Structural constraints in expansion segments from a midge 26S rDNA.


:DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displayed a local bias in nucleotide composition toward AT. These regions were identified as expansion segments D3, D4, D5, D6, D7a, and D12. Besides base sequence divergence, differences in length were observed between the respective variable domains of the two species, particularly for D7a. Prediction of secondary structure showed that the folding of the Chironomus expansion segments analyzed is in agreement with the general patterns proposed for eukaryotic LSU rRNA. The comparison with Drosophila revealed also that the Chironomus secondary structures of the variable domains are supported by multiple compensatory substitutions or even compensatory insertions. Chironomus D7a displayed an unusual structural feature with respect to the insect D7a models that have been inferred up to now. The structural constraint observed in the expansion segments of Diptera so distantly related as midges and Drosophila suggests that these regions contribute to some functional role. Concerning the D7a of insects so far analyzed, there can be, in addition to a conserved secondary structure, a nucleotide composition constraint that might be important for the process giving rise to the alpha and beta halves of the 26S rRNA.


J Mol Evol


Gorab E,Garcia de Lacoba M,Botella LM




Has Abstract


1995-12-01 00:00:00












  • The evolution of hexamerins and the phylogeny of insects.

    abstract::The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergen...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Burmester T,Massey HC Jr,Zakharkin SO,Benes H

    更新日期:1998-07-01 00:00:00

  • Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes).

    abstract::The gene content of a mitochondrial (mt) genome, i.e., 37 genes and a large noncoding region (LNR), is usually conserved in Metazoa. The arrangement of these genes and the LNR is generally conserved at low taxonomic levels but varies substantially at high levels. We report here a variation in mt gene content and gene ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Shao R,Barker SC,Mitani H,Takahashi M,Fukunaga M

    更新日期:2006-08-01 00:00:00

  • The major histocompatability complex (MHC) contains conserved polymorphic genomic sequences that are shuffled by recombination to form ethnic-specific haplotypes.

    abstract::The major histocompatibility complex (MHC) consists of polymorphic frozen blocks (PFBs) that are linked to form megabase haplotypes. These blocks consist of polymorphic sequences and define regions where recombination appears to be inhibited. We have been able to show, using a highly polymorphic sequence centromeric o...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Gaudieri S,Leelayuwat C,Tay GK,Townend DC,Dawkins RL

    更新日期:1997-07-01 00:00:00

  • Protein Evolution in the Flaviviruses.

    abstract::Proteins are commonly used as molecular targets against pathogens such as viruses and bacteria. However, pathogens can evolve rapidly permitting their populations to increase in protein diversity over time and thus escape to the activity of a molecular therapy. Subsequently, in order to design more durable and robust ...

    journal_title:Journal of molecular evolution

    pub_type: 信件


    authors: Arenas M

    更新日期:2020-08-01 00:00:00

  • Experimental evolution of a novel pathway for glycerol dissimilation in Escherichia coli.

    abstract::Wild-type Escherichia coli utilizes glycerol aerobically through an inducible pathway mediated by an ATP-dependent kinase and a glycerol 3-phosphate dehydrogenase which is a flavoprotein. A mutant, strain ECL424, employing a novel pathway for glycerol utilization was isolated. The novel pathway is mediated by an NAD-l...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Jin RZ,Tang JC,Lin EC

    更新日期:1983-01-01 00:00:00

  • Molecular evolution of the puroindoline-a, puroindoline-b, and grain softness protein-1 genes in the tribe Triticeae.

    abstract::The genome organization of the Hardness locus in the tribe Triticeae constitutes an excellent model for studying the mechanisms of evolution that played a role in the preservation and potential functional innovations of duplicate genes. Here we applied the nonsynonymous-synonymous rate ratio (d ( N )/d ( S ) or omega)...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Massa AN,Morris CF

    更新日期:2006-10-01 00:00:00

  • FLAVI: An Amino Acid Substitution Model for Flaviviruses.

    abstract::Amino acid substitution models represent substitution rates among amino acids during the evolution. The models play an important role in analyzing protein sequences, especially inferring phylogenies. The rapid evolution of flaviviruses is expanding the threat in public health. A number of models have been estimated fo...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Le TK,Vinh LS

