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PubMed1993

Evolution and expression of the Leishmania surface proteinase (gp63) gene locus.

The Leishmania surface proteinase, gp63, is the most abundant, surface-exposed protein on the promastigote form of the parasite. It is the product of a multigene family that, in some Leishmania species, shows marked heterogeneity among its members. The differential expression of structurally distinct gp63 genes shows circumstantial correlation with the differential processing and localization of the protein in the intracellular, amastigote form of Leishmania mexicana. The recent cloning and sequencing of a homologous gene in the monoxenous trypanosomatid, Crithidia fasciculata, provides a reference sequence for comparison with ten Leishmania gp63 genes sequenced to date. The amino terminal and the carboxy terminal regions of the protein sequences suggest different evolutionary histories within some of the genes. The evolutionary significance of the structure, organization, and regulation of the gp63 genes from different Leishmania species is described and speculated upon.

Amino Acid Sequence↗
PubMed1998

Emergence of a brain-expressed variant melanin-concentrating hormone gene during higher primate evolution: a gene "in search of a function".

Two related but distinct melanin-concentrating hormone (MCH) gene systems, i.e., the authentic and variant genes, have been characterized in the human, while only a single MCH gene has been found in the rat. We previously established that the variant gene corresponds to exon-I-deleted copies of the authentic gene mapped on chromosomes 5 and 12, respectively. In this report, we examined the expression of the authentic and variant MCH genes in the human brain. Mature mRNAs of the authentic MCH gene appeared to be predominantly expressed in the hypothalamus, whereas putative unprocessed transcripts of the variant MCH gene were found in other brain areas but not in the hypothalamus. Several products of the variant MCH gene were identified by RACE-PCR in the fetal human brain. One of these transcripts encoded a putative protein of 72 amino acids, while another transcript may potentially generate a protein of 35 amino acids. Thereafter, we explored the question of MCH gene transposition during Primate evolution. Southern blotting, PCR analyses using several genomic DNAs of Primates, and in situ hybridization on metaphase chromosomes led us to define at least three types of genetic events associated with the emergence of the variant MCH gene: (1) translocation of an exon II-exon III copy of the authentic MCH gene onto the equivalent of the human chromosome 5p arm of Anthropoidea ancestors (between 25 and 55 MYA); (2) exon II truncation and mutations before divergence of the Hylobatidae (about 15 MYA); and (3) duplication of the variant gene on the equivalent of the human chromosome 5p and 5q arms in the Hominidae, i.e., 5-10 MYA. Taken together, these results support the hypothesis that transposition/gene rearrangement processes could underlie the evolutionary emergence of new MCH-related genes expressed differentially in the brains of higher Primates, illustrating the concept of genes "in search of function" instead of true "pseudogenes."

Animals↗
PubMed2006

Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog.

This is the first detailed study of the evolution, phylogenetic distribution, and transcription of one young retroposed gene, CG13732, and its parental gene CG15645, whose functions are unknown. CG13732 is a recognizable retroposed copy of CG15645 retaining the signals of this process. We name the parental gene Cervantes and the retrogene Quijote. To determine when this duplication occurred and the phylogenetic distribution of Quijote, we employed polymerase chain reaction, Southern blotting, and the available information on sequenced Drosophila genomes. Interestingly, these analyses revealed that Quijote is present only in 4 species of Drosophila (Drosophila melanogaster, Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana) and that retroposed copies of Cervantes have also originated in the lineages leading to Drosophila yakuba and Drosophila erecta independently in the 3 instances. We name the new retrogene in the D. yakuba lineage Rocinante and the new retrogene in the D. erecta lineage Sancho. In this work, we present data on Quijote and its parental gene Cervantes. Polymorphism analysis of the derived gene and divergence data for both parental and derived genes were used to determine that both genes likely produce functional proteins and that they are changing at a fast rate (KA/KS approximately 0.38). The negative value of H of Fay and Wu in the non-African sample reveals an excess of derived variants at high frequency. This could be explained either by positive selection in the region or by demographic effects. The comparative expression pattern shows that both genes express in the same adult tissues (male and female germ line) in D. melanogaster. Quijote is also expressed in male and female in D. simulans, D. sechellia, and D. mauritiana. We argue that the fast rate of evolution of these genes could be related to their putative germ line function and are further studying the independent recruitment of Cervantes-derived retrogenes in multiple lineages.

