PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “regulatory evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,549 records · Page 86Linked to original sources
PubMed2004

The effect of stress on genome regulation and structure.

BACKGROUND: Stresses exert evolutionary pressures on all organisms, which have developed sophisticated responses to cope and survive. These responses involve cellular physiology, gene regulation and genome remodelling. SCOPE: In this review, the effects of stress on genomes and the connected responses are considered. Recent developments in our understanding of epigenetic genome regulation, including the role of RNA interference (RNAi), suggest a function for this in stress initiation and response. We review our knowledge of how different stresses, tissue culture, pathogen attack, abiotic stress, and hybridization, affect genomes. Using allopolyploid hybridization as an example, we examine mechanisms that may mediate genomic responses, focusing on RNAi-mediated perturbations. CONCLUSIONS: A common response to stresses may be the relaxation of epigenetic regulation, leading to activation of suppressed sequences and secondary effects as regulatory systems attempt to re-establish genomic order.

Climate↗
PubMed1989

Unusual promoter-independent transcription reactions with bacteriophage RNA polymerases.

Efficient transcription reactions of DNA-dependent RNA polymerases require the presence of a specific promoter sequence. This report shows that in the absence of their cognate promoter, two bacteriophage RNA polymerases are capable of performing unusual transcription reactions: (i) the DNA template serves also as a primer for RNA synthesis and this leads to hybrid DNA/RNA molecules, (ii) if the DNA template forms a hairpin structure, the linear DNA can be transcribed via the 'rolling circle' mechanism.

Biological Evolution↗
PubMed2006

The initiator caspase, caspase-10beta, and the BH-3-only molecule, Bid, demonstrate evolutionary conservation in Xenopus of their pro-apoptotic activities in the extrinsic and intrinsic pathways.

Two major apoptotic signaling pathways have been defined in mammals, the extrinsic pathway, initiated by ligation of death receptors, and the intrinsic pathway, triggered by cytochrome c release from mitochondria. Here, we identified and characterized the Xenopus homologs of caspase-10 (xCaspase-10beta), a novel initiator caspase, and Bid (xBid), a BH3-only molecule of the Bcl-2 family involved in both the extrinsic and intrinsic pathways. Exogenous expression of these molecules induced apoptosis of mammalian cells. By biochemical and cytological analyses, we clarified that xCaspase-10beta and xBid exhibit structural and functional similarities to their mammalian orthologues. We also detected xCaspase-10beta and xBid transcripts during embryogenesis by whole-mount in situ hybridization and RT-PCR analysis. Microinjection of mRNA encoding a protease-defect xCaspase-10beta mutant into embryos resulted in irregular development. Enforced expression of active xBid induced cell death in developing embryos. Using transgenic frogs established to allow monitoring of caspase activation in vivo, we confirmed that this form of cell death is caspase-dependent apoptosis. Thus, we demonstrated that the machinery governing the extrinsic and intrinsic apoptotic pathways are already established in Xenopus embryos. Additionally, we propose that the functions of the initiator caspase and BH3-only molecule are evolutionarily conserved in vertebrates, functioning during embryonic development.

Amino Acid Sequence↗
PubMed1988

Mutational analysis of the catalytic and feedback sites of the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase of Escherichia coli.

The nucleotide sequence of aroH, the structural gene for the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase [DAHPS(Trp)], is presented, and the deduced amino acid sequence of AroH is compared with that of the tyrosine-sensitive (AroF) and phenylalanine-sensitive (AroG) DAHPS isoenzymes. The high degree of sequence similarity among the three isoenzymes strongly indicates that they have a common evolutionary origin. In vitro chemical mutagenesis of the cloned aroH gene was used to identify residues and regions of the polypeptide essential for catalytic activity and for tryptophan feedback regulation. Missense mutations leading either to loss of catalytic activity or to feedback resistance were found interspersed throughout the polypeptide, suggesting overlapping catalytic and regulatory sites in DAHPS(Trp). We conclude that the specificity of feedback regulation of the isoenzymes was probably acquired by the duplication and divergent evolution of an ancestral gene, rather than by domain recruitment.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed1995

Circadian variations of adenosine and of its metabolism. Could adenosine be a molecular oscillator for circadian rhythms?

