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At least 649 records · Page 36Linked to original sources
PubMed2000

Knots in the family tree: evolutionary relationships and functions of knox homeobox genes.

Knotted-like homeobox (knox) genes constitute a gene family in plants. Class I knox genes are expressed in shoot apical meristems, and (with notable exceptions) not in lateral organ primordia. Class II genes have more diverse expression patterns. Loss and gain of function mutations indicate that knox genes are important regulators of meristem function. Gene duplication has contributed to the evolution of families of homeodomain proteins in metazoans. We believe that similar mechanisms have contributed to the diversity of knox gene function in plants. Knox genes may have contributed to the evolution of compound leaves in tomato and could be involved in the evolution of morphological traits in other species. Alterations in cis-regulatory regions in some knox genes correlate with novel patterns of gene expression and distinctive morphologies. Preliminary data from the analysis of class I knox gene expression illustrates the evolution of complex patterns of knox expression is likely to have occurred through loss and gain of domains of gene expression.

Evolution, Molecular↗
PubMed1987

Xenopus cytoskeletal actin and human c-fos gene promoters share a conserved protein-binding site.

Xenopus laevis cytoskeletal actin gene promoters contain a 20-bp sequence homologous to the serum response element (SRE) required for transient human c-fos gene transcription in response to serum factors. Both sequences bind the same factor in HeLa cell extracts, as shown by binding competition, DNase I and dimethylsulphate (DMS) protection and DMS interference assays. A similar protein is present in Xenopus laevis oocytes. Sequences containing the SRE homology are essential for constitutive activity of the actin promoter in both Xenopus and mouse cells, and a synthetic SRE functions as a promoter element in these cells. In mouse cells, transcription of both transfected Xenopus actin and actin/c-fos fusion genes is activated following serum stimulation. These data suggest that the SRE and its cognate protein form part of a regulatory pathway that has been highly conserved during evolution.

Actins↗
PubMed1992

Differential splicing of the GHF1 primary transcript gives rise to two functionally distinct homeodomain proteins.

The POU domain protein GHF-1 has a critical role in generation, proliferation and phenotypic expression of three pituitary cell types. GHF-1 functions in part by binding to and transactivating the promoters of both the growth hormone (GH) and prolactin (PRL) genes and that of the GHF1 gene itself. We describe a naturally occurring isoform of GHF-1, GHF-2, in which an additional 26 amino acids are inserted into the activation domain of the protein as a result of alternative splicing. GHF-2 retains the DNA binding activity of GHF-1 and can activate the GH promoter but has lost the ability to activate the PRL and GHF1 promoters. These results suggest that GHF-2 may function in differential target gene activation during differentiation of the somatotrophic lineage. Both GHF-1 and GHF-2 transcripts are specifically expressed in the anterior pituitary. Analysis of the genomic GHF1 gene shows that most of the distinct functional domains of GHF-1 (and GHF-2) are encoded by separate exons. Gene segment duplication and exon shuffling may have contributed to the evolution of this cell type-specific transcriptional regulatory gene.

Amino Acid Sequence↗
PubMed1993

Divergence of gene expression in neurohypophysial hormone precursors among salmonids.

Salmonid fish have pairs of genes for various hypothalamic and pituitary hormones including neurohypophysial hormones, vasotocin, and isotocin, probably because they are tetraploid. The problem here is whether two genes for the same hormone are expressed equally or differently. We therefore examined expression patterns of vasotocin and isotocin genes in four salmonid species using Northern blot analysis with chum salmon cDNAs as hybridization probes. The presence of two vasotocin and also two isotocin genes was confirmed by Southern blot analysis in rainbow trout and sockeye salmon which were not examined previously. Prior to Northern blot analysis, isotocin-I cDNA of sockeye salmon was determined and compared to those of chum salmon and masu salmon, since molecular probes are so specific that cross-species hybridization often leads misinterpretation in a quantitative study. The nucleotide sequence of sockeye salmon isotocin-I cDNA showed sufficiently high homology (> 96.0%) to those of chum salmon and masu salmon for cross-species hybridization among salmonids. Northern blot analysis showed that both isotocin-I and isotocin-II genes were well expressed in all species examined. Expression of isotocin-I gene tended to be relatively higher than that of isotocin-II gene in all species. However, expression pattern of vasotocin-I and vasotocin-II genes did not coincide among species. Expression of vasotocin-II genes was very weak or scarce in masu salmon and rainbow trout, while that in sockeye salmon was stronger than vasotocin-I gene expression. The present result may reflect complicated molecular evolution of salmonid vasotocin genes probably both in regulatory and coding regions.