Animals↗
PubMed2006

Class prediction from time series gene expression profiles using dynamical systems kernels.

We present a kernel-based approach to the classification of time series of gene expression profiles. Our method takes into account the dynamic evolution over time as well as the temporal characteristics of the data. More specifically, we model the evolution of the gene expression profiles as a Linear Time Invariant (LTI) dynamical system and estimate its model parameters. A kernel on dynamical systems is then used to classify these time series. We successfully test our approach on a published dataset to predict response to drug therapy in Multiple Sclerosis patients. For pharmacogenomics, our method offers a huge potential for advanced computational tools in disease diagnosis, and disease and drug therapy outcome prognosis.

Artificial Intelligence↗
PubMed1985

Characterization, expression, and evolution of the mouse embryonic zeta-globin gene.

We have determined the complete sequence of the embryonic alpha-like, zeta (zeta)-globin gene of the BALB/c mouse. The structure of this gene establishes the amino acid sequence of the mouse embryonic zeta-globin polypeptide chain and allows us to identify sequences within the gene that may be important for its expression. One of these is a 300-base segment that is tightly conserved between mice and humans and is located at the 5' end of the zeta-globin gene. By introducing the cloned gene into permanently transfected mouse erythroleukemic cell lines and comparing its transcript with that of zeta-globin mRNA derived from embryonic yolk sac erythrocytes, we are able to show that the cloned gene is transcriptionally active and that its transcript is correctly initiated and processed. Interestingly, the zeta-globin gene is also active when permanently transfected into an immunoglobulin-producing B-cell, a cell that presumably has tissue-specific requirements for gene expression. Further, a comparison of the amino acid coding sequence of the mouse zeta-globin gene to that of zeta-like globin genes of other species supports a revised evolutionary lineage in which goats and humans are closely related, whereas mice are further removed.

Amino Acid Sequence↗
PubMed1986

Structure, expression, and evolution of a heat shock gene locus in Caenorhabditis elegans that is flanked by repetitive elements.

A locus containing two hsp16 genes in Caenorhabditis elegans has been characterized by DNA sequencing. Each gene encodes a 16-kDa polypeptide which is expressed following heat induction. The two genes, designated hsp16-2 and hsp16-41, are arranged in divergent orientations, and each contains a single intron of 46 and 58 base pairs, respectively. Although both gene transcripts are spliced efficiently in vivo, hsp16-41 corresponds to a previously isolated cDNA which contains an unspliced intron sequence. The 5'-noncoding regions of both genes contain TATA boxes preceded 18 or 19 nucleotides upstream by a heat shock regulatory sequence. The 3'-noncoding regions contain polyadenylation signals (AATAAA) either downstream (hsp16-2) or immediately adjacent (hsp16-41) to a sequence capable of forming a hairpin. This pair of hsp16 genes is flanked by three copies of an approximately 200-bp dispersed repetitive element (two copies on one side and a single one on the other side of the locus) which occurs in at least 70 copies throughout the C. elegans genome, and has been designated CeRep-16. Together with data described previously (Russnak, R. H., and Candido, E. P. M. (1985) Mol. Cell. Biol. 5, 1268-1278), the results presented here define a family of four distinct, related small heat shock protein genes. These are arranged in divergently transcribed pairs at two loci. The hsp16-48/41 genes code for one class of HSP16, 143-amino acid residues long, while the hsp16-1/2 genes encode the other class, which is 2 amino acid residues longer. Thus each locus codes for the two major types of HSP16. The two loci differ in a number of respects, including the presence of a tandem inverted duplication of two heat shock protein genes at one locus, and of repetitive elements at the other. Sequence comparisons allow us to propose a scheme for the evolution of the four genes and reveal conserved features of noncoding regions which may be involved in the regulation of their transcription, RNA processing, or translation. Using locus-specific hybridization probes, we have found that the genes at locus hsp16-2/41 are expressed at levels approximately 20-40-fold higher than those at locus hsp16-1/48.

