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PubMed1988

A mammalian viral enhancer confers transcriptional regulation in yeast.

Transcriptional enhancers are DNA sequences that regulate RNA transcription from linked promoters by binding to cellular proteins (trans-activators). In the mammalian virus SV40, initiation of transcription is controlled, in part, by a strong 72-base pair enhancer. We show that yeast cells contain a factor that binds specifically to a key DNA motif in the SV40 enhancer, the P element that is essential for viral transcription in mammalian cells. The P element shows sequence similarity to a yeast DNA transcriptional regulatory element, GCN4, that controls transcription of genes that code for amino acid biosynthetic enzymes. Insertion of the SV40 enhancer or single or multiple copies of the P element itself upstream from the cytochrome Cyc-1 promoter places the hybrid viral-yeast transcription unit under metabolic control in yeast cells. These studies suggest that the SV40 P element and its complementary trans-activator represent a conserved transcriptional control mechanism that operates on widely divergent functions in evolution.

Base Sequence↗
PubMed1985

Jellyfish mesogloea collagen. Characterization of molecules as alpha 1 alpha 2 alpha 3 heterotrimers.

The mesogloea collagen of a primitive animal, the jellyfish Stomolophus nomurai, belonging to the class Scyphozoa in the Coelenterata, was studied with respect to its chain structure. Most of the mesogloea collagen was solubilized by limited digestion with pepsin and isolated by selective precipitation at 0.9 m NaCl in 0.5 M acetic acid. Upon denaturation, the pepsin-solubilized collagen produced three distinct alpha chains, alpha 1, alpha 2, and alpha 3, in comparable amounts which were separable by CM-cellulose chromatography. The nonidentity of these alpha chains was confirmed by amino acid and carbohydrate analyses and peptide mapping. Furthermore, the introduction of intramolecular cross-links into native molecules by formaldehyde yielded a large proportion of gamma 123 chain with chain structure alpha 1 alpha 2 alpha 3, as judged by chromatographic behavior and peptide maps. We concluded that mesogloea collagen is comprised of alpha 1 alpha 2 alpha 3 heterotrimers and is chemically like vertebrate Type V collagen. On the other hand, sea anemone mesogloea collagen from the class Anthozoa was previously reported to comprise (alpha)3 homotrimers (Katzman, R. L., and Kang, A. H. (1972) J. Biol. Chem. 247, 5486-5489). On the basis of these findings, we assume that alpha 1 alpha 2 alpha 3 heterotrimers arose in evolution with the divergence of Scyphozoa and Anthozoa.

Amino Acids↗
PubMed1988

Characterization of the proteins purified with monoclonal antibodies to glutamic acid decarboxylase.

Immunoaffinity columns are prepared from the monoclonal antibody (MAb) GAD-1. These columns are used to enrich glutamic acid decarboxylase (GAD) from the cytosolic fraction of rat brain homogenates and from Triton X-100 extracts of the brain membrane fraction. In each case enzyme activity is enriched over 400-fold. The immunopurified fractions were analyzed by SDS-PAGE. Fractions purified from the cytosol consisted of a quantitatively major band of 59 kDa, and one band of 63 kDa, as well as a group centered around 55 kDa. Fractions purified from membranes consisted primarily of the 59 and 63 kDa components; only traces of the lower-molecular-weight components were present. The entire set of proteins purified on GAD-1 immunoaffinity columns is strongly recognized by 2 widely used antisera to GAD, those described in Saito et al. (1974) and Oertel et al. (1981). The 59 kDa protein from the cytosolic fraction was purified to homogeneity by preparative SDS-PAGE; a partial amino acid sequence of this protein was obtained. The 59 kDa protein has a high degree of sequence homology with the deduced amino acid sequence of the protein that was coded for by a cDNA for feline GAD (Kaufman et al., 1986; Kobayashi et al., 1987). Thus, these proteins are either products of a single gene that diverged during the evolution of rat and cat from a common ancestor, or are members of a closely related set of genes found in both species. The MAb GAD-6 recognizes the 59 kDa band and the group of bands centered around 55 kDa on Western blots. Therefore, these proteins are immunochemically related. GAD-6 does not recognize the 63 kDa band. In Western blots of unfractionated homogenates of the whole brain, the only band recognized by GAD-6 is a 59 kDa band.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

[International harmonization of regular requirements for the registration of drugs: necessity, frena limitations].