Amino Acid Sequence↗
PubMed2001

Structure of the human zinc finger protein HIVEP3: molecular cloning, expression, exon-intron structure, and comparison with paralogous genes HIVEP1 and HIVEP2.

Here we report the cloning and characterization of HIVEP3, the newest member in the human immunodeficiency virus type 1 enhancer-binding protein family that encodes large zinc finger proteins and regulates transcription via the kappaB enhancer motif. The largest open reading frame of HIVEP3 contains 2406 aa. and is approximately 80% identical to the mouse counterpart. The HIVEP3 gene is located in the chromosomal region 1p34 and is at least 300 kb with 10 exons. RNA studies show that multiple HIVEP3 transcripts are differentially expressed and regulated. Additionally, transcription termination occurs in the ultimate exon, exon 10, or in exon 6. Therefore, HIVEP3 may produce protein isoforms that contain or exclude the carboxyl DNA binding domain and the leucine zipper by alternative RNA splicing and differential polyadenylation. Sequence homologous to HIVEP3 exon 6 is not found in mouse nor are the paralogous genes HIVEP1 and HIVEP2. Zoo-blot analysis suggests that sequences homologous to the human exon 6 are present only in primates and cow. Therefore, a foreign DNA harboring a termination exon likely was inserted into the HIVEP3 locus relatively recently in evolution, resulting in the acquisition of novel gene regulatory mechanisms as well as the generation of structural and functional diversity.

Amino Acid Sequence↗
PubMed2005

Palindrome content of the yeast Saccharomyces cerevisiae genome.

Palindromic sequences are important DNA motifs involved in the regulation of different cellular processes, but are also a potential source of genetic instability. In order to initiate a systematic study of palindromes at the whole genome level, we developed a computer program that can identify, locate and count palindromes in a given sequence in a strictly defined way. All palindromes, defined as identical inverted repeats without spacer DNA, can be analyzed and sorted according to their size, frequency, GC content or alphabetically. This program was then used to prepare a catalog of all palindromes present in the chromosomal DNA of the yeast Saccharomyces cerevisiae. For each palindrome size, the observed palindrome counts were significantly different from those in the randomly generated equivalents of the yeast genome. However, while the short palindromes (2-12 bp) were under-represented, the palindromes longer than 12 bp were over-represented, AT-rich and preferentially located in the intergenic regions. The 44-bp palindrome found between the genes CDC53 and LYS21 on chromosome IV was the longest palindrome identified and contained only two C-G base pairs. Avoidance of coding regions was also observed for palindromes of 4-12 bp, but was less pronounced. Dinucleotide analysis indicated a strong bias against palindromic dinucleotides that could explain the observed short palindrome avoidance. We discuss some possible mechanisms that may influence the evolutionary dynamics of palindromic sequences in the yeast genome.

DNA, Intergenic↗
PubMed2003

Regulatory regions and nuclear factors involved in nodule-enhanced expression of a soybean phosphoenolpyruvate carboxylase gene: implications for molecular evolution.