Animals↗
PubMed2006

Evolutionary origin and maintenance of coexpressed gene clusters in mammals.

Gene order is not random with regard to gene expression in mammals: coexpressed genes, and in particular housekeeping genes, are clustered along chromosomes more often than expected by chance. To understand the origin of these clusters and to quantify the impact of this phenomenon on genome organization, we analyzed clusters of coexpressed genes in the human and mouse genomes. We show that neighboring genes experience continuous concerted expression changes during evolution, which leads to the formation of coexpressed gene clusters. The pattern of expression within these clusters evolves more slowly than the genomic average. Moreover, by studying gene order evolution, we show that some clusters are maintained by natural selection and, therefore, have a functional significance. However, we also demonstrate that some coexpressed gene clusters are the result of neutral coevolution effects, as illustrated by the clustering of genes escaping inactivation on the X chromosome. Moreover, we show that, although statistically significant, constraints on gene orders have a limited impact on mammalian genome organization, affecting only 3-5% of the pool of human and murine genes. It had been hypothesized that coexpressed gene clusters might correspond to large chromatin domains. In contradiction, we find that most of these clusters contain only 2 genes whose coexpression may be due to transcriptional read-through or the activity of bidirectional promoters.

Animals↗
PubMed2004

Molecular evolution of sex-biased genes in Drosophila.

Studies of morphology, interspecific hybridization, protein/DNA sequences, and levels of gene expression have suggested that sex-related characters (particularly those involved in male reproduction) evolve rapidly relative to non-sex-related characters. Here we report a general comparison of evolutionary rates of sex-biased genes using data from cDNA microarray experiments and comparative genomic studies of Drosophila. Comparisons of nonsynonymous/synonymous substitution rates (d(N)/d(S)) between species of the D. melanogaster subgroup revealed that genes with male-biased expression had significantly faster rates of evolution than genes with female-biased or unbiased expression. The difference was caused primarily by a higher d(N) in the male-biased genes. The same pattern was observed for comparisons among more distantly related species. In comparisons between D. melanogaster and D. pseudoobscura, genes with highly biased male expression were significantly more divergent than genes with highly biased female expression. In many cases, orthologs of D. melanogaster male-biased genes could not be identified in D. pseudoobscura through a Blast search. In contrast to the male-biased genes, there was no clear evidence for accelerated rates of evolution in female-biased genes, and most comparisons indicated a reduced rate of evolution in female-biased genes relative to unbiased genes. Male-biased genes did not show an increased ratio of nonsynonymous/synonymous polymorphism within D. melanogaster, and comparisons of polymorphism/divergence ratios suggest that the rapid evolution of male-biased genes is caused by positive selection.

Animals↗
PubMed2006

Gene structure and expression pattern analysis of three monodehydroascorbate reductase (Mdhar) genes in Physcomitrella patens: implications for the evolution of the MDHAR family in plants.

The ascorbate-glutathione pathway plays a major role in the detoxification of reactive oxygen species (ROS) in vascular plants. One of the key enzymes in this pathway is monodehydroascorbate reductase (MDHAR), a FAD enzyme that catalyses the reduction of the monodehydroascorbate radical. To elucidate the evolution and functional role of MDHAR we identified and characterised MDHARs from the moss Physcomitrella patens. Expressed sequence tag (EST) databases containing approximately 100.000 ESTs from Physcomitrella were searched and three isoforms of monodehydroascorbate reductase (PpMDHAR1, PpMDHAR2 and PpMDHAR3) were identified. In vascular plants MDHAR is found in the cytosol, chloroplast, mitochondria and peroxisome. Surprisingly, all three PpMDHARs resembled the cytosolic isoforms from vascular plants lacking the NH(2)-terminal or COOH-terminal extension found in organelle targeted MDHARs. The number and position of introns was also conserved between PpMDHARs and cytosolic MDHARs from vascular plants. Phylogenetic analysis revealed that cytosolic MDHARs are monophyletic in origin and the ancestral gene evolved before the divergence of bryophytes more than 400 million years ago. Transcript analyses showed that expression of PpMdhar1 and PpMdhar3 was increased up to 5-fold under salt stress, osmotic stress or upon exposure to abscisic acid. In contrast, PpMdhar transcription levels were unchanged upon chilling, UV-B exposure or oxidative stress. The conservation of cytosolic MDHAR in the land-plant lineage and the transcriptional upregulation under water deficiency suggest that the evolution of cytosolic MDHAR played an essential role in stress protection for land plants when they inhabited the dry terrestrial environment.

