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PubMed2005

Evolution of transcription factor DNA binding sites.

In bioinformatics, binding of transcription regulatory factors to the cognate binding sites is usually described by sequence-specific binding energy, which is estimated from a training sample of sites. This model implies that all binding sites with binding energy above some threshold are functional and site sequence variations should be considered neutral until they do not reduce this energy below the threshold. To quantify this energy, the binding profile (positional weight matrix, PWM) model or consensus-based model is usually applied. Here we show that in many cases available data are not sufficient to construct a relevant PWM, and modified consensus-based model could be more effective to describe binding properties. Further, using the data about binding sites of several transcription factors, we demonstrate that some non-consensus nucleotides in "orthologous sites" (that is, binding sites of the same factor upstream of orthologous genes), which have been believed to be irrelevant or even hindering the regulation, are evolutionary very stable and specific for the regulated gene. For each two considered genomes, the number of substitutions between non-consensus nucleotides is far less than the expected number of neutral substitutions. Moreover, in several positions of binding sites regulating different genes, there are non-consensus nucleotides conserved in distant genomes. It means that there exists a selection pressure, which results in the stability of non-consensus nucleotides.

Base Sequence↗

PubMed2006

FW2.2 and cell cycle control in developing tomato fruit: a possible example of gene co-option in the evolution of a novel organ.

fw2.2 is one of the few QTLs thus far isolated from plants and the first one known to control fruit size. While it has been established that FW2.2 is a regulator (either directly or indirectly) of cell division, FW2.2 does not share sequence homology to any protein of known function (Frary et al. Science 289:85-88, 2000; Cong et al. Proc Natl Acad Sci USA 99:13606-13611, 2002; Liu et al. Plant Physiol 132:292-299, 2003). Thus, the mechanism by which FW2.2 mediates cell division in developing fruit is currently unknown. In an effort to remedy this situation, a combination of yeast two-hybrid screens, in vitro binding assays and cell bombardment studies were performed. The results provide strong evidence that FW2.2 physically interacts at or near the plasma membrane with the regulatory (beta) subunit of a CKII kinase. CKII kinases are well-studied in both yeast and animals where they form part of cell cycle related signaling pathway. Thus while FW2.2 is a plant-specific protein and regulates cell division in a specialized plant organ (fruit), it appears to participate in a cell-cycle control signal transduction pathway that predates the divergence of single- and multi-cellular organisms. These results thus provide a glimpse into how ancient and conserved regulatory processes can be co-opted in the evolution of novel organs such as fruit.

Amino Acid Sequence↗

PubMed1996

Molecular cloning of frog secretogranin II reveals the occurrence of several highly conserved potential regulatory peptides.

Secretogranin II (SgII) is an acidic secretory protein present in large dense core vesicles of neuronal and endocrine cells. Based on the sequence of a peptide derived from the processing of SgII in the brain of the frog Rana ridibunda, degenerate oligonucleotides were used to clone the cDNA encoding frog SgII from a pituitary cDNA library. This cDNA encodes a 574 amino acid protein which exhibits 46-48% sequence identity with mammalian SgII and contains 11 pairs of basic amino acids. Four potential processing products delimited by pairs of basic residues exhibited a much higher degree of identity (68-82%) with the corresponding mammalian SgII sequences. The frog SgII mRNA is approximately 4 kb in length and is differentially expressed in the brain and endocrine tissues. The present data reveal that several SgII-derived peptides have been highly conserved during evolution, suggesting that these peptides may play important neuroendocrine regulatory functions.

Amino Acid Sequence↗

PubMed2000

The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons.

Mammalian LINE-1 (L1) elements belong to the superfamily of autonomously replicating retrotransposable elements that lack the long terminal repeated (LTR) sequences typical of retroviruses and retroviral-like retrotransposons. The non-LTR superfamily is very ancient and L1-like elements are ubiquitous in nature, having been found in plants, fungi, invertebrates, and various vertebrate classes from fish to mammals. L1 elements have been replicating and evolving in mammals for at least the past 100 million years and now constitute 20% or more of some mammalian genomes. Therefore, L1 elements presumably have had a profound, perhaps defining, effect on the evolution, structure, and function of mammalian genomes. L1 elements contain regulatory signals and encode two proteins: one is an RNA-binding protein and the second one presumably functions as an integrase-replicase, because it has both endonuclease and reverse transcriptase activities. This work reviews the structure and biological properties of L1 elements, including their regulation, replication, evolution, and interaction with their mammalian hosts. Although each of these processes is incompletely understood, what is known indicates that they represent challenging and fascinating biological phenomena, the resolution of which will be essential for fully understanding the biology of mammals.