The present review describes the biological implications of the periodic changes of adenosine concentrations in different tissues of the rat. Adenosine is a purine molecule that could have been formed in the prebiotic chemical evolution and has been preserved. The rhythmicity of this molecule, as well as its metabolism and even the presence of specific receptors, suggests a regulatory role in eukaryotic cells and in multicellular organisms. Adenosine may be considered a chemical messenger and its action could take place at the level of the same cell (autocrine), the same tissue (paracrine), or on separate organs (endocrine). Exploration of the circadian variations of adenosine was planned considering the liver as an important tissue for purine formation, the blood as a vehicle among tissues, and the brain as the possible acceptor for hepatic adenosine or its metabolites. The rats used in these studies were adapted to a dark-light cycle of 12 h with an unrestrained feeding and drinking schedule. The metabolic control of adenosine concentration in the different tissues studied through the 24-h cycle is related to the activity of adenosine-metabolizing enzyme: 5'-nucleotidase adenosine deaminase, adenosine kinase, and S-adenosylhomocysteine hydrolase. Some possibilities of the factors modulating the activity of these enzymes are commented upon. The multiphysiological action of adenosine could be mediated by several actions: (i) by interaction with extracellular and intracellular receptors and (ii) through its metabolism modulating the methylation pathway, possibly inducing physiological lipoperoxidation, or participating in the energetic homeostasis of the cell. The physiological meaning of the circadian variations of adenosine and its metabolism was focused on: maintenance of the energetic homeostasis of the tissues, modulation of membrane structure and function, regulation of fasting and feeding metabolic pattern, and its participation in the sleep-wake cycle. From these considerations, we suggest that adenosine could be a molecular oscillator involved in the circadian pattern of biological activity in the rat.

Adenosine↗
PubMed1998

Evolution in functional complexity of heart rate dynamics: a measure of cardiac allograft adaptability.

The capacity of self-organized systems to adapt is embodied in the functional organization of intrinsic control mechanisms. Evolution in functional complexity of heart rate variability (HRV) was used as measure of the capacity of the transplanted heart to express newly emergent regulatory order. In a cross-sectional study of 100 patients after (0-10 yr) heart transplantation (HTX), heart rate dynamics were assessed using pointwise correlation dimension (PD2) analysis. A new observation is that, commencing with the acute event of allograft transplantation, the dynamics of rhythm formation proceed through complex phase transitions. At implantation, the donor heart manifested metronome-like chronotropic behavior (PD2 approximately 1.0). At 11-100 days, dimensional complexity of HRV reached a peak (PD2 approximately 2.0) associated with resurgence in the high-frequency component (0.15-0.5 Hz) of the power spectral density. Subsequent dimensional loss to PD2 approximately 1.0 at 20-30 mo after HTX was followed by a progressive near-linear gain in system complexity, reaching PD2 approximately 3.0 7-10 yr after HTX. The "dynamic reorganization" in the allograft rhythm-generating system, seen in the first 100 days, is a manifestation of the adaptive capacity of intrinsic control mechanisms. The loss of HRV 2 yr after HTX implies a withdrawal of intrinsic autonomic control and/or development of an entrained dynamic pattern characteristic of extrinsic sympathetic input. The subsequent long-term progressive rise in dimensional complexity of HRV can be attributed to the restoration of a functional order patterning parasympathetic control. The recognition that the decentralized heart can restitute the multidimensional state space of HR generator dynamics independent of external autonomic signaling may provide a new perspective on principles that constitute homeodynamic regulation.

Adaptation, Physiological↗
PubMed2007

Diversity of brain morphology in teleosts: brain and ecological niche.

Modern teleosts have more copies of developmental regulatory genes than other vertebrates, probably due to a whole genome duplication that occurred specifically at the base of the lineage of ray-finned fishes. The genome duplication generates duplicated genes (including their regulatory regions), and one of the duplicates might become redundant and free from selective pressures. These redundant genes might be more easily mutated during evolution. Brain morphogenesis is a process that is dependent on a large genetic program in which a subprogram for the regionalization of the brain is coupled with that for cell-proliferation control. If beneficial mutations took place in key genes within the genetic program for brain morphogenesis, it might result in the enhancement of region-specific cell proliferation and cell survival in the corresponding brain subdivisions. This mechanism might account for the appearance of various forms of teleost brains, which have been preserved under selection pressure in diverse environments. It is conceivable that variously modified brains might evolve under the conditions of natural selection so that the brains help fit the teleost species for diverse ecological niches.

Animals↗
PubMed2006

Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin.