We have determined the genomic organization of two closely related phosphoenolpyruvate carboxylase genes in soybean, GmPEPC7, which is expressed at high levels in root nodules, and the housekeeping gene GmPEPC15. Their nucleotide sequences, including most introns and 5;-flanking regions within 600 bp upstream from the transcription start sites, are well conserved, suggesting that they were duplicated quite recently. To gain insights into the process of evolution of the tissue-specifically expressed GmPEPC7gene, we produced chimeric constructs carrying either the GmPEPC7or GmPEPC15promoter fused to the beta-glucuronidase gene. The expression patterns of the reporter observed in nodules that developed on transgenic hairy roots reflected the levels of mRNA levels produced by the genes in wild-type soybean plants, indicating that the GmPEPC7promoter directs nodule-specific expression. Loss-of-function experiments showed that the segment of GmPEPC7between -466 and -400, designated as the "switch region" (SR), was necessary for expression in nodules, although proteins that bind to SR were not detectable in a gel-retardation assay. Another gel-retardation assay indicated that putative nodule nuclear proteins bind specifically to the region of GmPEPC7between -400 and -318, designated as the "amplifier region" (AR). Both SR and AR have characteristic sequences that are not found in the GmPEPC15promoter. Furthermore, experiments using hybrid promoters derived from GmPEPC15demonstrated that AR confers high-level expression in nodules only in combination with SR. When wild-type soybean plants were subjected to prolonged darkness and subsequently illuminated, the level of GmPEPC7mRNA in nodules decreased and then recovered. This study suggests that the acquisition of two interdependent cis-acting elements resulted in molecular evolution of the nodule-enhanced GmPEPC7gene.

Base Sequence↗
PubMed1989

Isolation and characterization of the discrete N- and C-terminal halves of rat brain hexokinase: retention of full catalytic activity in the isolated C-terminal half.

Selective stabilization of either the N- or C-terminal half (by ligands binding to these regions) of rat brain hexokinase against partial denaturation with guanidine hydrochloride and subsequent digestion with trypsin has provided a means for isolating these regions, referred to as N fragment and C fragment, respectively, in quantities adequate for characterization. The N fragment (mol wt 52 kDa) is devoid of catalytic activity. In contrast, the C fragment (mol wt 51 kDa) has a specific activity of about 110 U/mg, nearly twice that (60 U/mg) of the intact 100-kDa enzyme, indicating that the kappa cat is virtually identical for both species. Unlike the parent enzyme, the C fragment is quite sensitive to inhibition by Pi (competitive vs ATP, noncompetitive vs Glc); sulfate and arsenate, but not acetate, inhibit with effectiveness similar to that seen with Pi. The Glc-6-P analog, 1,5-anhydroglucitol-6-P, also inhibits the C fragment (competitive vs ATP, uncompetitive vs Glc). Both N and C fragments bind to Affi-Gel Blue, an affinity matrix bearing a covalently attached analog of ATP, and are eluted by hexose 6-phosphates competitive with nucleotide binding to the parent enzyme. Based on the ability of various hexoses and hexose 6-phosphates (and analogs) to protect against guanidine-induced denaturation and subsequent proteolysis it is concluded that both fragments contain discrete sites for hexoses and hexose 6-phosphates, with specificities resembling those seen for the binding of these ligands to the parent enzyme. Synergistic interactions between the hexose and hexose-6-P binding sites, previously seen with the parent enzyme, are also observed with the C fragment but not the N fragment. The existence of binding sites for hexoses and hexose 6-phosphates on both halves conflicts with previous binding studies demonstrating a single hexose binding site and a single hexose 6-phosphate binding site on the intact 100-kDa enzyme, leading to the conclusion that one of each pair of sites must be latent in the intact enzyme, becoming manifest only in the isolated discrete halves. Several investigators have previously suggested that the 100-kDa mammalian hexokinases evolved by duplication and fusion of a gene encoding an ancestral 50-kDa Glc-6-P-insensitive hexokinase, similar to the present-day yeast enzyme, with sensitivity to Glc-6-P resulting from evolution of a duplicated catalytic site into a regulatory site.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1992

The primary structure of a PYY-related peptide from chicken intestine suggests an anomalous site of cleavage of the signal peptide in preproPYY.