3' Untranslated Regions↗

PubMed2006

[Retroviruses-derived sequences in the human genome. Human endogenous retroviruses (HERVs)].

Retroviruses-derived elements in the human genome constitute 90% of non-coding mobile sequences. Reverse transcriptase (RT) plays an essential role in their transposition as do long terminal repeats (LTRs), which contain promotors, enhancers, and regulatory sequences. Some retroelements (pseudogens and retrogenes, e.g. SINE) are non-autonomic and do not possess their own RT. These elements are dependent on autonomic elements (retroposons, e.g. LINE, retrotransposons, exo- and endogenous retroviruses). The genome of retroviruses is composed of gag, pol, and env genes flanked by long terminal repeats. Endogenous retroviruses are probably the remnants of ancient germ cell infection by exogenous retroviruses and are transmissible to the next generation in a Mendelian way. Most of them are defective (because of mutation accumulation), but some are still active and their expression is regulated by different factors (UV radiation, inflammatory cytokines, steroid hormones, and exogenous virus products). Retroelements as well as their gene products exert influence on the organism's functions. They influence the plasticity and evolution of genomes, are a source of promotors and regulatory sequences, but they also supply additional signals of transcription initiation, mRNA splicing, and STOP codons. One of the positive aspects of human endogenous retroviruses (HERVs) is the participation of their products in normal syncytiotrophoblast formation. They also block exogenous retrovirus replication by receptor interference or antisense mRNA. Their presence is considered to be connected with a number of autoimmunological diseases (multiple sclerosis, insulin-dependent diabetes mellitus, systemic lupus erythematosus), cancer, or even psychiatric disorders (schizophrenia). There are also other problems connected with the potential role of ERVs in genomic therapy (with retroviruses vectors) and transplantology (xenotransplantation).

Autoimmune Diseases↗

PubMed2005

Conserved genomic organisation of Group B Sox genes in insects.

BACKGROUND: Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. RESULTS: We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. CONCLUSION: The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and Dichaete, and two Group B2 genes. The genomic organisation of Dichaete and another two Group B genes in a cluster, suggests they may be under concerted regulatory control. Our analysis suggests a simple model for the evolution of group B Sox genes in insects that differs from the proposed evolution of vertebrate Group B genes.

Animals↗

PubMed2001

Review: How was metazoan threshold crossed? The hypothetical Urmetazoa.

The origin of Metazoa remained--until recently--the most enigmatic of all phylogenetic problems. Sponges [Porifera] as "living fossils", positioned at the base of multicellular animals, have been used to answer basic questions in metazoan evolution by molecular biological techniques. During the last few years, cDNAs/genes coding for informative proteins have been isolated and characterized from sponges, especially from the marine demosponges Suberites domuncula and Geodia cydonium. The analyses of their deduced amino acid sequences allowed a molecular biological resolution of the monophyly of Metazoa. Molecules of the extracellular matrix/basal lamina, with the integrin receptor, fibronectin and galectin as prominent examples, cell-surface receptors (tyrosine kinase receptors), elements of nerve system/sensory cells (metabotropic glutamate receptor), homologs/modules of an immune system [immunoglobulin-like molecules, SRCR- and SCR-repeats, cytokines, (2-5)A synthetase], as well as morphogens (myotrophin) classify the Porifera as true Metazoa. As "living fossils", provided with simple, primordial molecules allowing cell-cell and cell-matrix adhesion, as well as processes of signal transduction as known in a more complex manner from higher Metazoa, sponges also show peculiarities. Tissues of sponges are rich in telomerase activity, suggesting a high plasticity in the determination of cell lineages. It is concluded that molecular biological studies with sponges as models will not only help to understand the evolution to the Metazoa but also the complex, hierarchical regulatory network of cells in higher Metazoa [reviewed in Progress in Molecular Subcellular Biology, vols. 19, 21 (1998) Springer Verlag]. The hypothetical ancestral animal, the Urmetazoa, from which the metazoan lineages diverged (more than 600 MYA), may have had the following characteristics: cell adhesion molecules with intracellular signal transduction pathways, morphogens/growth factors forming gradients, a functional immune system, and a primordial nerve cell/receptor system.

Amino Acid Sequence↗

PubMed1975

Intrinsic asymmetry of oligomer transitions and biomolecular evolution.

Structural transitions in oligomeric proteins due to ligand binding are important in biomolecular regulatory processes. The transitions may occur on the secondary, tertiary or quarternary structure levels. Detailed consideration of the time sequence of ligand binding to the oligomer shows that there is an intrinsic dynamic asymmetry in all oligomer transitions, even if the initial and the final state are completely symmetric. This asymmetry has important bearing on the evolution and the divergence of the primary structure (amino acid sequence) of oligomeric proteins. It may explain (at least in part) the occurrence of oligomeric proteins with similar but not identical protomers. Certain specific groups of oligomers are shown to be under greater evolutionary pressure for protomer structure divergence. The dynamic asymmetry of oligomer transitions also results in higher complexity in reaction kinetics. Some implications on ribosome structural evolution are discussed.

