Evidence for a type-IV-related collagen in Drosophila melanogaster. Evolutionary constancy of the carboxyl-terminal noncollagenous domain

Type IV collagen, a major structural component of basement membrane, has been characterized only in vertebrates. It is unique among the collagenous proteins in that it forms specific lattice networks by end-to-end interactions. In particular, in mammals the C-terminal noncollagenous domain (NCl) of collagen IV was shown to be one of the major cross-linking sites in the network assembly. Here, we give the first direct evidence of type-IV-related collagen in invertebrates by sequence analysis of cDNA and genomic DNA clones for the 3'-end of a previously characterized Drosophila collagen gene. The data describe the C-terminal 190 amino acid residues of the triple helix and the entire noncollagenous domain (231 amino acids) of the chain encoded for by this gene. Comparison with data reported for human and mouse alpha 1(IV) chains reveals that triple-helix regions are quite different, while NC1 structures are very similar. This suggests different constraints on triple-helix and NC1 domains during evolution. Present data support the assumption that the NC1 structure originated from duplication of an ancestral sequence; the extent of both interspecies and intramolecular homologies suggests the maintenance in vertebrates and invertebrates of an ancestral specific function.     

Developmental evolution of the insect retina: insights from standardized numbering of homologous photoreceptors

The canonical number of eight photoreceptors and their arrangement in the ommatidia of insect compound eyes is very conserved. However significant variations exist in selective groups, such as the Lepidoptera and Hymenoptera, which independently evolved additional photoreceptors. For this and historical reasons, heterogeneous labeling conventions have been in use for photoreceptor subtypes, despite developmentally and structurally well-defined homologies. Extending earlier efforts, we introduce a universal photoreceptor subtype classification key that relates to the Drosophila numbering system. Its application is demonstrated in major insect orders, with detailed information on the relationship to previous conventions. We then discuss new insights that result from the improved understanding of photoreceptor subtype homologies. This includes evidence of functionally imposed ground rules of differential opsin expression, the underappreciated role of R8 as ancestral color receptor, the causes and consequences of parallel R7 photoreceptor addition in Hymenoptera and Lepidoptera, and the ancestral subfunctionalization of outer photoreceptors cells, which may be only developmentally recapitulated in Drosophila. We conclude with pointing out the need for opsin expression data from a wider range of insect orders.     

Hypothesis testing in evolutionary developmental biology: a case study from insect wings

Developmental data have the potential to give novel insights into morphological evolution. Because developmental data are time-consuming to obtain, support for hypotheses often rests on data from only a few distantly related species. Similarities between these distantly related species are parsimoniously inferred to represent ancestral aspects of development. However, with limited taxon sampling, ancestral similarities in developmental patterning can be difficult to distinguish from similarities that result from convergent co-option of developmental networks, which appears to be common in developmental evolution. Using a case study from insect wings, we discuss how these competing explanations for similarity can be evaluated. Two kinds of developmental data have recently been used to support the hypothesis that insect wings evolved by modification of limb branches that were present in ancestral arthropods. This support rests on the assumption that aspects of wing development in Drosophila, including similarities to crustacean epipod patterning, are ancestral for winged insects. Testing this assumption requires comparisons of wing development in Drosophila and other winged insects. Here we review data that bear on this assumption, including new data on the functions of wingless and decapentaplegic during appendage allocation in the red flour beetle Tribolium castaneum.     

Opsins and cell fate in the Drosophila Bolwig organ: tricky lessons in homology inference

The Drosophila Bolwig organs are small photoreceptor bundles that facilitate the phototactic behavior of the larva. Comparative literature suggests that these highly reduced visual organs share evolutionary ancestry with the adult compound eye. A recent molecular genetic study produced the first detailed account of the mechanisms controlling differential opsin expression and photoreceptor subtype determination in these enigmatic eyes of the Drosophila larva. Here, the evolutionary implications are examined, taking into account the dynamic diversification of opsin genes and the spatial regulation of opsin homolog expression in other insects. It is concluded that, consistent with their common evolutionary roots, the Drosophila larval and adult eyes use the same mechanisms for the regulation of opsin expression and photoreceptor cell fate specification. Strikingly, the structurally highly derived Bolwig organs retained a more ancestral state of opsin expression and regulation. Inconspicuous in size, the Drosophila larval eyes deliver useful lessons in the reconstruction of homology between neuronal cell types with gene expression data, and on the conservative nature of gene regulatory network evolution during the emergence of novel organs from ancestral templates.     

Six class homeobox genes in drosophila belong to three distinct families and are involved in head development.

