Multilocus enzymes, gene regulation, and genetic sufficiency

That 70s show: regulation, evolution and development beyond molecular genetics

This paper argues that the "long 1970s" (1969-1983) is an important though often overlooked period in the development of a rich landscape in the research of metabolism, development, and evolution. The period is marked by: shrinking public funding of basic science, shifting research agendas in molecular biology, the incorporation of new phenomena and experimental tools from previous biological research at the molecular level, and the development of recombinant DNA techniques. Research was reoriented towards eukaryotic cells and development, and in particular towards "giant" RNA processing and transcription. We will here focus on three different models of developmental regulation published in that period: the two models of eukaryotic genetic regulation at the transcriptional level that were developed by Georgii P. Georgiev on the one hand, and by Roy Britten and Eric Davidson on the other; and the model of genetic sufficiency and evolution of regulatory genes proposed by Emile Zuckerkandl. These three bases illustrate the range of exploratory hypotheses that characterised the challenging landscape of gene regulation in the 1970s, a period that in hindsight can be labelled as transitional, between the biology at the laboratory bench of the preceding period, and the biology of genetic engineering and intensive data-driven research that followed.

Further studies on the alcohol dehydrogenases in barley: evidence for a third alcohol dehydrogenase locus and data on the effect of an alcohol dehydrogenase – 1 null mutation in homozygous and in heterozygous condition

This paper presents evidence that the alcohol dehydrogenases (ADHs) in barley are specified by three loci. Six distinct ADH isozymes are observed following native slab polyacrylamide gel electrophoresis of crude extracts from flooded wild-type roots. Three of these isozymes are missing in flooded roots of plants homozygous for the Adhl-M9 mutation. The results also indicate that a simple binomial model (incorporating random dimerization and no inhibitive interaction of the two subunit species within heterodimers) is unable to account for the distribution of the total ADH activity between the ADH isozymes observed. Finally, the level and distribution of ADH activity in heterozygous (Adhl+ / Adhl-M9) flooded roots is not what would be expected if these contain only one-half of the available ADH1 protomers and the same frequency of available ADH2 and ADH3 protomers as is contained in the flooded roots of wild-type homozygotes (Adhl + / Adhl + ).

Patterns of expansion and expression divergence in the plant polygalacturonase gene family

Analysis of Arabidopsis and rice polygalacturonases suggests that polygalacturonases duplicates underwent rapid expression divergence and that the mechanisms of duplication affect the divergence rate.

Background

Polygalacturonases (PGs) belong to a large gene family in plants and are believed to be responsible for various cell separation processes. PG activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, fruit softening and decay, xylem cell formation, and pollen tube growth, thus illustrating divergent roles for members of this gene family. A close look at phylogenetic relationships among Arabidopsis and rice PGs accompanied by analysis of expression data provides an opportunity to address key questions on the evolution and functions of duplicate genes.

Results

We found that both tandem and whole-genome duplications contribute significantly to the expansion of this gene family but are associated with substantial gene losses. In addition, there are at least 21 PGs in the common ancestor of Arabidopsis and rice. We have also determined the relationships between Arabidopsis and rice PGs and their expression patterns in Arabidopsis to provide insights into the functional divergence between members of this gene family. By evaluating expression in five Arabidopsis tissues and during five stages of abscission, we found overlapping but distinct expression patterns for most of the different PGs.

Conclusion

Expression data suggest specialized roles or subfunctionalization for each PG gene member. PGs derived from whole genome duplication tend to have more similar expression patterns than those derived from tandem duplications. Our findings suggest that PG duplicates underwent rapid expression divergence and that the mechanisms of duplication affect the divergence rate.

Is ectopic expression caused by deregulatory mutations or due to gene-regulation leaks with evolutionary potential?