Although the amino acid sequence of members of the pancreatic polypeptide (PP)-family of regulatory peptides has been poorly conserved during vertebrate evolution, the overall length of the peptides (36 amino acid residues) has remained constant. Nucleotide sequence analysis of cloned cDNAs and/or genomic fragments has shown the PP-related sequence immediately follows the signal peptide in the prepropeptides. A peptide tyrosine-tyrosine (PYY)-related peptide with 37 residues has been isolated from the chicken intestine, and its primary structure was established as: Ala-Tyr-Pro-Pro-Lys-Pro-Glu-Ser-Pro-Gly10-Asp-Ala-Ala-Ser-P ro-Glu-Glu-Ile-Ala-Gln20-Tyr-Phe-Ser-Ala-Leu-Arg-His-Tyr-Il e-Asn30-Leu-Val-Thr-Arg-Gln-Arg-Tyr.CONH2. The presence of an additional alanine residue at the NH2-terminus of the peptide suggests that the site of cleavage of the signal peptide in chicken preproPYY is different from the site of cleavage in other PP-family prepropeptides.

Amino Acid Sequence↗
PubMed1993

Evolution by DNA turnover in the control region of vertebrate mitochondrial DNA.

The control region of animal mitochondrial DNA is heterogeneous, including both highly conserved and highly variable sequences. Within the variable regions, variable number tandem repeat sequences have been described for numerous species. Repeats at one location, just upstream of the origin of replication, show an unprecedented level of length variation in somatic tissue. Recent comparison of these sequences in different species indicates a pattern of DNA turnover acting at different rates and over motifs of various sizes.

Animals↗
PubMed2004

Unexpected conserved non-coding DNA blocks in mammals.

The significance of non-coding DNA is a longstanding riddle in the study of molecular evolution. Using a comparative genomics approach, Dermitzakis and colleagues have recently shown that at least some non-coding sequence, frequently ignored as meaningless noise, might bear the signature of natural selection. If functional, it could mark a turning point in the way we think about the evolution of the genome.

Animals↗
PubMed1999

Hsc40, a new member of the hsp40 family, exhibits similar expression profile to that of hsc70 in mammalian cells.

Here, we report the identification and characterization of a new hsp40 family member, heat shock cognate 40 (hsc40), which may be a specific functional partner for hsc70. The hsc40 gene consists of five exons and four introns. The previously characterized hsp40 gene contains only three exons and two introns. Despite this difference in the numbers of exons and introns, the structures of these two genes are actually quite similar. If the first two exons and introns of the hsc40 gene are excluded, the rest is essentially the same as the whole hsp40 gene. The intron/exon boundaries of the hsc40 and hsp40 genes are conserved with respect to amino acid coding, indicating that the hsp40 gene might have arisen from a duplicated hsc40 gene, which developed a new transcription-regulatory mechanism in the second intron. Hsc40 is evolutionally conserved. There is over 95% sequence identity between the putative mouse and human hsc40 proteins. However, there is only 60% sequence identity between the hsc40 and hsp40 proteins from either human or mouse cells. Northern blot analysis of various tissues and cells in culture revealed that this gene was expressed under normal conditions, and its expression was further increased after various stress treatments. The expression pattern of the hsc40 gene is very similar to that of the hsc70 gene under both normal and stress conditions, whereas the hsp40 gene exhibited an expression pattern more similar to that of hsp70 genes on the same Northern blots. These results, considered along with the high rate of sequence conservation between the same proteins from different species and high rate of variation between the two different proteins from the same species, strongly suggest that hsc40 and hsp40 may perform different functions and/or have different specificities in the cell.

3T3 Cells↗
PubMed2005

Topology of biological networks and reliability of information processing.

Survival of living cells and organisms is largely based on highly reliable function of their regulatory networks. However, the elements of biological networks, e.g., regulatory genes in genetic networks or neurons in the nervous system, are far from being reliable dynamical elements. How can networks of unreliable elements perform reliably? We here address this question in networks of autonomous noisy elements with fluctuating timing and study the conditions for an overall system behavior being reproducible in the presence of such noise. We find a clear distinction between reliable and unreliable dynamical attractors. In the reliable case, synchrony is sustained in the network, whereas in the unreliable scenario, fluctuating timing of single elements can gradually desynchronize the system, leading to nonreproducible behavior. The likelihood of reliable dynamical attractors strongly depends on the underlying topology of a network. Comparing with the observed architectures of gene regulation networks, we find that those 3-node subgraphs that allow for reliable dynamics are also those that are more abundant in nature, suggesting that specific topologies of regulatory networks may provide a selective advantage in evolution through their resistance against noise.