The vertebrate Six genes are homologues of the Drosophila homeobox gene sine oculis (so), which is essential for development of the entire visual system. Here we describe two new Six genes in Drosophila, D-Six3 and D-Six4, which encode proteins with strongest similarity to vertebrate Six3 and Six4, respectively. In addition, we report the partial sequences of 12 Six gene homologues from several lower vertebrates and show that the class of Six proteins can be subdivided into three major families, each including one Drosophila member. Similar to so, both D-Six3 and D-Six4 are initially expressed at the blastoderm stage in narrow regions of the prospective head and during later stages in specific groups of head midline neurectodermal cells. D-Six3 may also be essential for development of the clypeolabrum and several head sensory organs. Thus, the major function of the ancestral Six gene probably involved specification of neural structures in the cephalic region.     

New perspectives on the evolution of protochordate sensory and locomotory systems, and the origin of brains and heads

Cladistic analyses generally place tunicates close to the base of the chordate lineage, consistent with the assumption that the tunicate tail is primitively simple, not secondarily reduced from a segmented trunk. Cephalochordates (i.e. amphioxus) are segmented and resemble vertebrates in having two distinct locomotory modes, slow for distance swimming and fast for escape, that depend on separate sets of motor neurons and muscle cells. The sense organs of both amphioxus and tunicate larvae serve essentially as navigational aids and, despite some uncertainty as to homologies, current molecular and ultrastructural data imply a close relationship between them. There are far fewer signs of modification and reduction in the amphioxus central nervous system (CNS), however, so it is arguably the closer to the ancestral condition. Similarities between amphioxus and tunicate sense organs are then most easily explained if distance swimming evolved before and escape behaviour after the two lineages diverged, leaving tunicates to adopt more passive means of avoiding predation. Neither group has the kind of sense organs or sensory integration centres an organism would need to monitor predators, yet mobile predators with eyes were probably important in the early Palaeozoic. For a predator, improvements in vision and locomotion are mutually reinforcing. Both features probably evolved rapidly and together, in an 'arms race' of eyes, brains and segments that left protochordates behind, and ultimately produced the vertebrate head.     

Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest.     

Replication of UV-damaged DNA: new insights into links between DNA polymerases, mutagenesis and human disease

The existence of homologous genes in diverse species is intriguing. A detailed comparison of the structure and function of gene families may provide important insights into gene regulation and evolution. An unproven assumption is that homologous genes have a common ancestor. During evolution, the original function of the ancestral gene might be retained in the different species which evolved along separate courses. In addition, new functions could have developed as the sequence began to diverge. This may also explain partly the presence of multipurpose genes, which have multiple functions at different stages of development and in different tissues. The Drosophila gene snail is a multipurpose gene; it has been demonstrated that snail is critical for mesoderm formation, for CNS development, and for wing cell fate determination. The related vertebrate Snail and Slug genes have also been proposed to participate in mesoderm formation, neural crest cell migration, carcinogenesis, and apoptosis. In this review, we will discuss the Snail/Slug family of regulators in species ranging from insect to human. We will present the protein structures, expression patterns, and functions based on molecular genetic analyses. We will also include the studies that helped to elucidate the molecular mechanisms of repression and the relationship between the conserved and divergent functions of these genes. Moreover, the studies may enable us to trace the evolution of this gene family.     

Structure, function and evolution of sex-determining systems in Dipteran insects

Nature has evolved an astonishing variety of genetic and epigenetic sex-determining systems which all achieve the same result, the generation of two sexes. Genetic and molecular analyses, mainly performed during the last 20 years, have gradually revealed the mechanisms that govern sexual differentiation in a few model organisms. In this review, we will introduce the sex-determining system of Drosophila and compare the fruitfly to the housefly Musca domestica and other Dipteran insects. Despite the ostensible variety, all these insects use the same basic strategy: a primary genetic signal that is different in males and females, a key gene that responds to the primary signal, and a double-switch gene that eventually selects between two alternative sexual programmes. These parallels, however, do not extend to the molecular level. Except for the double-switch gene doublesex at the end of the cascade, no functional homologies were found between more distantly related insects. In particular, Sex-lethal, the key gene that controls sexual differentiation in Drosophila, does not have a sex-determining function in any other genus studied so far. These results show that sex-determining cascades, in comparison to other regulatory pathways, evolve much more rapidly.     

Differential loss of ancestral gene families as a source of genomic divergence in animals

A phylogenetic approach was used to reconstruct the pattern of an apparent loss of 2106 ancestral gene families in four animal genomes (Caenorhabditis elegans, Drosophila melanogaster, human and fugu). Substantially higher rates of loss of ancestral gene families were found in the invertebrates than in the vertebrates. These results indicate that the differential loss of ancestral gene families can be a significant factor in the evolutionary diversification of organisms.     

