deuterostomes. First, recent results of molecular phylogeny imply that none of the currently living animals correspond to evolutionary intermediates between protostomes and deuterostomes, thus making it impossible to infer the morphological organization of an ancestral bilaterian brain from living specimens. Second, recent molecular genetic evidence provides support for the body axis inversion hypothesis, which implies that a dorsoventral inversion of the body axis occurred in protostomes versus deuterostomes, leading to the inverted location of neurogenic regions in these animal groups. Third, recent developmental genetic analyses are uncovering the existence of structurally and functionally homologous genes that have comparable and interchangeable functions in early brain development in insect and vertebrate model systems. Thus, development of the anteriormost part of the embryonic brain in both insects and vertebrates depends upon the otd/Otx and ems/Emx genes; development of the posterior part of the embryonic brain in both insects and vertebrates involves homologous control genes of the Hox cluster. These findings, which demonstrate the conserved expression and function of key patterning genes involved in embryonic brain development in insects and vertebrates support the hypothesis that the brains of protostomes and deuterostomes are of monophyletic, urbilaterian origin.     

The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera

Background

Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera.

Results

The mitogenome of Zorotypus medoensis with an A + T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A + T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees.

Conclusions

Characterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1156) contains supplementary material, which is available to authorized users.