Biological Evolution↗

PubMed1990

Vitellogenin protein diversity in the Hawaiian Drosophila.

Egg and female hemolymph proteins were resolved via SDS-polyacrylamide gel electrophoresis in a diverse array of 33 endemic Hawaiian drosophilids, encompassing 17 picture-winged species, 3 of the antopocerus species group, 9 fungus feeders, 1 species from each of the modified mouthparts, crassifemur and ciliated tarsus groups, and 1 Scaptomyza species. Molecular weights of the two (10 species) or three vitellogenin bands (22 species) were highly variable, spanning a 7-kD range. The largest vitellogenin, V1, was the most variable, showing a change of some 10% in its mean size of 47.6 kD. The smallest V3 vitellogenin, mean size 44.1 kD, was evolutionarily the most conservative in size. The species Drosophila hawaiiensis was found to be polymorphic for two/three vitellogenin bands and, also, polymorphic with respect to the size of the V1 protein. No inter- or intrapopulation variability in vitellogenin size was detected in 10 other species examined. The major features of vitellogenin protein evolution in the Hawaiian Drosophila are change in molecular weight and regulatory differences that result in quantitative differences between species in patterns of vitellogenin protein production.

Animals↗

PubMed2006

Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes.

Abstract We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes (Coregonus clupeaformis, Salmonidae) is accompanied by parallelism in gene transcription. The most striking phenotypic differences between these forms implied energetic metabolism and swimming activity. Therefore, we predicted that genes showing parallel expression should mainly belong to functional groups associated with these phenotypes. Transcriptome profiles were obtained from white muscle by using a 3557 cDNA gene microarray developed for the Atlantic salmon (Salmo salar). A total of 1181 genes expressed in both lake populations hybridized on the array. Significant differential expression between ecotypes was detected for 134 (11.3%) and 195 (16.5%) gene clones in Cliff Lake and Indian Pond, respectively. Fifty-one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression. Candidate genes associated with parallelism in swimming activity and energetic metabolism based on their level and variance in expression were identified. These results add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints. It also provides further evidence for the determinant role of divergent natural selection in driving phenotypic divergence, and perhaps reproductive isolation, in the adaptive radiation of lake whitefish. This study adds to a nascent field employing microarrays as powerful tools for investigating the evolutionary processes of adaptive divergence among natural populations.

Animals↗

PubMed1979

Evolution of human longevity: a critical overview.

Evolution of longevity of the ungulates, carnivores and primates is reviewed. Special emphasis is focused on recent evolutionary history of longevity along the hominid ancestral-descendant sequence leading to modern man. Maximum life span potential (MLP) or the change in MLP is predicted in extinct species by (1) a phylogenetic analysis of the MLP of present living species and (2) an empirical equation using brain and body weight estimates from fossils. Both of these methods indicate MLP generally increased during mammalian evolution and at an extremely fast rate during the appearance of the hominid species. These results suggest that relatively few genetic alterations were necessary during the recent evolutionary history of man to significantly extend his innate ability to maintain mental and physical health. Much evidence indicates these genetic alterations principally involve regulatory genes, which control a conserved set of structural genes. Evolution of longevity in man could therefore be a result of simple changes in temporal and quantitative expression. Whether these genetic alterations result from mutational changes and/or chromosomal rearrangement cannot yet be evaluated.

Aging↗

PubMed2005

Genomic sources of regulatory variation in cis and in trans.

Regulatory variation results from genetic changes with both cis and trans acting effects on gene expression. Here I describe the types of genetic variants that alter cis and trans regulation and discuss differences in the potential for cis and trans changes among different classes of genes. I argue that the molecular function of the protein encoded by each gene and how the gene is wired into the genomic regulatory network may influence its propensity for cis and trans regulatory changes.

Animals↗

PubMed2004

Gene regulatory network growth by duplication.

We are beginning to elucidate transcriptional regulatory networks on a large scale and to understand some of the structural principles of these networks, but the evolutionary mechanisms that form these networks are still mostly unknown. Here we investigate the role of gene duplication in network evolution. Gene duplication is the driving force for creating new genes in genomes: at least 50% of prokaryotic genes and over 90% of eukaryotic genes are products of gene duplication. The transcriptional interactions in regulatory networks consist of multiple components, and duplication processes that generate new interactions would need to be more complex. We define possible duplication scenarios and show that they formed the regulatory networks of the prokaryote Escherichia coli and the eukaryote Saccharomyces cerevisiae. Gene duplication has had a key role in network evolution: more than one-third of known regulatory interactions were inherited from the ancestral transcription factor or target gene after duplication, and roughly one-half of the interactions were gained during divergence after duplication. In addition, we conclude that evolution has been incremental, rather than making entire regulatory circuits or motifs by duplication with inheritance of interactions.