It has long been thought that gene expression is tightly regulated in multicellular eukaryotes, so that expression profiles match functional profiles. This conception emerged from the assumption that gene activity is synonymous with gene function. This paradigm was first challenged by comparative protein electrophoresis studies showing extensive differences in expression patterns among related species. The paradigm is now being challenged by evolutionary transcriptomics using microarray technologies. Most gene expression profiles display features that lack any obvious functional significance. The so-called "ectopic" expression refers to the expression of genes at times and locations where the target gene is not known to have a function. However, ectopic expression might be associated with genuine function even if this function is not essential or has yet to be ascertained. Alternatively, ectopic expression might come about as a superfluous by-product of regulatory systems, which would call for a revision of prevailing ideas about the specificity of gene regulation. We herein review available evidence for ectopic expression and the hypotheses proposed for its origin and evolution. We propose that ectopic expression must be regarded as part of an integrated phenotypic whole. It seems likely that ectopic expression represents a leak in the evolution of regulatory systems, but one that is endowed with considerable evolutionary possibilities.

Specialized metabolism and biochemical suppression during aestivation of the extant South American lungfish--Lepidosiren paradoxa

Lepidosiren paradoxa (pirambóia) is the single representative of Dipnoan (lungfish) in South America. This species is considered a living fossil, in spite of some reports describing this fish as having a very specialized life style. It aestivates during the dry season, and has developed metabolic adaptations to cope with both flooding and drought. The literature describing its tissue ultra-structure shows high glycogen stored in the muscle, suggesting a strong dependence on anaerobic glycolysis. The present paper reports tissue enzyme levels of LDH, MDH, and CS, and isozymic tissue distribution of LDH, MDH, ADH, PGI, SOD, and PGM of 7 aestivating specimens from Lago do Canteiro in the Amazonas River. Animals were caught while burrowed in mud during the aestivation period. Our findings reveal high anaerobic capacity of both skeletal and heart muscles, even during the aestivation period, when enzymes showed suppressed levels compared to those of non-aestivating animals (data from the literature). Isozymic patterns suggest loss of duplicate condition in most analyzed loci, a characteristic that occurs mainly in higher vertebrate categories. These data indicate that, compared to the fish group, lungfish may be considered advanced, despite retaining primitive morphological characters.

Junk DNA and sectorial gene repression

Transcriptional repression in eukaryotes often involves tens or hundreds of kilobase pairs, two to three orders of magnitude more than the bacterial operator/repressor model does. Classical repression, represented by this model, was maintained over the whole span of evolution under different guises, and consists of repressor factors interacting primarily with promoters and, in later evolution, also with enhancers. The use of much larger amounts of DNA in the other mode of repression, here called the sectorial mode ('superrepression'), results in the conceptual transfer of so-called junk DNA to the domain of functional DNA. This contribution to the solution of the c-value paradox involves perhaps 15% of genomic 'junk,' and encompasses the bulk of the introns, thought to fill a stabilizing role in sectorially repressed chromatin structures. In the case of developmental genes, such structures appear to be heterochromatoid in character. However, solid clues regarding general structural features of superrepressed terminal differentiation genes remain elusive. The competition among superrepressible DNA sectors for sectorially binding factors offers, in principle, a molecular mechanism for developmental switches. Position effect variegation may be considered an abnormal manifestation of normal processes that underly development and involve heterochromatoid sectorial repression, which is apparently required for local elimination or modulation of morphological features (morpholysis). Sectorial repression of genes participating either in development or in terminal differentiation is considered instrumental in establishing stable cell types, and provides a basis for the distinction between determination and cell type specification. The gamut of possible stable cell types may have been broadened by the appearance in evolution of heavy isochores. Additional types of relatively frequent GC-rich cis-acting DNA motifs may offer reiterated binding sites to factors endowed with a selective (though not individually strong) affinity for these motifs. The majority of sequence motifs thought to be used in superrepression need not be individually maintained by natural selection. It is re-emphasized that the dispensability of sequences is not an indicator of their nonfunctionality and that in many cases, along noncoding sequences, nucleotides tend to fill functions collectively, rather than individually.

Tracking heterochromatin

The Second International Workshop on Drosophila Heterochromatin, held in Honolulu from January 4-7, 1995, brought together about 70 scientists from the US, Canada, Germany, Italy, Russia, and the Netherlands. After the first of these international meetings, five years ago, Mary Lou Pardue and Wolfgang Hennig, in these columns, commented on its proceedings, and on heterochromatin in general. Although the questions that they raised cannot yet be answered exhaustively, important and sometimes surprising new observations have been made, some previously tentative answers have been firmed up, and some theoretical views underwent significant shifts. We wish to reflect here a few of the data presented at the second workshop, and express some thoughts suggested to us by these recent findings.