Amino Acid Sequence↗
PubMed2006

Dlx3 is expressed in the ventral forebrain of chicken embryos: implications for the evolution of the Dlx gene family.

The archetypal genomic arrangement of vertebrate Dlx genes is as three bigene clusters (Dlx1/2, Dlx3/4, Dlx5/6). Phylogenetic sequence analysis of mouse and zebrafish Dlx clusters supports the notion that the Dlx3/4 cluster is more derived and the absence of expression of either Dlx3 or Dlx4 in the central nervous system, as reported to date, is consistent with this. Together, these observations have prompted a model in which cis-regulatory elements, responsible for directing Dlx gene transcription in the forebrain, were lost from the Dlx3/4 bigene cluster prior to the divergence of tetrapods from fish. Here, we describe Dlx3 expression in the forebrain of chicken embryos; this constitutes the first documented evidence of expression of either Dlx3 or Dlx4 in the central nervous system of a vertebrate. Our observations have implications for models of the evolutionary history of the Dlx gene family, for the genomic organization of Dlx genes in birds and for functional redundancy of Dlx gene function during avian forebrain development.

Animals↗
PubMed2026

Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.

BACKGROUND: The brown rat (Rattus norvegicus) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene family in rats has remained elusive. RESULTS: In this study, we performed a genome-wide identification of 61 RnbZIP genes, which were categorized into 10 distinct subfamilies based on phylogenetic relationships and chromosomal localization. Structural analysis revealed conserved motif arrangements within subfamilies, while collinearity analysis identified significant gene duplication events-predominantly tandem and segmental duplications-that have driven the evolutionary expansion of the RnbZIP family. Quantitative analysis showed that members within the same subfamily shared 45%-92% sequence similarity (calculated using the BLOSUM62 scoring matrix), and all duplicated gene pairs underwent strong purifying selection (Ka/Ks&#x2009;<&#x2009;1). Comparative genomics across seven rodent species further underscored the evolutionary conservation and divergence of these factors. Expression profiling across diverse organs and brain developmental stages indicated that RnbZIP genes exhibit high tissue specificity. Notably, 10 candidate genes, including RnbZIP01, RnbZIP02, and RnbZIP08, demonstrated dynamic expression patterns during brain maturation, suggesting their essential roles in neurodevelopmental processes. CONCLUSIONS: Our findings provide a comprehensive structural and evolutionary framework for the RnbZIP gene family, highlighting their potential regulatory functions in rat organogenesis and brain development. This study establishes a valuable resource for further functional characterization of specific bZIP members in mammalian neurological systems.

Animals↗
PubMed1996

Polyclonal antisera elicited bý lysozymes: insights into antigenic structure and evolution.

Polyclonal antisera elicited by evolutionary variants of bird lysozymes c played a major role in the development of the multideterminant-regulatory model to describe the antigenic structure of globular proteins and in the demonstration that there is a strong correlation between immunological differences and amino acid sequence differences. This chapter reviews the evidence and calculations used to show, for lysozyme c and several other proteins, the essentially the entire surface of globular proteins is antigenic, that nearly all evolutionary substitutions affect immunological cross-reactivity, and that there is empirical and theoretical support for the use of immunological distances to infer genealogical relationships and establish approximate evolutionary time scales. In addition this chapter discusses several examples of the use of polyclonal antisera to lysozymes c and g to gain insights into molecular and organismal evolution and the regulation of gene expression.

Animals↗
PubMed2006

Neutral and adaptive variation in gene expression.

