Regulatory Genes and Adaptation

Genomic signatures of the evolution of a diurnal lifestyle in Strigiformes

Understanding the targets of selection associated with changes in behavioral traits represents an important challenge of current evolutionary research. Owls (Strigiformes) are a diverse group of birds, most of which are considered nocturnal raptors. However, a few owl species independently adopted a diurnal lifestyle in their recent evolutionary history. We searched for signals of accelerated rates of evolution associated with a diurnal lifestyle using a genome-wide comparative approach. We estimated substitution rates in coding and noncoding conserved regions of the genome of seven owl species, including three diurnal species. Substitution rates of the noncoding elements were more accelerated than those of protein-coding genes. We identified new, owl-specific conserved noncoding elements as candidates of parallel evolution during the emergence of diurnality in owls. Our results shed light on the molecular basis of adaptation to a new niche and highlight the importance of regulatory elements for evolutionary changes in behavior. These elements were often involved in the neuronal development of the brain.

The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.

CONSERVATION OF MOLECULAR PREPATTERNS DURING THE EVOLUTION OF CUTICLE MORPHOLOGY IN DROSOPHILA LARVAE

We are using patterns of cuticle specialization in Drosophila larvae as models to investigate the molecular, genetic, and developmental bases of morphological evolution. Members of the virilis species group differ markedly from one another in the distribution of hairs on the dorsal surface of first instar larvae. In particular, characteristic bands of hairs cover about 20% of each trunk segment in some species but about 70% in others. These major types do not correlate with recently proposed phylogenetic relationships, suggesting that similar phenotypes have arisen independently in different lineages. The patterns of expression of several genes that control or reflect intrasegmental patterning are indistinguishable in species with very different cuticle morphologies. We conclude that, in this case, morphology probably has evolved via altered response to a conserved molecular prepattern.

Inheritance of protein amounts: comparison of two-dimensional electrophoresis patterns of leaf sheaths of two maize lines (Zea mays L.) and their hybrids

Denatured total proteins of two maize lines and their reciprocal F1 hybrids were analysed by two-dimensional electrophoresis. Quantitative (spot more or less intense) and qualitative (presence or absence of spots) differences exist between the lines, and correspond to 11% of the total reproducible spots. Non-additive effects on spot intensities were found in the hybrids, which display spots similar to the more intense parental spot for 11% of varying spots. This may correspond to dominance for regulatory systems controlling the protein amounts. Such interactions contrast with additivity classically described for enzymes or DNA.

Protein polymorphism between 2 Picea abies populations revealed by 2-dimensional gel electrophoresis and tandem mass spectrometry

In species with high gene flow and consequent low interpopulation differentiation over wide geographic ranges, differential gene expression along ecological gradients often reveals adaptive significance. We investigated potential differences in protein expression between Picea abies ecotypes adapted to contrasting altitude conditions. Protein expression patterns were compared between needles and roots of 2-month-old P. abies seedlings by means of 2-dimensional electrophoresis. Proteins exhibiting differential expression between the 2 ecotypes were analyzed by tandem mass spectrometry. A total of 19 proteins exhibited qualitative or quantitative polymorphism between the 2 populations. These proteins exhibited organ-specific expression, and the level of interpopulation protein polymorphism was organ dependent. Among differentially expressed proteins, we identified proteins involved in photosynthesis, photorespiration, root tracheary element differentiation, and transmitochondrial membrane transport. Our results show that P. abies seedlings from locally adapted ecotypes exhibit consistent differences in protein expression. The expression polymorphism of some of these proteins has potential adaptive significance.

Similar tissue-specific expression of the Adh genes from different Drosophila species is mediated by distinct arrangements of cis-acting sequences

In Drosophila melanogaster transformants, the alcohol dehydrogenase (Adh) genes from D. affinidisjuncta and D. grimshawi show similar levels of expression except in the adult midgut where the D. affinidisjuncta gene is expressed about 10- to 20-fold more strongly. To study the arrangement of cis-acting sequences responsible for this regulatory difference, homologous restriction sites were used to create a series of chimeric genes that switched fragments from the 5' and 3' flanking regions of these two genes. Chimeric genes were introduced into the germ-line of D. melanogaster, and Adh gene expression was analyzed by measuring RNA levels. Various gene fragments in the promoter region and elsewhere influence expression in the adult midgut and in whole larvae and adults. Comparison of these results with earlier studies involving chimeras between the D. affinidisjuncta and D. hawaiiensis genes indicates that expression in the adult midgut is influenced by multiple regulatory sequences and that distinct arrangements of regulatory sequences can result in similar levels of expression both in the adult midgut and in the whole organism.

VARIATION IN ALCOHOL DEHYDROGENASE ACTIVITY AND FLOOD TOLERANCE IN WHITE CLOVER, TRIFOLIUM REPENS

Flooding results in induction of anaerobic metabolism in many higher plants. As an important component of anaerobic energy production, alcohol dehydrogenase (ADH) activity increases markedly in response to flooding in white clover, Trifolium repens. Significant inter-individual variation in flood-induced ADH activity exists in natural populations of T. repens. The genetic basis of this variation was analyzed by offspring-midparent regression of data from 75 greenhouse reared families; the estimated heritability of flood-induced ADH activity was 0.55 (±0.13). Genetic variation in flood-induced ADH activity has pronounced effects on physiological response and flood tolerance in this species. ADH activity is positively correlated with the rate of ethanol production, indicating that observed in vitro activity differences are manifested in in vivo physiological function. T. repens plants with higher ADH activities during flooding have greater flood tolerance (measured as growth rate when flooded/unflooded growth rate). Variation in ADH activity during flooding accounts for more than 79% of the variance in flood tolerance. On the basis of a limited field survey of populations occupying three sites differing in exposure to flooding conditions, individuals from site C, the most frequently flooded site, expressed significantly higher average ADH activity when flooded than individuals from site A, a site with no history of flooding. Since ADH activity levels are not correlated with electrophoretic mobility variation in T. repens, this work supports previous suggestions that regulatory variation in enzyme activity may play a central role in biochemical adaptations to environmental stress.