Considering the necessity of internationalisation, the Pharmaceutical Industry fears the regulatory variations that may result from national evolutions, parallel or divergent, which sometimes impose on it some repeated works, hence causing an undesirable extension of development duration and also higher costs. Therefore it is quite evident to that Industry that a worldwide harmonization is necessary. For the whole collectivity, such an harmonization allows a better utilization of manpower, of animal experimentation, and also of the material means available for the new pharmaceutical products development. The strong interest showed by the Pharmaceutical industry in France for the International regulatory harmonization, confirms that this Profession has effectively taken into account the worldwide dimension for the medicinal products of the year 2000.

Humans↗
PubMed1994

Molecular cloning and chromosome localization of a putative basolateral Na(+)-K(+)-2Cl- cotransporter from mouse inner medullary collecting duct (mIMCD-3) cells.

Electroneutral Na(+)-K(+)-2Cl- cotransporters represent one of the major routes for Cl- movement in epithelia. A secretory form of the cotransporter has been described in the basolateral membrane of a variety of epithelia from fish to mammals. We isolated a putative bumetanide-sensitive Na(+)-K(+)-2Cl- cotransporter cDNA, BSC2, from mIMCD-3 cells. Northern analysis indicates that in contrast to BSC1, the recently cloned renal-specific apical isoform of the cotransporter, BSC2 is expressed in secretory epithelia and thus appears to represent the basolateral isoform. Furthermore, BSC2 is also expressed in non-polarized cells, such as red cells and myocytes. Sequence comparison and chromosome localization demonstrate that BSC2 and BSC1 are different genes that diverged before the evolution of vertebrates.

Amino Acid Sequence↗
PubMed1996

Zebrafish translation elongation factor EF1 alpha mRNA: sequence and secondary structures.

We have determined the complete sequence of the translation elongation factor EF1 subunit alpha (EF1 alpha) mRNA of zebrafish, and the 3'-untranslated sequence of EF1 alpha mRNA of halibut. The 5'-untranslated leader sequence of the EF1 alpha mRNA starts with a polypyrimidine tract. This feature is shared with the mRNAs for ribosomal proteins, where it affects the utilization of mRNA by ribosomes. However, the secondary structures of these leader sequences may differ. 5'-Polypyrimidine tracts of vertebrate EF1 alpha mRNAs participate in the formation of stable stem-loop structures, whereas those of 15 randomly chosen mRNAs for ribosomal proteins do not. This difference may provide a basis for differential control of translation for the two classes of mRNA. The 3'-untranslated sequences of vertebrate EF1 alpha mRNA have diverged little during evolution. Analyses of sequence and putative secondary structures suggest that both sequence-specific interactions and secondary structures may have contributed to sequence conservation.

Amino Acid Sequence↗
PubMed1997

[Divergence between "early" genes from defective phages of various strains of soil bacilli, close to Bacillus subtilis 168].

The extent of xre gene divergence was studied in nine soil bacillus strains with different degrees of relationship to Bacillus subtilis 168. This gene product is a repressor of defective phages. Bac. subtilis 168 recipient strains were transformed by DNA from these bacillus strains for the xhi-1479 marker and ten markers of amino acid and nitrous bases metabolism. The efficiency of soil strain DNA hybridization with Bac. subtilis 168 DNA was assessed. Eight strains were close to Bac. subtilis 168 with respect to the efficiency of heterotransformation for all markers and hybridization, and one strain (1621) strongly differed from other strains with regard to these parameters. As determined by the degree of differences in heterotransformation for all markers, the nucleotide sequence of the xre gene diverged in the evolution process at a rate similar to that of the nucleotide sequences of the housekeeping genes. All examined genes were shown to have similar selective value.

Bacillus Phages↗
PubMed1997

[Karyological differentiation of three species of coarse-haired mice of the genus Lophuromys (Murinae, Rodentia) from the Bale Mountain National Part in Ethiopia].

Three karyotypically differentiated species of harsh-furred mice, Lophuromys melanonyx (2n = 60, NFa = 90; 24m,sm + 8st + 26a + Xm + Ya), Lophuromys sp. A (2n = 54, NFa = 60; 8m,sm + 44a + Xa + Ya), and Lophuromys sp. B (2n = 68, NFa = 78; 8m,sm + 4st + 54a + Xst + Ya), were found at the Bale Mountains National Park, Ethiopia. Comparative analysis of chromosomes showed that G-banding patterns of 2 to 17 chromosome banding patterns or chromosome arms were identical in all species. Apparently, the formation of the studied species was associated with their independent karyotypic divergence during early evolution. The results obtained indicate that the rate of karyotypic alterations is not associated with the degree of morphological differentiation in this group of species.