Gene content evolution on the X chromosome

Compared with autosomes, the X chromosome shows different patterns of evolution as a result of its hemizygosity in males. Additionally, inactivation of the X during spermatogenesis can make the X chromosome an unfavorable location for male-specific genes. These factors can help to explain why in many species gene content of the X chromosome differs from that of autosomes. Indeed, the X chromosome in mouse is enriched for male-specific genes while they are depleted on the X in Drosophila but show neither of these trends in mosquito. Here, we will discuss recent findings on the ancestral and neo-X chromosomes in Drosophila that support sexual antagonism as a force shaping gene content evolution of sex chromosomes and suggest that selection could be driving male-biased genes off the X.     

Evolution of type II DNA methyltransferases. A gene duplication model

On the basis of consensus sequences, which had previously been defined for two groups of closely related cytosine-specific and adenine-specific DNA methyltransferases, homologies can be detected that indicate a common origin for these proteins. Intramolecular comparisons of several of these enzymes reveal homology relationships, which suggests that gene duplication is a phylogenetic principle in the evolution of the Mtases. One or two duplications of an ancestral gene encoding a 12,000 to 16,000 Mr protein, followed by divergent evolution, may have led to very different protein structures and could explain the differences in amino acid sequences, molecular weights and biochemical properties. Intermolecular and intramolecular homologies were also recognized in type II restriction endonucleases, suggesting a very similar evolutionary pathway.     

Analysis of the chicken TBP-like protein(tlp) gene: evidence for a striking conservation of vertebrate TLPs and for a close relationship between vertebrate tbp and tlp genes.

TLP (TBP-like protein), which is a new protein dis-covered by us, has a structure similar to that of the C-terminal conserved domain (CCD) of TBP, although its function has not yet been elucidated. We isolated cDNA and genomic DNA that encode chicken TLP (cTLP) and determined their structures. The predicted amino acid sequence of cTLP was 98 and 91% identical to that of its mammalian and Xenopus counterparts, respectively, and its translation product was ubiquitously observed in chicken tissues. FISH detection showed that chicken tlp and tbp genes were mapped at 3q2.6-2.8 and 3q2.4-2.6 of the same chromosome, respectively. Genome analysis revealed that the chicken tlp gene was spliced with five introns. Interestingly, the vertebrate tbp genes were also found to be split by five introns when we focused on the CCDs, and their splicing points were similar to those of tlp. On the contrary, another TBP-resembling gene of Drosophila, trf1, is split by only one intron, as is the Drosophila 's tbp gene. These results support our earlier assumption that vertebrate TLPs did not directly descend from Drosophila TRF1. On the basis of these results together with phylogenetical exam-ination, we speculate that tlp diverged from an ancestral tbp gene through a process of gene duplication and point mutations.     

Early events in the development of Drosophila peripheral nervous system

1. We have analysed the development of the larval PNS of Drosophila, with the aim of understanding the genetic programme that underlies this development. 2. The achaete-scute gene complex (AS-C), which is required for the development of the adult PNS, is also necessary for the larval PNS. The analysis of different AS-C lesions shows that the larval PNS results from the superimposition of two independent subpatterns, each of which depends on one AS-C gene. 3. The analysis of the two subpatterns reveals hidden homologies between the very different arrangements of sense organs observed on different segments, suggesting that the initial pattern is the same in all segments and is later modified in the different segments. 4. The early arrangement of sensory mother cells can be visualised in a special transgenic line, A37. In this line the initial repetitive pattern inferred above can be directly observed. Furthermore this line makes it possible to decide whether a given mutation acts on the very early steps of the PNS development (determination) or at later stages (differentiation). 5. The line A37 has been used to show that mutations that reduce the PNS such as AS-C- or da- alter the very first steps of the process, while mutations which result in a hypertrophied PNS such as N seem to alter a subsequent step. We end up with an overview of the genetic operations that generate the arrangement of sense organs and sensory neurons.     

N-Terminal homology in three cysteinyl proteases from Papaya latex

Sequences to residue 17 have been determined for the three Papaya cysteinyl proteases, chymopapain and papaya peptidase A and B. Extensive homologies were found for these three enzymes and with papain and bromelain. These results suggest that the five sulphydryl enzymes discussed derive from a common ancestral gene.     

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition.     

Subdivision in an ancestral species creates asymmetry in gene trees

We consider gene trees in three species for which the species tree is known. We show that population subdivision in ancestral species can lead to asymmetry in the frequencies of the two gene trees not concordant with the species tree and, if subdivision is extreme, cause the one of the nonconcordant gene trees to be more probable than the concordant gene tree. Although published data for the human-chimp-gorilla clade and for three species of Drosophila show asymmetry consistent with our model, sequencing error could also account for observed patterns. We show that substantial levels of persistent ancestral subdivision are needed to account for the observed levels of asymmetry found in these two studies.