    更新日期:2020-07-01 00:00:00

  • Discovery and molecular characterization of a plasmid localized in Buchnera sp. bacterial endosymbiont of the aphid Rhopalosiphum padi.

    abstract::We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum padi. Evidence which suggests that the plasmid occurs localized within the bacterial endosymbionts is presented. The plasmid contains the four genes that constitute the entire leucine operon. This fact makes it really uni...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Bracho AM,Martínez-Torres D,Moya A,Latorre A

    更新日期:1995-07-01 00:00:00

  • A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila.

    abstract::Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Droso...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Heames B,Schmitz J,Bornberg-Bauer E

    更新日期:2020-05-01 00:00:00

  • Cotranscriptional 3'-End Processing of T7 RNA Polymerase Transcripts by a Smaller HDV Ribozyme.

    abstract::In vitro run-off transcription by T7 RNA polymerase generates heterogeneous 3'-ends because the enzyme tends to add untemplated adenylates. To generate homogeneous 3'-termini, HDV ribozymes have been used widely. Their sequences are added to the 3'-terminus such that co-transcriptional self-cleavage generates homogene...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Akoopie A,Müller UF

    更新日期:2018-08-01 00:00:00

  • Domesticated P elements in the Drosophila montium species subgroup have a new function related to a DNA binding property.

    abstract::Molecular domestication of a transposable element is defined as its functional recruitment by the host genome. To date, two independent events of molecular domestication of the P transposable element have been described: in the Drosophila obscura species group and in the Drosophila montium species subgroup. These P ne...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Reiss D,Nouaud D,Ronsseray S,Anxolabéhère D

    更新日期:2005-10-01 00:00:00

  • An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances.

    abstract::Recent experience with molecular phylogeny has shown that all molecular markers have strengths and weaknesses. Nonetheless, despite several notable discrepancies with phylogenies obtained from protein data, the merits of the small subunit ribosomal RNA (SSU rRNA) as a molecular phylogenetic marker remain indisputable....

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Van de Peer Y,Baldauf SL,Doolittle WF,Meyer A

    更新日期:2000-12-01 00:00:00

  • Enzyme-coding genes as molecular clocks: the molecular evolution of animal alpha-amylases.

    abstract::We constructed a cDNA library for the beetle, Tribolium castaneum. This library was screened using a cloned amylase gene from Drosophila melanogaster as a molecular probe. Beetle amylase cDNA clones were isolated from this bank, and the nucleotide sequence was obtained for a cDNA clone with a coding capacity for 228 a...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Hickey DA,Benkel BF,Boer PH,Genest Y,Abukashawa S,Ben-David G

    更新日期:1987-01-01 00:00:00

  • Genetic, comparative genomic, and expression analyses of the Mc1r locus in the polychromatic Midas cichlid fish (Teleostei, Cichlidae Amphilophus sp.) species group.

    abstract::Natural populations of the Midas cichlid species in several different crater lakes in Nicaragua exhibit a conspicuous color polymorphism. Most individuals are dark and the remaining have a gold coloration. The color morphs mate assortatively and sympatric population differentiation has been shown based on neutral mole...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Henning F,Renz AJ,Fukamachi S,Meyer A

    更新日期:2010-05-01 00:00:00

  • Misexpression of testicular microRNA in sterile Xenopus hybrids points to tetrapod-specific microRNAs associated with male fertility.

    abstract::Spermatogenesis is one of the most complex biological processes undergone by any organism, making it susceptible to perturbations that result in male sterility. Research has demonstrated that mutant phenotypes can be obtained from the disruption of epigenetic modifications, which are commonly microRNA guided. Employin...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Madison-Villar MJ,Michalak P

    更新日期:2011-12-01 00:00:00

  • Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.

    abstract::Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We obs...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Runnels CM,Lanier KA,Williams JK,Bowman JC,Petrov AS,Hud NV,Williams LD

    更新日期:2018-12-01 00:00:00

  • Structural comparisons of muscle and nonmuscle actins give insights into the evolution of their functional differences.

    abstract::Actin is a highly conserved protein although many isoforms exist. In vertebrates and insects the different actin isoforms can be grouped by their amino acid sequence and tissue-specific gene expression into muscle and nonmuscle actins, suggesting that the different actins may have a functional significance. We ask her...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Mounier N,Sparrow JC