BACKGROUND: Structural genes of the phenyl-propanoid pathway which encode flavonoid 3'- and 3',5'-hydroxylases (F3'H and F3'5'H) have long been invoked to explain the biosynthesis of cyanidin- and delphinidin-based anthocyanin pigments in the so-called red cultivars of grapevine. The relative proportion of the two types of anthocyanins is largely under genetic control and determines the colour variation among red/purple/blue berry grape varieties and their corresponding wines. RESULTS: Gene fragments of VvF3'H and VvF3'5'H, that were isolated from Vitis vinifera 'Cabernet Sauvignon' using degenerate primers designed on plant homologous genes, translated into 313 and 239 amino acid protein fragments, respectively, with up to 76% and 82% identity to plant CYP75 cytochrome P450 monooxygenases. Putative function was assigned on the basis of sequence homology, expression profiling and its correlation with metabolite accumulation at ten different ripening stages. At the onset of colour transition, transcriptional induction of VvF3'H and VvF3'5'H was temporally coordinated with the beginning of anthocyanin biosynthesis, the expression being 2-fold and 50-fold higher, respectively, in red berries versus green berries. The peak of VvF3'5'H expression was observed two weeks later concomitantly with the increase of the ratio of delphinidin-/cyanidin-derivatives. The analysis of structural genomics revealed that two copies of VvF3'H are physically linked on linkage group no. 17 and several copies of VvF3'5'H are tightly clustered and embedded into a segmental duplication on linkage group no. 6, unveiling a high complexity when compared to other plant flavonoid hydroxylase genes known so far, mostly in ornamentals. CONCLUSION: We have shown that genes encoding flavonoid 3'- and 3',5'-hydroxylases are expressed in any tissues of the grape plant that accumulate flavonoids and, particularly, in skin of ripening red berries that synthesise mostly anthocyanins. The correlation between transcript profiles and the kinetics of accumulation of red/cyanidin- and blue/delphinidin-based anthocyanins indicated that VvF3'H and VvF3'5'H expression is consistent with the chromatic evolution of ripening bunches. Local physical maps constructed around the VvF3'H and VvF3'5'H loci should help facilitate the identification of the regulatory elements of each isoform and the future manipulation of grapevine and wine colour through agronomical, environmental and biotechnological tools.

Anthocyanins↗
PubMed1999

Sequence variation and evolution of the mitochondrial DNA control region in the musk shrew, Suncus murinus.

The complete mitochondrial DNA (mtDNA) control region was cloned and sequenced in the musk shrew, Suncus murinus, Insectivora. The general aspect was similar to that found in other mammals. We have found in two locations of this region the presence of arrays of tandem repeats like those in other shrew species. One array was located in the left domain containing the termination-associated sequences (TAS) and the length of a copy was 77 bp. The other repeats were situated upstream from the recognition site for the end of H-strand replication in the right domain and were 20 bp long. The left halves of the control region containing the former repeats were sequenced and compared in several laboratory lines and wild animals from different localities, variations in copy number of repeated sequences were found both among individuals and within an individual. A comparative study of repeated sequences provides useful indication for the origin and evolution of tandem repeated sequences. Strand slippage and mispairing during replication of mtDNA with concerted manner is currently regarded as a dominant theory to account molecular mechanism for tandemly repeated sequences, and the pattern of sequence and length variation in our study supports this theory. Our results, however, suggest that the evolution of the repeated sequences containing the TAS in the musk shrew might go through the process of two steps; at the first step one complete repeated and several incomplete repeated sequences had reproduced in common ancestor of the shrew, and the second stage step-up of complete repeated sequences occurred with concerted evolution after differentiation into continental and insular groups.

Animals↗
PubMed2003

The Food and Drug Administration's Osteoporosis Guidance Document: past, present, and future.

In December 1979, the Food and Drug Administration's (FDA) Division of Metabolic and Endocrine Drug Products issued its Guidelines for the Clinical Evaluation of Drugs Used in the Treatment of Osteoporosis. The Guidance Document recommended study designs, patient populations for study, and techniques for evaluating skeletal mass and fracture frequency that were considered central to showing the efficacy and safety of drugs used to treat and prevent postmenopausal osteoporosis (PMO). In this paper, I discuss the evolution of the Osteoporosis Guidance as it relates to the pharmaceutical industry's efforts to develop effective and safe anti-osteoporosis drugs. Current regulatory policy on osteoporosis drugs and thoughts on the future direction of the Osteoporosis Guidance are also provided.

Female↗
PubMed1992

Expression of the myogenic gene MRF4 during Xenopus development.