Animals↗
PubMed1998

Janus kinases and focal adhesion kinases play in the 4.1 band: a superfamily of band 4.1 domains important for cell structure and signal transduction.

The band 4.1 domain was first identified in the red blood cell protein band 4.1, and subsequently in ezrin, radixin, and moesin (ERM proteins) and other proteins, including tumor suppressor merlin/schwannomin, talin, unconventional myosins VIIa and X, and protein tyrosine phosphatases. Recently, the presence of a structurally related domain has been demonstrated in the N-terminal region of two groups of tyrosine kinases: the focal adhesion kinases (FAK) and the Janus kinases (JAK). Additional proteins containing the 4.1/JEF (JAK, ERM, FAK) domain include plant kinesin-like calmodulin-binding proteins (KCBP) and a number of uncharacterized open reading frames identified by systematic DNA sequencing. Phylogenetic analysis of amino acid sequences suggests that band 4.1/JEF domains can be grouped in several families that have probably diverged early during evolution. Hydrophobic cluster analysis indicates that the band 4.1/JEF domains might consist of a duplicated module of approximately 140 residues and a central hinge region. A conserved property of the domain is its capacity to bind to the membrane-proximal region of the C-terminal cytoplasmic tail of proteins with a single transmembrane segment. Many proteins with band 4.1/JEF domains undergo regulated intra- or intermolecular homotypic interactions. Additional properties common to band 4.1/JEF domains of several proteins are binding of phosphoinositides and regulation by GTPases of the Rho family. Many proteins with band 4. 1/JEF domains are associated with the actin-based cytoskeleton and are enriched at points of contact with other cells or the extracellular matrix, from which they can exert control over cell growth. Thus, proteins with band 4.1/JEF domain are at the crossroads between cytoskeletal organization and signal transduction in multicellular organisms. Their importance is underlined by the variety of diseases that can result from their mutations.

Amino Acid Sequence↗
PubMed1996

Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs.

We have examined and dated primate divergences by applying a newly established molecular/ paleontological reference, the evolutionary separation between artiodactyls and cetaceans anchored at 60 million years before present (MYBP). Owing to the morphological transformations coinciding with the transition from terrestrial to aquatic (marine) life and the large body size of the animals (which makes their fossils easier to find), this reference can be defined, paleontologically, within much narrower time limits compared to any local primate calibration marker hitherto applied for dating hominoid divergences. Application of the artiodactyl/ cetacean reference (A/C-60) suggests that hominoid divergences took place much earlier than has been concluded previously. According to a homogeneous-rate model of sequence evolution, the primary hominoid divergence, i.e., that between the families Hylobatidae (gibbons) and Hominidae, was dated at approximately 36 MYBP. The corresponding dating for the divergence between Pongo (orangutan) and Gorilla-Pan (chimpanzee) -Homo is approximately 24.5 MYBP, that for Gorilla vs Homo-Pan is approximately 18 MYBP, and that for Homo vs Pan approximately 13.5 MYBP. The split between Sumatran and Bornean orangutans was dated at approximately 10.5 MYBP and that between the common and pygmy chimpanzees at approximately 7 MYBP. Analyses of a single gene (cytochrome b) suggest that the divergence within the Catarrhini, i.e., between Hominoidea and Old World monkeys (Cercopithecoidea), took place > 40 MYBP; that within the Anthropoidea, i.e., between Catarrhini and Platyrrhini (New World monkeys), > 60 MYBP; and that between Anthropoidea and Prosimii (lemur), approximately 80 MYBP. These separation times are about two times more ancient than those applied previously as references for the dating of hominoid divergences. The present findings automatically imply a much slower evolution in hominoid DNA (both mitochondrial and nuclear) than commonly recognized.

Animals↗
PubMed1994

Evolution of murine alpha 1-proteinase inhibitors: gene amplification and reactive center divergence.