Molecular pathways to parallel evolution: I. Gene nexuses and their morphological correlates

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently "unrelated" organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counterpart to parallel evolution. Specific macromolecular interactions leading to the regulation of the c-fos gene are given as an example of a "controller node" defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for "controller gene diseases," a process that would spontaneously tend to lead to increased regulatory and organismal complexity. Despite the inferred increase in gene interaction complexity, whose course over evolutionary time is unknown, the number of homology groups for the functional and structural protein units designated as domains has probably remained rather constant, even as, in some of its branches, evolution moved toward "higher" organisms. In connection with this process, the question is raised of parallel evolution within the purview of activating and repressing master switches and in regard to the number of levels into which the hierarchies of genic master switches will eventually be resolved.

Revisiting junk DNA

The distribution of functions within genomes of higher organisms relative to processes that lead to the spread of mutations in populations is examined in its general outlines. A number of points are enumerated that collectively put in question the concept of junk DNA: the plausible compatibility of DNA function with rapid substitution rates; the likelihood of superimposed functions along much of eukaryotic DNA; the potential for a merely conditional functionality in sequence repeats; the apparent adoption of macromolecular waste as a strategy for maintaining a function without selective grooming of individual sequence repeats that carry out the function; the likely requirement that any DNA sequence must be "polite" vis-'a-vis (compatible with) functional sequences in its genomic environment; the existence in germ-cell lineages of selective constraints that are not apparent in populations of individuals; and the fact that DNA techtonics - the appearance and disappearance of genomic DNA - are not incompatible with function. It is pointed out that the inverse correlation between functional constraints and rates of substitution cannot be claimed to be pillar of the neutral theory, because it is also predicted from a selectionist viewpoint. The dispensability of functional structures is brought into relation with the concept of reproductive sufficiency the survivability of genotypes in the absence of fitter alleles.

Evolutionary implications of the cDNA sequence of the single lactate dehydrogenase of a lamprey

All vertebrates other than lampreys exhibit multiple loci encoding lactate dehydrogenase +ADL-LDH; (S)-lactate:NAD+ oxidoreductase, EC 1.1.1.27+BD. Of these loci, Ldh-A is expressed predominantly in muscle, Ldh-B is expressed predominantly in heart, and Ldh-C (where present) exhibits different tissue-restricted patterns of expression depending on the taxon. To examine the relationship of the single LDH of lampreys to other vertebrate LDHs, we have determined the cDNA sequence of the LDH of the sea lamprey Petromyzon marinus and compared it to previously published sequences from bacteria, plants, and vertebrates. The lamprey sequence exhibits a mixture of features of both LDH-A and LDH-B at the amino acid level that may account for its intermediate kinetic properties. Both distance and maximum parsimony analyses strongly reject a relationship of lamprey LDH with mammalian LDH-C but do not significantly distinguish among remaining alternative phylogenetic hypotheses. Evolutionary parsimony analyses suggest that the lamprey LDH is related to Ldh-A and that the single locus condition has arisen as a result of the loss of Ldh-B (prior to the appearance of Ldh-C). The collection of LDH sequences for further studies of the evolution of the vertebrate LDH gene family will be facilitated by the PCR approach that we have used to obtain the lamprey sequence.

Evidence for a genetic duplication involving alcohol dehydrogenase genes in Ceratitis capitata

An Adh duplication is described in the medfly Ceratitis capitata. Evidence is presented for two separate Adh1 and Adh2 structural loci mapping at a distance of 0.49 recombination unit from each other. By deletion mapping the Adh region has been cytologically located near the free end of the left arm of the second chromosome within an area between 2C;3A segments of the polytene chromosome. The genetic analysis of the region around Adh has identified seven neighboring genes (Acon1, Mpi, Est6, Aox, Xdh, Mdh2, Lsp1) which identify the linkage group D. The orientation of loci with regard to the centromere sets the origin of the map of the left arm of the second chromosome close to the two Adh loci.

