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PubMed1993

Evolution and expression of a beta-like globin gene of the Australian marsupial Sminthopsis crassicaudata.

A beta-like globin gene was isolated from the Australian dasyurid marsupial Sminthopsis crassicaudata. Nucleotide-sequence analysis of promoter and coding regions of the gene revealed that it was orthologous to eutherian early-expressed (epsilon, gamma, eta) beta-like globin genes. Comparison of the conceptually translated sequence of the gene with a partial amino acid sequence of the adult beta-globin chain from S. crassicaudata provided evidence that the gene was not expressed in adult tissues. In addition, Northern analysis of RNA isolated from an embryo, pouch young, and adult bone marrow indicated that the gene was expressed predominantly in embryonic tissues and that there was a significant reduction in the expression of the gene within a day of birth. These results provide strong support for the hypothesis of Koop and Goodman [Koop, B. F. & Goodman, M. (1988) Proc. Natl. Acad. Sci. USA 85, 3893-3897] that an embryonic beta-like globin gene existed prior to the divergence of the eutherian and marsupial lineages and that this gene was already differentiated with respect to its promoter regions and developmental expression. The observation that epsilon-globin mRNA was present at least until day 4 postpartum suggests that the epsilon-globin chain may play some role in influencing the physiological properties of hemoglobin in S. crassicaudata neonates.

Aging↗
PubMed2003

Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses.

MADS-box genes encode transcription factors involved in various important aspects of development and differentiation in land plants, metazoans, and other organisms. Three types of land plant MADS-box genes have been reported. MIKCC- and MIKC*-type genes both contain conserved MADS and K domains but have different exon/intron structures. M-type genes lack a K domain. Most MADS-box genes previously analyzed in land plants are expressed in the sporophyte (diploid plant body); few are expressed in the gametophyte (haploid plant body). Land plants are believed to have evolved from a gametophyte (haploid)-dominant ancestor without a multicellular sporophyte (diploid plant body); most genes expressed in the sporophyte probably originated from those used in the gametophyte during the evolution of land plants. To analyze the evolution and diversification of MADS-box genes in land plants, gametophytic MADS-box genes were screened using macroarray analyses for 105 MADS-box genes found in the Arabidopsis genome. Eight MADS-box genes were predominantly expressed in pollen, the male gametophyte; all but one of their expression patterns was confirmed by Northern analyses. Analyses of the exon/intron structure of these seven genes revealed that they included two MIKCC-type, one M-type, and four MIKC*-type MADS-box genes. Previously, MIKC*-type genes have been reported only from a moss and a club moss, and this is the first record in seed plants. These genes can be used to investigate the unknown ancestral functions of MADS-box genes in land plants. The macroarray analyses did not detect expression of 56 of 61 M-type MADS-box genes in any tissues examined. A phylogenetic tree including all three types of Arabidopsis MADS-box genes with representative genes from other organisms showed that M-type genes were polyphyletic and that their branch lengths were much longer than for the other genes. This finding suggests that most M-type genes are pseudogenes, although further experiments are necessary to confirm this possibility. Our global phylogenetic analyses of MADS-box genes did not support the previous classification of MADS-box genes into type I and II groups, based on smaller scale analyses. An evolutionary scenario for the evolution of MADS-box genes in land plants is discussed.

Arabidopsis↗
PubMed1996

The Pem homeobox gene: rapid evolution of the homeodomain, X chromosomal localization, and expression in reproductive tissue.

A hallmark of homeobox genes is their high degree of sequence conservation in distantly related species. Here, we report the chromosomal localization, sequence, and expression pattern of an orphan homeobox gene, Pem, that encodes a homeodomain (HD) that has undergone a surprisingly high rate of evolutionary change. The N-terminal portion of the Pem HD, which includes the first two alpha-helices, exhibits only 44% sequence identity between rat Pem (r.Pem) and mouse Pem (m.Pem). This N-terminal subdomain exhibited an extremely high frequency of nonsynonymous substitutions, severalfold higher than other regions of the Pem protein. In contrast, the third helix, which is known to confer most of the base-specific contacts of HDs with DNA, was almost identical in r. Pem and m.Pem. Several lines of evidence suggested that the rat and mouse genes that we identified as Pem genes are true homologues: (1) the r.Pem and m.Pem genes both reside on the X chromosome; (2) they possess identical exon/intron splice junctions; (3) they both encode a distinctive motif upstream of the HD that is unique to Pem; and (4) the only m.Pem-like gene we were able to identify in the rat genome other than r.Pem was a pseudogene, r.Pem-ps, whose sequence and chromosomal localization indicated that it was derived by reverse transcription and reinsertion into the genome. The functional r.Pem gene is selectively expressed in placenta, testis, epididymis, and ovary. This expression pattern is of interest since other genes transcribed in reproductive tissue have also been shown to undergo high rates of sequence divergence. The high rate of amino acid substitutions in the N-terminal region of the Pem HD suggests the possibility of species-specific directional selection.