The organization and sequence of genes encoding the alpha 1-proteinase inhibitor (alpha 1PI), a major serine proteinase inhibitor of the mammalian bloodstream, have been compared in several species, including murine rodents (genus Mus). Analysis of gene copy number indicates that amplification of alpha 1PI genes occurred at some time during evolution of the Mus genus, leading to fixation of a family of about three to five genes in several existing species (e.g., M. domesticus and M. saxicola), and only a single gene in others (e.g., M. caroli). A phylogeny for the various mammalian alpha 1PI mRNAs was constructed based upon synonymous substitutions within coding regions. The mRNAs in different murine species diverged from a common ancestor before the formation of the first species lineages of the Mus genus, i.e., about 10-13 million years ago. Thus, alpha 1PI gene amplification must have occurred prior to Mus speciation; gene families were retained in some, but not all, murine species. The reactive center region of the alpha 1PI polypeptide, which determines target protease specificity, has diverged rapidly during evolution of the Mus species, but not during evolution of other mammalian species included in the analysis. It is likely that this accelerated evolution of the reactive center, which has been noted previously for serine proteinase inhibitors, was driven by some sort of a positive Darwinian selection that was exerted in a taxon-specific manner. We suggest that evolution of alpha 1PI genes of murine rodents has been characterized by both modification of gene copy number and rapid reactive center divergence. These processes may have resulted in a broadened repertoire of proteinase inhibitors that was evolutionarily advantageous during Mus speciation.

Amino Acid Sequence↗
PubMed2004

Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957-1972: evidence for genetic divergence and multiple reassortment events.

Phylogenic analysis of all gene segments of human H2N2 viruses isolated from 1957 to 1968 was undertaken to better understand the evolution of this virus subtype. Human H3N2 viruses isolated from 1968 to 1972 were also examined to investigate genetic events associated with their emergence in humans and to identify the putative H2N2 ancestral virus. All gene segments of human H2N2 viruses demonstrated divergent evolution into two distinct clades (I and II) among late H2N2 isolates. All gene segments of 1968 H3N2 viruses that were retained from human H2N2 viruses were most similar to clade I H2N2 genes. However, genes of both clades were found among H3N2 isolates of 1969-1971. Unique phylogenic topologies reflected multiple reassortment events among late H2N2 or H3N2 viruses that resulted in a variety of different genome constellations. These results suggest that H2N2 viruses continued to circulate after 1968 and that establishment of H3N2 viruses in humans was associated with multiple reassortment events that contributed to their genetic diversity.

Amino Acid Sequence↗
PubMed2002

Mosaic organization of orthologous sequences in grass genomes.

Although comparative genetic mapping studies show extensive genome conservation among grasses, recent data provide many exceptions to gene collinearity at the DNA sequence level. Rice, sorghum, and maize are closely related grass species, once sharing a common ancestor. Because they diverged at different times during evolution, they provide an excellent model to investigate sequence divergence. We isolated, sequenced, and compared orthologous regions from two rice subspecies, sorghum, and maize to investigate the nature of their sequence differences. This study represents the most extensive sequence comparison among grasses, including the largest contiguous genomic sequences from sorghum (425 kb) and maize (435 kb) to date. Our results reveal a mosaic organization of the orthologous regions, with conserved sequences interspersed with nonconserved sequences. Gene amplification, gene movement, and retrotransposition account for the majority of the nonconserved sequences. Our analysis also shows that gene amplification is frequently linked with gene movement. Analyzing an additional 2.9 Mb of genomic sequence from rice not only corroborates our observations, but also suggests that a significant portion of grass genomes may consist of paralogous sequences derived from gene amplification. We propose that sequence divergence started from hotspots along chromosomes and expanded by accumulating small-scale genomic changes during evolution.

Chromosomes, Plant↗
PubMed2000

Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans.

The concept of recent hominoid divergences has been a mainstay in molecular primatology since the 1970's. However, the ages allocated to the calibration points used to establish these divergence times and the estimates resulting from their application, notably the commonly accepted divergence between Pan (chimpanzees) and Homo 5 million years before present (MYBP), are now palaeontologically refutable. Here we estimate the ages of various primate divergences using three references with a more detailed fossil record than any of the traditional primate calibration points. Our findings suggest that the latter yield datings that are too recent by a factor of about two. For example, our estimates place the divergence between Pan and Homo 10.5-13 MYBP. The revised estimates of primate divergence times suggest a new hypothesis for primate evolution and dispersal: that the divergence between strepsirhines (lorises, lemurs) and anthropoids was contemporary with the break-up of Southern continents about 90 MYBP, with strepsirhines becoming isolated on Madagascar and later dispersing to Africa (and Asia) and anthropoids evolving in South America and subsequently colonizing Africa (and Asia), or possibly North America. In addition we present a new hypothesis, which accommodates the strikingly similar coalescence times for human mitochondrial DNA and the Y-chromosome. This hypothesis posits a common mitochondrial and Y-chromosome bottleneck about 400,000 years ago, associated with the origination of the human 2n = 46 karyotype, obstructing genetic exchange with the 2n = 48 Homo contemporaries.