Variation among populations in gene expression should be related to the accumulation of random-neutral changes and evolution by natural selection. The following evolutionary analysis has general applicability to biological and medical science because it accounts for genetic relatedness and identifies patterns of expression variation that are affected by natural selection. To identify genes evolving by natural selection, we allocate the maximum among-population variation to genetic distance and then examine the remaining variation relative to a hypothesized important ecological parameter (temperature). These analyses measure the expression of metabolic genes in common-gardened populations of the fish Fundulus heteroclitus whose habitat is distributed along a steep thermal gradient. Although much of the variation in gene expression fits a null model of neutral drift, the variation in expression for 22% of the genes that regress with habitat temperature was far greater than could be accounted for by genetic distance alone. The most parsimonious explanation for among-population variation for these genes is evolution by natural selection. In addition, many metabolic genes have patterns of variation incongruent with neutral evolution: They have too much or too little variation. These patterns of biological variation in expression may reflect important physiological or ecological functions.

Animals↗
PubMed2004

How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution?

We used the yeast genome sequences of gene families, microarray profiles and regulatory motif data to test the current wisdom that there is a strong correlation between regulatory motif structure and gene expression profile. Our results suggest that duplicate genes tend to be co-expressed but the correlation between motif content and expression similarity is generally poor, only approximately 2-3% of expression variation can be explained by the motif divergence. Our observations suggest that, in addition to the cis-regulatory motif structure in the upstream region of the gene, multiple trans-acting factors in the gene network can influence the pattern of gene expression significantly.

Evolution, Molecular↗
PubMed2006

Multiple lineage specific expansions within the guanylyl cyclase gene family.

BACKGROUND: Guanylyl cyclases (GCs) are responsible for the production of the secondary messenger cyclic guanosine monophosphate, which plays important roles in a variety of physiological responses such as vision, olfaction, muscle contraction, homeostatic regulation, cardiovascular and nervous function. There are two types of GCs in animals, soluble (sGCs) which are found ubiquitously in cell cytoplasm, and receptor (rGC) forms which span cell membranes. The complete genomes of several vertebrate and invertebrate species are now available. These data provide a platform to investigate the evolution of GCs across a diverse range of animal phyla. RESULTS: In this analysis we located GC genes from a broad spectrum of vertebrate and invertebrate animals and reconstructed molecular phylogenies for both sGC and rGC proteins. The most notable features of the resulting phylogenies are the number of lineage specific rGC and sGC expansions that have occurred during metazoan evolution. Among these expansions is a large nematode specific rGC clade comprising 21 genes in C. elegans alone; a vertebrate specific expansion in the natriuretic receptors GC-A and GC-B; a vertebrate specific expansion in the guanylyl GC-C receptors, an echinoderm specific expansion in the sperm rGC genes and a nematode specific sGC clade. Our phylogenetic reconstruction also shows the existence of a basal group of nitric oxide (NO) insensitive insect and nematode sGCs which are regulated by O2. This suggests that the primordial eukaryotes probably utilized sGC as an O2 sensor, with the ligand specificity of sGC later switching to NO which provides a very effective local cell-to-cell signalling system. Phylogenetic analysis of the sGC and bacterial heme nitric oxide/oxygen binding protein domain supports the hypothesis that this domain originated from a cyanobacterial source. CONCLUSION: The most salient feature of our phylogenies is the number of lineage specific expansions, which have occurred within the GC gene family during metazoan evolution. Our phylogenetic analyses reveal that the rGC and sGC multi-domain proteins evolved early in eumetazoan evolution. Subsequent gene duplications, tissue specific expression patterns and lineage specific expansions resulted in the evolution of new networks of interaction and new biological functions associated with the maintenance of organismal complexity and homeostasis.

Animals↗
PubMed2003

Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli.

Twelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.

Biological Evolution↗
PubMed1998

The neuronal zootype. An hypothesis.

We present an hypothesis, derived from the zootype concept of Slack, Holland and Graham. The main point of this hypothesis is to postulate that the primordial function of the zootype genes is to design an appropriate neuronal network in bilaterian animals, by controlling the genes involved in the specificity of the axon pathways. This would be the primary function of the zootype genes in development and their primitive function in evolution. The hypothesis is discussed in view of the current knowledge on the Hox genes, their evolution, their genomic organization, their expression and their targets.

Animals↗