Alternative Splicing↗
PubMed2005

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression.

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

Adaptation, Physiological↗
PubMed2006

Evolutionary comparison of the reproductive genes, DAZL and BOULE, in primates with and without DAZ.

Genes of the DAZ (Deleted in AZoospermia) gene family, DAZ, DAZL (DAZ-Like), and BOULE, encode closely related RNA-binding proteins that are required for fertility in numerous organisms, yet the genomes of different organisms possess different complements of DAZ family genes. Thus, invertebrates such as flies and worms contain just a single DAZ homolog, boule, while genomes of vertebrates, other than catarrhine primates (Old World monkeys and hominids), possess both Boule and Dazl genes. Finally, catarrhine primates possess BOULE, DAZL, and DAZ genes. Since the DAZ genes arose recently in evolution in the catarrhine lineage, we sought to examine how the sequences and expression of this gene family may have changed after the introduction of a new member, DAZ. Based on previous results, we hypothesized that the introduction of a new member of the DAZ gene family into catarrhines could reduce functional constraint on DAZL. Surprisingly, however, we found that platyrrhine DAZL demonstrated significantly more sequence divergence than catarrhine DAZL (p=0.0006 for nucleotide and p=0.05 for amino acid sequence); however, comparison of K (a)/K (s) ratios suggests that the DAZL and BOULE genes are under similar functional constraints regardless of lineage. Thus, our data are most consistent with the hypothesis that the introduction of DAZ did not affect the evolution of DAZL or BOULE, and that a higher neutral mutation rate in platyrrhines than in catarrhines, along with the greater tolerance of DAZL for variation relative to BOULE, may be the foundation for the observed differences in sequence divergence in this gene family.

Amino Acid Sequence↗
PubMed1987

Characterization and evolution of the expressed rat ferritin light subunit gene and its pseudogene family. Conservation of sequences within noncoding regions of ferritin genes.

The iron storage protein ferritin consists of two types of subunits of different molecular weight, heavy (H) and light (L). The rat genome contains approximately 20 copies of the ferritin L-subunit gene, of which we have sequenced seven. One is an expressed ferritin gene containing three introns located between the alpha-helical domains of the L-subunit protein. The remaining six have the characteristics of processed pseudogenes. Sequence divergence suggest that these pseudogenes arose approximately 3-12 X 10(6) years ago, well within the 30 X 10(6) years of divergence of rat and mouse. By using intron probes derived from the expressed ferritin L-gene, a homologous second copy has been identified in some Fischer rats. Comparison of the 5'-untranslated region of the rat L-gene with the published sequences of this region of the human L (Santoro, C., Marone, M., Ferrone, M., Costanzo, F., Colombo, M., Minganti, C., Cortese, R., and Silengo, L. (1986) Nucleic Acids Res. 14, 2863-2876) and H (Costanzo, F., Colombo, M., Staempfli, S., Santoro, C., Marone, M., Frank, R., Delius, H., and Cortese, R. (1986) Nucleic Acids Res. 14, 721-735) genes and of a bullfrog cDNA (Didsbury, J. R., Theil, E. C., Kaufman, R. E., and Dickey, L. F. (1986) J. Biol. Chem. 261, 949-955) show a strongly conserved 28-base pair sequence, suggesting a translational regulatory function. The 5' flanking region of the rat L-gene contains sequences homologous to those in the flanking areas of the human L- and H-genes. The implications of these conserved sequences for control of ferritin expression are discussed.

Amino Acid Sequence↗
PubMed1997

The evolution of the differentiation-specific histone H1 gene basal promoter.