Africa↗
PubMed1991

Rapid evolution of prostatic protein PSP94 suggested by sequence divergence between rhesus monkey and human cDNAs.

Comparison of the protein coding region of mRNA for the prostatic secretory protein PSP94 in human (hPSP94) with that in rhesus monkey (rmPSP94) indicates that, for the most part, its sequence has evolved with few constraints and at a relatively fast rate. Interestingly, half of the 22 residue differences between the two species involve charge changes, reflected by the acidic pI (5.4) of hPSP94 and the basic pI (10.6) of rmPSP94. However, the 10 cysteines and 5 of the 6 prolines of PSP94 were unaffected, suggesting that the three-dimensional conformations of the human and the monkey proteins may be similar. Rapid evolution of this gene might explain the apparent absence in nonprimates of homologous sequences detectable by hybridization.

Amino Acid Sequence↗
PubMed1990

Evolution of the autosomal chorion cluster in Drosophila. IV. The Hawaiian Drosophila: rapid protein evolution and constancy in the rate of DNA divergence.

Autosomal chorion genes s18, s15, and s19 are shown to diverge at extremely rapid rates in closely related taxa of Hawaiian Drosophila. Their nucleotide divergence rates are at least as fast as those of intergenic regions that are known to evolve more extensively between distantly related species. Their amino acid divergence rates are the fastest known to date. There are two nucleotide replacement substitutions for every synonymous one. The molecular basis for observed length and substitution mutations is analyzed. Length mutations are strongly associated with direct repeats in general, and with tandem repeats in particular, whereas the rate for an average transition is twice that for an average transversion. The DNA sequence of the cluster was used to construct a phylogenetic tree for five taxa of the Hawaiian picture-winged species group of Drosophila. Assignment of observed base substitutions occurring in various branches of the tree reveals an excess of would-be homoplasies in a centrally localized 1.8-kb segment containing the s15 gene. This observation may be a reflection of ancestral excess polymorphisms in the segment. The chorion cluster appears to evolve at a constant rate regardless of whether the central 1.8-kb segment is included or not in the analysis. Assuming that the time of divergence of Drosophila grimshawi and the planitibia subgroup coincides with the emergence of the island of Kauai, the overall rate of base substitution in the cluster is estimated to be 0.8% million years, whereas synonymous sites are substituted at a rate of 1.2% million years.

Amino Acid Sequence↗
PubMed2002

REM and NREM sleep as natural accompaniments of the evolution of warm-bloodedness.

Divergence of primitive sleep into REM and NREM states is thought to have occurred in the nocturnal Triassic ancestors of mammals as a natural accompaniment of the evolution of warm-bloodedness. As ambient temperatures during twilight portions of primitive sleep traversed these evolving ancestors' core temperature, mechanisms of thermoregulatory control that employ muscle contractions became superfluous. The resulting loss of need for such contractions during twilight sleep led to muscle atonia. With muscle tone absent, selection favored the persistence of the fast waves of nocturnal activity during twilight sleep. Stimulations by these waves reinforce motor circuits at the increasing temperatures of evolving warm-bloodedness without leading to sleep-disturbing muscle contractions. By these and related interlinked adaptations, twilight sleep evolved into REM sleep. The daytime period of sleep became NREM sleep. The evolution of NREM and REM sleep following this scenario has implications for sleep's maintenance processes for long-term memories. During NREM sleep, there is an unsynchronized, uncoordinated stimulation and reinforcement of individual distributed component circuits of consolidated memories by slow wave potentials, a process termed 'uncoordinated reinforcement'. The corresponding process during REM sleep is the coordinated stimulation and reinforcement of these circuits by fast wave potentials. This action temporally binds the individual component circuit outputs into fully formed memories, a process termed 'coordinated reinforcement'. Sequential uncoordinated and coordinated reinforcement, that is, NREM followed by REM sleep, emerges as the most effective mechanism of long-term memory maintenance in vertebrates. With the evolution of this two-stage mechanism of long-term memory maintenance, it became adaptive to partition sleep into several NREM-REM cycles, thereby achieving a more lengthy application of the cooperative sequential actions.

Adaptation, Physiological↗
PubMed1989

Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family.

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. We have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that they have low sequence identity (approximately 50%) with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.

Amino Acid Sequence↗