Complexity in evolved regulatory variation for alcohol dehydrogenase genes in Hawaiian Drosophila

The alcohol dehydrogenase gene (Adh gene) of Drosophila affinidisjuncta is expressed at a higher level in the larval midgut and Malpighian tubules than the homologous gene from Drosophila hawaiiensis. This study analyzed the cis-acting sequences responsible for these regulatory differences in larval tissues of Drosophila melanogaster transformants. A series of 10 chimeric and deleted Adh genes was introduced into the germ line of D. melanogaster, and tissue-specific expression levels were quantified by gel electrophoresis of tissue extracts. Sequences in the upstream region of the two genes had the strongest influence on enzyme production in the midgut and Malpighian tubules. Other sequence elements also showed effects, some of which were tissue specific. Most gene fragments displayed context-dependent effects, thus supporting the proposed model of polygenic regulation of Adh gene expression.

Genetic aspects of variation of protein amounts in maize and pea

Using high-resolution two-dimensional polyacrylamide gel electrophoresis we studied the polymorphism of protein amounts in some genotypes of maize and pea. This type of variability seems to be rather common and insensitive to environmental conditions, as attested by the comparison of the patterns of two maize lines harvested in two different years. A large-scale experiment involving 5 lines, 7 of their hybrids, and 6 organs (or physiological stages) of maize allowed us to examine numerous polypeptides regarding their genetic variability, their amount differences between organs and the inheritance of their abundance. Genetic and organ variations are not independent: polypeptides whose amount varies from one organ to another are, for the most part, genetically variable (59%), while the stable polypeptides are not often genetically variable (18%). We found a striking organ specificity for (i) the extent of quantitative variability (from 2.3-15.4% of the polypeptides), (ii) the occurrence and the type of variation for a given polypeptide (an intensity difference seen in an organ can disappear or even be reversed in another one), (iii) the kind of inheritance (additive/non-additive): combining the 6 organs and the 7 hybrids we found 101 cases of non-additivity (4% of the total) which concern as many as 72 different spots, that is to say that in most cases a polypeptide displaying nonadditivity in an organ seems to display additivity in the other ones. Moreover, for most of the polypeptides with nonadditive inheritance the hybrid spot presents an intensity similar to that of the most intense parental spot.(ABSTRACT TRUNCATED AT 250 WORDS)

Is the polymorphism of protein amounts related to phenotypic variability? A comparison of two-dimensional electrophoresis data with morphological traits in maize

The hypothesis that the quantitative variations in gene product levels could be a more important basis for morphological and adaptative change than the classical qualitative variability revealed by electrophoretic techniques was studied by comparing five maize lines from three sets of variables: (i) qualitative variations of proteins (presence/absence) revealed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE), at a physiological seedling stage; (ii) quantitative variations in proteins (spots more or less intense) revealed by 2D PAGE, at the same physiological stage; (iii) general combining abilities of fourteen heritable, morphological or agronomical characters measured at various juvenile and adult stages. Distances between lines were defined, based on qualitative and quantitative variations of proteins. These distances do not appear to be correlated and do not give the same patterns of divergence between lines, as shown by principal coordinate analyses. Mahalanobis distances computed from the general combining abilities of the morphological characters are significantly correlated (r=0.75) to quantitative but not to qualitative distances. The comparison of the first planes of the principal coordinate analyses performed on the three kinds of distances clearly confirms this finding. Our results are discussed in connection with the possible genetic meaning of the two molecular distances and with the hypothesis that regulatory processes are primarily implicated in morphological variation.

Chromosomal localization of structural genes and regulators in wheat by 2D electrophoresis of ditelosomic lines

Among the 782 spots observed in two-dimensional gel electrophoresis of denatured proteins from etiolated wheat shoots, 185 were found to be variable between the euploid and 26 ditelosomic lines of 'Chinese Spring'. Thirty-five structural genes were located on 17 chromosome arms. Numerous intensity changes showing alterations in protein levels were observed and led to the following statements: 1) regulators are frequently found and can be assigned for a same polypeptide to various chromosome arms; 2) for most polypeptides homoeologous arms do not manifest similar effects; 3) nevertheless, when affecting the same polypeptide, homoeologous arms display in most cases identical regulatory effects; 4) gene dosage compensation is observed in only one out of four homoeoallelic situations.

Regulatory gene evolution: adaptive differences in expression of alcohol dehydrogenase in Drosophila melanogaster and Drosophila simulans

In Drosophila melanogaster X D. simulans hybrids, the alcohol dehydrogenase (ADH) electromorphs characteristic of the two parents display tissue- and stage-specific differences in relative level of expression. This implies distinct cis-acting regulatory elements associated with the respective Adh alleles. These cis-acting elements account in part, but not completely, for markedly different overall patterns of ADH expression in the two species. The regulatory patterns seem to be adaptively significant since they correlate with species-specific patterns of ethanol tolerance. The activity differences are accounted for by different levels of enzyme protein, but the underlying mechanisms have not been fully analysed and may be complex. Independent evolution of various aspects of the ADH developmental programme may relate to use of different promoters for transcription of the Adh locus in different developmental contexts. This system illustrates the potential importance of regulatory genes in evolution and provides a model for investigating the molecular basis of evolved regulatory differences.