Biological Evolution↗
PubMed1994

Universal signals control slime mold stalk formation.

The primitive slime mold Dictyostelium minutum does not display oscillations during aggregation, cannot form migrating slugs, and does not form a prestalk/prespore pattern, all of which are characteristic for development of its advanced relative Dictyostelium discoideum. We used D. minutum to investigate whether slime molds share common mechanisms controlling development. In D. discoideum, the morphogen differentiation inducing factor (DIF) can induce stalk-cell differentiation in vitro. However, stalk formation in vivo is supposedly triggered by local depletion of DIF antagonists such as ammonia or cAMP. A homologue of the D. discoideum stalk gene ecmB was cloned in D. minutum that encodes a 3.4-kb mRNA, and its deduced amino acid sequence shows repeats of 24 amino acids that are characteristic for the D. discoideum ecmB gene. Remarkably, DIF effectively induces expression of the D. minutum ecmB gene and ammonia inhibits its expression. D. discoideum cells were transformed with a construct of the D. minutum ecmB promoter fused to the lacZ reporter gene and showed expression in the stalk, but not in the upper and lower cup of the fruiting body, which also express the D. discoideum ecmB gene. In D. discoideum, the D. minutum ecmB and the ecmB promoter are similarly activated by DIF and repressed by both cAMP and ammonia, suggesting that additional signaling is required for ecmB expression in upper and lower cup cells. Our data indicate that the extracellular signals controlling stalk formation and their intracellular signaling cascades including gene regulatory proteins remained highly conserved during slime mold evolution.

Amino Acid Sequence↗
PubMed1997

The policy implications of using hospital and physician volumes as "indicators" of quality of care in a changing health care environment.

There is growing interest in the quality of health care and in using quality measures to direct patients to hospitals and providers offering high quality, low cost health care. The dilemma is that, while there is an increasing need for quality indicators as a result of a changing health care environment, this changing environment has important implications for the use of some of these measures. Since the 1970s, a growing body of research in the U.S. has addressed the empirical relationship between the number of patients with a specific diagnosis of surgical procedure and their outcomes after treatment in a particular hospital or by a particular physician ("volume-outcome" studies). In this paper, we examine the policy implications of using hospital and physician volume information as an "indicator" of quality in a rapidly changing health care environment with new players and new incentives. We begin by describing the evolution of the use of volumes within both regulatory and market-oriented contexts in the U.S. We then discuss policy considerations and cautions in using volumes, along with suggestions for future research. Our purpose is to point out potential problems and clarify confusions about the use of volumes, so that policymakers and practitioners can be sensitive to the potential minefields they are traversing.

Decision Making, Organizational↗
PubMed2006

The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.

WRKY and GCM1 are metal chelating DNA-binding domains (DBD) which share a four stranded fold. Using sensitive sequence searches, we show that this WRKY-GCM1 fold is also shared by the FLYWCH Zn-finger domain and the DBDs of two classes of Mutator-like element (MULE) transposases. We present evidence that they share a stabilizing core, which suggests a possible origin from a BED finger-like intermediate that was in turn ultimately derived from a C2H2 Zn-finger domain. Through a systematic study of the phyletic pattern, we show that this WRKY-GCM1 superfamily is a widespread eukaryote-specific group of transcription factors (TFs). We identified several new members across diverse eukaryotic lineages, including potential TFs in animals, fungi and Entamoeba. By integrating sequence, structure, gene expression and transcriptional network data, we present evidence that at least two major global regulators belonging to this superfamily in Saccharomyces cerevisiae (Rcs1p and Aft2p) have evolved from transposons, and attained the status of transcription regulatory hubs in recent course of ascomycete yeast evolution. In plants, we show that the lineage-specific expansion of WRKY-GCM1 domain proteins acquired functional diversity mainly through expression divergence rather than by protein sequence divergence. We also use the WRKY-GCM1 superfamily as an example to illustrate the importance of transposons in the emergence of new TFs in different lineages.

Amino Acid Sequence↗
PubMed2007

Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata.

The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.

Adaptation, Biological↗