Concentration-affinity equivalence in gene regulation: convergence of genetic and environmental effects

It is proposed that equivalent phenotypic effects can be obtained by either structural changes in macromolecules involved in gene regulation or changes in activity of the structurally unaltered macromolecules. This equivalence between changes in activity (concentration) and changes in structure can come into play within physiologically plausible limits and seems to represent an important interface between environment and genome--namely, between environmentally determined and genetically determined gene expression. The equivalence principle helps explain the appearance of phenocopies. It also points to a general pathway favorable to the occurrence, during evolution, of frequent episodes corresponding to Waddington's genetic assimilation and is likely to represent one component of the system responsible for the high frequency of recurrence of parallel evolution.

Analysis of protein patterns from different organs and cell fractions of trisomy 19 mice

Proteins were extracted from liver, brain, and skin of 6-day-old mice with trisomy (Ts) 19 and fractionated into solubilized cell proteins and structure-bound cell proteins. The proteins were separated by two-dimensional electrophoresis, and protein patterns were compared in the combinations Ts/normal and normal/normal. Analysis of the protein patterns revealed protein spots (variants) with densities higher (h-type) or lower (l-type) in trisomies than in normal mice. Some of these variants were found in all Ts individuals investigated for a particular protein class. These variants, termed regular Ts-variants, constituted 0.8%-1.6% of the total number of spots. The proteins of the regular Ts variants were in most cases organ-nonspecific. However, in almost all cases a given quantitative variation was expressed in only one of the three organs investigated. To explain our results, we have presented models for the control of protein levels on the basis of gene regulation. New aspects in the conception of studies on trisomies in man could be gained.

On the molecular evolutionary clock

The conceptual framework surrounding the origin of the molecular evolutionary clock and circumstances of this origin are described. In regard to the quest for the best available molecular clocks, a return to protein clocks is conditionally recommended. On the basis of recent data and certain considerations, it is pointed out that the realm of neutrality in evolution is probably less extensive than is now commonly thought, in the three distinct senses of the term neutrality--neutrality as nonfunctionality of mutations, neutrality as equifunctionality of mutations, and neutrality as a mode of fixation of mutations. The possibility is raised that complex sets of interacting components forming a system that is bounded with respect to its environment may quite generally display an intrinsic trend to a quasi-clockwise evolutionary behavior.

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.

Qualitative and quantitative variability in different classes of proteins: comparison of mouse and rat

Proteins of membranes and cytosols were extracted from the livers and brains of mice (inbred strain DBA/6J) and rats (inbred strain DA/Han) and separated by two-dimensional electrophoresis (2-DE). The 2-DE patterns were compared with regard to qualitative (spot position) and quantitative (spot intensity) characteristics of the proteins of these two species. The following results were obtained: Brain had more (higher percentage) conservative proteins (proteins found in both mice and rats) than liver; plasma membranes had more conservative proteins than the cytosols; organ-unspecific proteins contained more conservative proteins than relatively organ-specific proteins; the pattern of distribution of genetic variability among different classes of proteins represented by findings 1-3 was the same for the qualitative and quantitative characteristics of the proteins; and some observations indicated that quantitative variability occurred more frequently among proteins than did qualitative variability. Our conclusion is that regulatory sequences in the DNA (regulatory genes) are subjected to functional constraints that differ in strength among different classes of proteins by the same ratios as the constraints acting on the structural genes. The overall effect of the selective pressure is, however, less stringent for regulatory genes than for structural genes. The results obtained here by comparing two different species are very similar to previous results we obtained by studying different subspecies (inbred strains of the mouse). From this finding arises a new concept: the study of molecular evolution on the basis of different classes of proteins. Our results were compared with data from the literature that were obtained in part from studies on cultured cells. The comparison suggested that cultured cells have lost their tissue-specific proteins, and so generate predominantly extremely conservative proteins.