In a search for myogenic genes in Xenopus, I have cloned homologs of the mammalian myogenic genes MRF4 and myogenin. The myogenin clone is a genomic fragment encoding an amino acid sequence with 62% identity to the N-terminal region of rat myogenin. No myogenin transcript has been detected and no cDNA has been isolated, suggesting that Xenopus myogenin, if it is expressed at all, is likely to be expressed at low levels or transiently during development. A Xenopus MRF4 cDNA has been isolated and encodes an amino acid sequence with 72% identity to rat MRF4. In adult frogs, MRF4 RNA is detectable only in skeletal muscle (whereas MyoD, unexpectedly, is also expressed at low levels in the heart). During embryonic development, MRF4 RNA appears later than MyoD, at a time when the embryonic musculature already shows many differentiated features. This implies that MRF4 is not involved in the commitment or early differentiation of muscle cells. The accumulation of Xenopus MRF4 RNA overlaps with the formation of neuromuscular connections, suggesting that it may be induced by innervation. Consistent with this possibility, the level of Xenopus MRF4, but not MyoD, RNA is reduced in response to denervation of adult frog muscle.

Amino Acid Sequence↗
PubMed1982

Somatostatin-28 encoded in a cloned cDNA obtained from a rat medullary thyroid carcinoma.

We have constructed and cloned in bacteria complementary DNAs derived from a transplantable rat medullary thyroid carcinoma. Using a hybridization probe encoding an anglerfish islet pre-prosomatostatin, a precursor of the tetradecapeptide somatostatin, we have identified and isolated a clone containing a 400-base pair complementary DNA encoding most of the rat carcinoma pre-prosomatostatin. The amino acid sequence of the tetradecapeptide somatostatin and of the amino-terminally extended form, somatostatin-28 was deduced from the nucleotide sequence of the complementary DNA. Somatostatin-28 was found at the COOH terminus of a polypeptide of at least 80 amino acids indicating that somatostatin-28 arises by cleavage from a large precursor. The sequences of somatostatin-28 and somatostatin-14 are strictly conserved between the rat and other mammals. Such conservation of these sequences indicates strong selective pressures during evolution to maintain the sequence and suggests that somatostatin-28 may serve some essential biologic functions apart from, or in addition to, the important regulatory actions of somatostatin-14. Additionally, we found a high degree of homology in the amino acid sequences of the NH2-terminal extension peptides in the anglerfish islet and the rat carcinoma pre-prosomatostatins pointing further to a possible biologic function of these extension peptides.

Amino Acid Sequence↗
PubMed2005

Tcf- and Vent-binding sites regulate neural-specific geminin expression in the gastrula embryo.

Vertebrate neural development has been extensively investigated. However, it is unknown for any vertebrate gene how the onset of neural-specific expression in early gastrula embryos is transcriptionally regulated. geminin expression is among the earliest markers of dorsal, prospective neurectoderm at early gastrulation in Xenopus laevis. Here, we identified two 5' sequence domains that are necessary and sufficient to drive neural-specific expression during gastrulation in transgenic Xenopus embryos. Each domain contained putative binding sites for the transcription factor Tcf, which can mediate Wnt signaling and for Vent homeodomain proteins, transcriptional repressors that mediate BMP signaling. Results from embryos transgenic for constructs with mutated Tcf or Vent sites demonstrated that signaling through the Tcf sites was required for dorsal-specific expression at early gastrulation, while signaling through the Vent sites restricted geminin expression to the prospective neurectoderm at mid-gastrulation. Consistent with these results, geminin 5' regulatory sequences and endogenous Xgem responded positively to Wnt signaling and negatively to BMP signaling. The two 5' sequence domains were also conserved among geminin orthologs. Together, these results demonstrate that signaling through Tcf and Vent binding sites regulates transcription of geminin in prospective neurectoderm during gastrulation.

Animals↗
PubMed1996

Molecular evolution of the 5'-flanking regions of the duplicated Amy genes in Drosophila melanogaster species subgroup.

The nucleotide sequences of the 5'-flanking regions of the duplicated Amy genes in eight sibling species belonging to the melanogaster species subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp immediately upstream of the translation initiation site of the two paralogous genes (the proximal and distal genes) has sequence similarities. However, we could not detect any significant sequence similarity in the region more upstream than -450. This result indicates that the coding regions of the ancestral Amy gene were duplicated together with 450 bp of the 5'-flanking region as one unit. Multiple alignment of these 450-bp sequences in the proximal and distal genes of all eight species revealed a mosaic pattern of highly conserved and divergent regions. The conserved regions included almost all the putative regulatory elements identified in previous analyses of the sequences. A phylogenetic analysis of the aligned sequences shows that these 450-bp sequences are clustered into the proximal and the distal groups. As a whole, the divergence between groups in this region is very large in contrast to that in the coding regions. Based on the divergence between groups, the 450-bp region is divided into two subregions. We found that the ratios of the divergence between groups to that within groups differ in the two subregions. From these observations, we discuss a possibility of positive selection acting on the subregion immediately upstream of the Amy coding region to cause divergence of regulatory elements of the paralogous genes.

Animals↗