The comparison of the rat H1 zero gene promoter sequence with that of known H1 zero genes showed a high evolutionary conservation of regulatory elements involved in the control of the basal transcription of the gene. This finding suggests that the regulation of H1 zero gene expression is also controlled by a very conserved mechanism within vertebrates. In order to confirm this hypothesis, we destroyed three major cis-acting elements in the H1 zero gene promoter by site-directed mutagenesis and showed that these mutations affect significantly the activity of this promoter in cell lines representative of different vertebrate classes (fishes, amphibians, reptiles, birds, and mammals). We concluded that H1 zero gene activity, which is a developmentally regulated process, has been under a great selective pressure during evolution to ensure the expression of the protein at crucial periods of vertebrate development. One of these elements, the H4 box, helps to define within vertebrate H1 genes those encoding differentiation-specific subtypes. Indeed, it is only present in the proximal promoter region of H1 zero and H5 encoding genes. Regarding this feature of the vertebrate differentiation-specific H1 genes, they appear closer to the invertebrate (sea urchin) H1 genes than to those encoding vertebrate replication-dependent (RD) H1. This observation suggests that histone H1 zero and H5 are members that diverged from the main group of histone H1 before the vertebrate histone H1 and that the regulation of vertebrate RD H1 genes has probably evolved toward a coordinate regulation with that of core histone genes.

Animals↗
PubMed1998

Characterization of AmphiF-spondin reveals the modular evolution of chordate F-spondin genes.

The F-spondin genes are a family of extracellular matrix molecules united by two conserved domains, FS1 and FS2, at the amino terminus plus a variable number of thrombospondin repeats at the carboxy terminus. Currently, characterized members include a single gene in Drosophila and multiple genes in vertebrates. The vertebrate genes are expressed in the midline of the developing embryo, primarily in the floor plate of the neural tube. To investigate the evolution of chordate F-spondin genes, I have used the basal position in chordate phylogeny of the acraniate amphioxus. A single F-spondin-related gene, named AmphiF-spondin, was isolated from amphioxus. Based on molecular phylogenetics, AmphiF-spondin is closely related to a particular subgroup of vertebrate F-spondin genes that encode six thrombospondin repeats. However, unlike these genes, expression of AmphiF-spondin is not confined to the midline but is found through most of the central nervous system. Additionally, AmphiF-spondin has lost three thrombospondin repeats and gained two fibronectin type III repeats, one of which has strong identity to a fibronectin type III repeat from Deleted in Colorectal Cancer (DCC). Taken together, these results suggest a complex evolutionary history for chordate F-spondin genes that includes (1) domain loss, (2) domain gain by tandem duplication and divergence of existing domains, and (3) gain of heterologous domains by exon shuffling.

Amino Acid Sequence↗
PubMed2006

Ubl4b, an X-derived retrogene, is specifically expressed in post-meiotic germ cells in mammals.

Post-translational modification by ubiquitin and ubiquitin-related proteins plays critical roles in protein degradation and in regulation of essential cellular processes. In mammals, transcription grinds to a halt during late spermiogenesis due to compaction of the spermatid genome, which creates a special need for robust post-transcriptional regulation. Here, we report the finding of a novel mouse ubiquitin-like protein, UBL4B. Ubl4b is a testis-specific autosomal gene. Ubl4b lacks introns and evidently arose from an X-linked intron-bearing housekeeping gene, Ubl4a, by retroposition during mammalian evolution. While Ubl4a is expressed throughout spermatogenesis, Ubl4b is restricted to post-meiotic germ cells. Ubl4a is highly conserved, but Ubl4b has undergone rapid evolution and may have evolved new functions. Our data suggest that evolution of Ubl4b is not due to meiotic sex chromosome inactivation (MSCI). Alternatively, origination of Ubl4b was due to MSCI, but Ubl4b eventually evolved to be restricted to post-meiotic germ cells.

Animals↗
PubMed2005

Phenogenetic drift in evolution: the changing genetic basis of vertebrate teeth.

Vertebrate mineralized tissues are vital to the adaptive evolution of various traits. Among these traits is the tooth, which consists of two characteristic mineralized tissues, a highly mineralized surface layer (enamel in tetrapods and enameloid in fish) and a softer body (dentin), both supported by basal bone. However, enamel and enameloid are significantly different in development, and dentin shows many histological variations; hence their evolution has been intensively studied. Nevertheless, their genetic basis has been revealed only in tetrapods. We previously reported that many genes involved in tetrapod tissue mineralization arose from a common ancestor and constitute the secretory calcium-binding phosphoprotein (SCPP) gene family. Now we show that teleost fish also use many SCPPs for enameloid and dentin mineralization, but none of these directly corresponds to tetrapod SCPPs. This finding suggests that teleost and tetrapod SCPP genes have experienced independent parallel duplication histories. Thus, through phenogenetic drift, the tooth has remained a stable trait in jawed vertebrates, while evolving distinct genetic bases in teleosts and tetrapods. The characteristics of teleost SCPP genes and their expression domains in tooth development suggest the possibility that enameloid arose from dentin and enamel from enameloid more than once in vertebrate evolution. In fugu (puffer fish), expression of SCPP genes is also detected in an unusual beak-like structure that shelters numerous teeth. Their expression pattern suggests that the jaw consists of the dentin beak and supportive bone. These findings illustrate the complexity of the homology concept in understanding evolution, particularly the evolution of mineralized tissues.