Bacterial Proteins↗

PubMed1995

Information requirements and regulatory approaches for heritable genetic risk assessment and risk communication.

With the evolution of genetic toxicology as a scientific discipline and the formation of the Environmental Mutagen Society (EMS), much thought was given to the study of chemicals in the human environment for their mutagenic effects. The Society's goal was to promote scientific investigation and dissemination of information related to genetic toxicology. Subsequently, the concern for chemically induced genetic damage in human germ cells and its potential impact on genetic diseases was detailed in the Committee 17 Report (1975). With new information on the involvement of genetic alterations in disease and on the ramifications of possible effects of exposures to environmental mutagens, it is becoming increasingly necessary to again focus our attention on the assessment of heritable genetic effects. Clearly, strategies for communication of genetic hazard/risk assessments to exposed individuals and to those charged with regulating environmental agents need to be developed.

Animals↗

PubMed1995

Isolation of a novel mouse gene MA-3 that is induced upon programmed cell death.

Typical programmed cell death requires de novo macromolecular synthesis and shares common morphological changes referred to as apoptosis. To elucidate the molecular mechanism of apoptosis, we isolated cDNA clones that are induced in various types of apoptosis by the differential display method. Among such clones, the MA-3 mRNA was induced in all apoptosis-inducible cell lines tested so far, including thymocytes, T cells, B cells and pheochromocytoma. The nucleotide sequence of the MA-3 cDNA predicted an amino acid (aa) sequence of 469 aa, which did not reveal significant similarity to any known proteins and functional aa motifs in databases. The MA-3 mRNA was strongly expressed in the thymus although small amounts of the MA-3 mRNA were ubiquitously expressed in mouse adult tissues. The MA-3 gene was highly conserved during evolution and cross-hybridization bands were found not only in vertebrates but also in Drosophila melanogaster.

Amino Acid Sequence↗

PubMed2005

Engineering regulatory RNAs.

RNA has long been a favoured medium for in vitro evolution and engineering. Functional RNAs produced in vitro can bind small molecules (aptamers), possess catalytic activity (ribozymes) or do both (aptazymes). A plethora of recent work has shown similar strategies used naturally for gene regulation in bacteria. Interest in these natural systems has inspired an effort to engineer and evolve this activity in vivo. A recent paper by Isaacs et al. describes the engineering and in vivo activity of a small RNA that removes translation inhibition by binding the 5' untranslated region of its target mRNA and making the ribosome-binding site accessible.

Animals↗

PubMed1986

Evolution in biosynthetic pathways: two enzymes catalyzing consecutive steps in methionine biosynthesis originate from a common ancestor and possess a similar regulatory region.

The metC gene of Escherichia coli K-12 was cloned and the nucleotide sequence of the metC gene and its flanking regions was determined. The translation initiation codon was identified by sequencing the NH2-terminal part of beta-cystathionase, the MetC gene product. The metC gene (1185 nucleotides) encodes a protein having 395 amino acid residues. The 5' noncoding region was found to contain a "Met box" homologous to sequences suggestive of operator structures upstream from other methionine genes that are controlled by the product of the pleiotropic regulatory metJ gene. The deduced amino acid sequence of beta-cystathionase showed extensive homology with that of the MetB protein (cystathionine gamma-synthase) that catalyzes the preceding step in methionine biosynthesis. The homology strongly suggests that the structural genes for the MetB and MetC proteins evolved from a common ancestral gene.

Amino Acid Sequence↗

PubMed2002

The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding.

Cyclic nucleotide phosphodiesterases (PDEs) regulate all pathways that use cGMP or cAMP as a second messenger. Five of the 11 PDE families have regulatory segments containing GAF domains, 3 of which are known to bind cGMP. In PDE2 binding of cGMP to the GAF domain causes an activation of the catalytic activity by a mechanism that apparently is shared even in the adenylyl cyclase of Anabaena, an organism separated from mouse by 2 billion years of evolution. The 2.9-A crystal structure of the mouse PDE2A regulatory segment reported in this paper reveals that the GAF A domain functions as a dimerization locus. The GAF B domain shows a deeply buried cGMP displaying a new cGMP-binding motif and is the first atomic structure of a physiological cGMP receptor with bound cGMP. Moreover, this cGMP site is located well away from the region predicted by previous mutagenesis and structural genomic approaches.

3',5'-Cyclic-AMP Phosphodiesterases↗