Quantitative protein profiling: determining lexotypes

The lexotype of a cell is defined as a set of quantitative characters of its informational macromolecular gene products, notably proteins, as observed under specified environmental conditions. This definition can be applied to cells in several ways that need to be distinguished. It can refer to the protein lexotype, to RNA lexotypes; to the steady-state lexotype, synthesis lexotype, functional protein lexotype; to the in situ lexotype and standard-environment lexotype. When used without qualification, the term lexotype may be applied to the standard-environment, steady-state protein lexotype. Some difficulties that currently limit our ability to determine lexotypes are assessed. Reasons are given why abnormal cellular states, such as states of disease, should often be characterizable by means of protein markers not themselves involved in the disease process and why one expects to find markers in tissues other than the one in which a certain pathological process may be anticipated to occur. There are three routes through which biological systems can produce secondary protein markers, namely through gene regulatory chains, through chromosomal gene linkage, and through "physiological linkage" of genes. The partly stable, partly shifting, yet defined relations between tissue lexotypes are considered. A number of potentially important fields of application of rigorous quantitative analyses of protein profiles are listed. One particular use of the technology is to investigate a hypothesis linking aging to degenerative diseases with late onset. According to this hypothesis, such diseases appear in later life as the cellular concentration of the active form of a protein passes a certain threshold in the course of the aging process.

An apparent progressive and recurrent evolutionary restriction in tissue expression of a gene, the lactate dehydrogenase-C gene, within a family of bony fish (Salmoniformes: Umbridae)

Unexpectedly large differences in the tissue patterns of lactate dehydrogenase-C (Ldh-C) gene regulation were observed among species of fish within the family Umbridae (Salmoniformes). Normally, all the species within a family or order of advanced fishes exhibit the same, tissue-restricted pattern of L-lactate dehydrogenase C4 isozyme synthesis--either eye- or liver-restricted expression, but not both. However, within the Umbridae the more anciently derived species had a more generalized (primitive) tissue expression, whereas the more recently derived species had a more tissue-restricted expression, predominating in the eye. Given the relative divergence times among the species estimated by genetic distance (using 51 protein-coding loci), divergence from the presumed primitive expression of the Ldh-C gene appears to have been proceeding more rapidly in some species lineages than others. This narrowing of Ldh-C gene tissue regulatory specificity within the family Umbridae is similar to the general trend observed over much greater evolutionary times within the class of bony fishes. The results support the hypothesis of repeated evolutionary canalizations of Ldh-C gene regulation from the generalized tissue expression in more primitive species to a predictable tissue-restricted expression (in either eye or liver) in advanced species. Furthermore, in the Umbridae, this progressive restriction of tissue expression of isozymes has taken place during the evolution of both the Ldh-C and Ldh-B genes. These evolutionary trends in the regulation of isozyme-locus tissue expression in the bony fishes are consistent with either an intrinsically conditioned trend of change in gene regulation or with a response to natural selection.

Analysis of two-dimensional protein patterns from mouse embryos with different trisomies

Two-dimensional protein patterns from whole mouse embryos with different trisomies (Ts) (Ts1, -12, -14, -19) and from different organs (normal or malformed) and developmental stages of Ts12 embryos were analyzed by comparison with control patterns. Quantitatively altered proteins were found, and a portion of these (21/approximately equal to 1,000, average) was attributable to the Ts conditions. Most of these variants were found always (regularly) in Ts embryos. They could be divided into two groups: group I shows characteristics (chromosome specific, density increased by a factor close to 1.5 +/- 0.12) compatible with proteins directly affected by the Ts; and group II (chromosome nonspecific, density decreased, seldom increased) results most likely from indirect effects. The incidence of group II variants (about 13/approximately equal to 1,000, average) was considerably greater than that of the group I variants (about 3/approximately equal to 1,000). The frequency of both types of variants, however, was far lower than was expected by a rough estimation. Apparently, a relatively small number of changes, rather than a complex, escalating effect, was induced at the protein level by the Ts. Some observations suggest that this is due to a stable regulation of protein concentrations. The proportion in which quantitative changes of different types occurred in the protein patterns did not correlate with the degree of developmental impairments (malformation, retardation, early death) of the embryos. The generalized occurrence of protein changes on the cellular level might explain the restricted viability of Ts mouse embryos.