Animals↗
PubMed2005

Structure, evolution and expression of a second subfamily of protein phosphatase 2A catalytic subunit genes in the rice plant (Oryza sativa L.).

Protein phosphatase 2A (PP2A) is one of the major serine/threonine protein phosphatases in the cell and plays a variety of regulatory roles in metabolism and signal transduction. Previously, we described the structure and expression of two genes encoding PP2A catalytic subunits (PP2Ac)--OsPP2A-1 and OsPP2A-3--in the rice plant (Yu et al. 2003). Here, we report the isolation and characterisation of a second structurally distinguishable PP2Ac subfamily comprised of three additional isogenes, OsPP2A-2, OsPP2A-4 (each containing ten introns) and OsPP2A-5 (which contains nine introns). Northern blot analysis demonstrated that the three isogenes are ubiquitously expressed in all rice tissues during plant development, and differentially expressed in response to high salinity and the combined stresses of drought and heat. Phylogenetic analyses indicated that the two PP2Ac subfamilies are descended from two ancient lineages, which derived from gene duplications that occurred after the monocotyledon-dicotyledon split. In the second subfamily, it is proposed that two duplication events were involved; in which, the initial duplication of a ten-intron primordial gene yielded OsPP2A-2 and the progenitor of OsPP2A-4 and OsPP2A-5. The OsPP2A-4/OsPP2A-5 progenitor, in turn, underwent a second duplication event, resulting in the present day OsPP2A-4 and OsPP2A-5. It is proposed that loss of the 5'-most intron from OsPP2A-5 occurred after these two duplication events.

Amino Acid Sequence↗
PubMed2006

Impact of transcriptional properties on essentiality and evolutionary rate.

We characterized general transcriptional activity and variability of eukaryotic genes from global expression profiles of human, mouse, rat, fly, plants, and yeast. The variability shows a higher degree of divergence between distant species, implying that it is more closely related to phenotypic evolution, than the activity. More specifically, we show that transcriptional variability should be a true indicator of evolutionary rate. If we rule out the effect of translational selection, which seems to operate only in yeast, the apparent slow evolution of highly expressed genes should be attributed to their low variability. Meanwhile, rapidly evolving genes may acquire a high level of transcriptional variability and contribute to phenotypic variations. Essentiality also seems to be correlated with the variability, not the activity. We show that indispensable or highly interactive proteins tend to be present in high abundance to maintain a low variability. Our results challenge the current theory that highly expressed genes are essential and evolve slowly. Transcriptional variability, rather than transcriptional activity, might be a common indicator of essentiality and evolutionary rate, contributing to the correlation between the two variables.

Animals↗
PubMed2004

Expression and evolution of delta9 and delta11 desaturase genes in the moth Spodoptera littoralis.

Desaturation of fatty acids is a key reaction in the biosynthesis of moth sex pheromones. The main component of Spodoptera littoralis sex pheromone blend is produced by the action of Delta11 and Delta9 desaturases. In this article, we report on the cloning of four desaturase-like genes in this species: one from the fat body (Sls-FL1) and three (Sls-FL2, Sls-FL3 and Sls-FL4) from the pheromone gland. By means of a computational/phylogenetic method, as well as functional assays, the desaturase gene products have been characterized. The fat body gene expressed a Delta9 desaturase that produced (Z)-9-hexadecenoic and (Z)-9-octadecenoic acids in a (1:4.5) ratio, whereas the pheromone gland Sls-FL2 expressed a Delta9 desaturase that produced (Z)-9-hexadecenoic and (Z)-9-octadecenoic acids in a (1.5:1) ratio. Although both Delta9 desaturases produced (Z)-9-tetradecenoic acid from myristic acid, transformed yeast grown in the presence of a mixture of myristic and (E)-11-tetradecenoic acids produced (Z,E)-9,11-tetradecadienoic acid, but not (Z)-9-tetradecenoic acid. The Sls-FL3 gene expressed a protein that produced a mixture of (E)-11-tetradecenoic, (Z)-11-tetradecenoic, (Z)-11-hexadecenoic and (Z)-11-octadecenoic acids in a 5:4:60:31 ratio. Despite having all the characteristics of a desaturase gene, no function could be found for Sls-FL4.

Amino Acid Sequence↗