Adaptative features of ectothermic enzymes--IV. Studies on malate dehydrogenase of Astyanax fasciatus (Characidae) from Lobo Reservoir (Såo Carlos, Såo Paulo, Brasil)

1. Skeletal muscle and heart supernatant malate dehydrogenase (s-MDH) from a subtropical fish, Astyanax fasciatus consists of three electrophoretically anodal bands. Each band is a dimer (AA, AB and BB) and two loci are active. 2. In A. fasciatus tissue extracts, A and B subunits are present at differing quantitative levels and their activities are almost season-independent. However, the relative activity of each homodimer in relation to total s-MDH estimated by densitometry of gels or of each homodimer purified by chromatography varies with temperature. The more anodic homodimer is thermolabile and the less anodic one is thermostable. 3. The pH optimum of s-MDH is 7.5, of AA is 6.5 and of BB is 7.8. 4. The BB isozyme is more sensitive to high concentrations of substrate and has a Km temperature-independent. The AA isozyme is not inhibited by high concentrations of oxaloacetate and shows a Km temperature-dependent with a fourteenfold increase between 20 degrees and 40 degrees C.

Adaptative features of ectothermic enzymes--I. Temperature effects on the malate dehydrogenase from a temperate fish Leiostomus xanthurus

1. Following electrophoresis the s-MDH activity of Leiostomus xanthurus and many other species of fish and amphibian appears in three sharp, equally-spaced, anodal bands. Each band is a dimer (AA, AB and BB) and two loci are active. 2. In Leiostomus tissue extracts A and B subunits are present are differing quantitative levels and their activities can be modified by changes in environment temperature. 3. Thermostability and thermal dependency tests show that, similar to what occurs during acclimatization, the AA isozyme is more stable to heat than is the BB isozyme. The BB isozyme is activated by low temperatures and is rapidly inactivated by high temperatures. 4. Extracts from a variety of fishes, amphibians, reptiles and birds suggest that when only one or two s-MDH bands are present, they behave as dose the AA homodimer in Leiostomus Xanthurus, i.e., are stable at elevated temperatures.

A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a 'c-value paradox' becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence 'motif' that is variable within certain limits. Noncoding sequences of the chickens ovalbumin gene furnish an appropriate example of a sequence motif. GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organisms, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.

Evolution of patterns of gene expression in hawaiian picture-winged Drosophila

The tissue and stage specificity of expression of five enzymes was examined by electrophoretic analysis of relative enzyme levels in extracts of 13 larval and adult tissues in 27 species of Hawaiian picture-winged Drosophila. The developmentally regulated patterns of enzyme expression thus characterized were compared to a modal standard phenotype. About 30% of the pattern features analyzed differed significantly from the standard in one or more species. Many of these regulatory differences are essentially qualitative, with tissue specific differences in enzyme activity in excess of 100 fold for some species pairs. The adaptive significance of these pattern differences in unknown, but the results provide strong direct evidence for rapid evolution of new patterns of gene regulation in this group of organisms.

Evolution of the differential regulation of duplicate genes after polyploidization

In the 50 million years since the polyploidization event that gave rise to the catostomid family of fishes the duplicate genes encoding isozymes have undergone different fates. Ample opportunity has been available for regulatory evolution of these duplicate genes. Approximately half the duplicate genes have lost their expressions during this time. Of the duplicate genes remaining, the majority have diverged to different extents in their expression within and among adult tissues. The pattern of divergence of duplicate gene expression is consistent with the accumulation of mutations at regulatory genes. The absence of a correlation of extent of divergence of gene expression with the level of genetic variability for isozymes at these loci is consistent with the view that the rates of regulatory gene and structural gene evolution are uncoupled. The magnitude of divergence of duplicate gene expressions varies among tissues, enzymes, and species. Little correlation was found with the extent of divergence of duplicate gene expression within a species and its degree of morphological "conservatism", although species pairs which are increasingly taxonomically distant are less likely to share specific patterns of differential gene expression. Probable phylogenetic times of origin of several patterns of differential gene expression have been proposed. Some patterns of differential gene expression have evolved in recent evolutionary times and are specific to one or a few species, whereas at least one pattern of differential gene expression is present in nearly all species and probably arose soon after the polyploidization event. Multilocus isozymes, formed by polyploidization, provide a useful model system for studying the forces responsible for the maintenance of duplicate genes and the evolution of these once identical genes to new spatially and temporally specific patterns of regulation.