    更新日期:1997-01-01 00:00:00

  • The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome.

    abstract::Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Cutler RW,Chantawannakul P

    更新日期:2007-06-01 00:00:00

  • Phylogenetic relationships between the chlorophyll a/b binding protein (CAB) multigene family: an intra- and interspecies study.

    abstract::The genome of Glycine max (L.) Merr. cv. "Dare" contains a chlorophyll a/b binding (Cab) protein gene family consisting of 10 genes. The primary structures of two linked Cab genes (Cab 4 and Cab 5) were determined. A comparison of the nucleic acid and predicted amino acid sequences of Cab 4 and Cab 5 revealed a high d...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Demmin DS,Stockinger EJ,Chang YC,Walling LL

    更新日期:1989-09-01 00:00:00

  • Nucleic acid-like structures. III. Oligomerization of 3'-deoxyadenosine 2',5'-diphosphoimidazolide.

    abstract::The activated dimonophosphate of 3'-deoxyadenosine (cordycepin) undergoes oligomerization to produce a new family of pyrophosphate-linked oligomers in which the average repeating unit involves a nine-atom structural group. The presence of a poly(U) template increases the relative yields of higher oligomers, although t...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Visscher J,Schwartz AW

    更新日期:1987-01-01 00:00:00

  • Conserved Critical Evolutionary Gene Structures in Orthologs.

    abstract::Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that mi...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Fuertes MA,Rodrigo JR,Alonso C

    更新日期:2019-04-01 00:00:00

  • Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes.

    abstract::Many eubacteria contain an ATP-dependent protease complex, which is built by multiple copies of the HslV and HslU proteins and is therefore called HslVU. HslU proteins are AAA + ATPases, while HslV proteins are proteases that show highly significant similarity to beta subunits of proteasomes. Therefore, the HslVU comp...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Ruiz-González MX,Marín I

    更新日期:2006-10-01 00:00:00

  • DNA methylation and Mycoplasma genomes.

    abstract::DNA methylation is one of the many hypotheses proposed to explain the observed deficiency in CpG dinucleotides in a variety of genomes covering a wide taxonomic distribution. Recent studies challenged the methylation hypothesis on empirical grounds. First, it cannot explain why the Mycoplasma genitalium genome exhibit...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Xia X

    更新日期:2003-01-01 00:00:00

  • The distribution of genes on chromosomes: a cytological approach.

    abstract::Studies during the last 20 years have shown that the chromosomes of many organisms, especially those of higher vertebrates, consist of a series of segments having different properties. These can be recognized as, for example, G- and R-bands. Recent studies have indicated that genes tend to lie in the R-bands rather th...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章,评审


    authors: Sumner AT,de la Torre J,Stuppia L

    更新日期:1993-08-01 00:00:00

  • Evolution of four human Y chromosomal unique sequences.

    abstract::Four cloned unique sequences from the human Y chromosome, two of which are found only on the Y chromosome and two of which are on both the X and Y chromosomes, were hybridized to restriction enzyme-treated DNA samples of a male and a female chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and pig-tailed macaqu...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Erickson RP

    更新日期:1987-01-01 00:00:00

  • Ubiquitin genes as a paradigm of concerted evolution of tandem repeats.

    abstract::Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken, Xenopus, Drosophila, barley, and yeast have re...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Sharp PM,Li WH

    更新日期:1987-01-01 00:00:00

  • Uneven distribution of repetitive trinucleotide motifs in human immunoglobulin heavy variable genes.

    abstract::Insertions and deletions of entire codons have recently been discovered as a mechanism by which B cells, in addition to conventional base substitution, evolve the antibodies produced by their immunoglobulin genes. These events frequently seem to involve repetitive sequence motifs in the antibody-encoding genes, and it...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Lantto J,Ohlin M

    更新日期:2002-03-01 00:00:00

  • Recent evolutionary history of human immunodeficiency virus type 1 subtype B: reconstruction of epidemic onset based on sequence distances to the common ancestor.

    abstract::We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3 (270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual men and injecting drug users (IDUs), as well as 77 env V3 sequences...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Lukashov VV,Goudsmit J

    更新日期:2002-05-01 00:00:00

  • Evolutionary sequence divergence within repeated DNA families of higher plant genomes. II. Analysis of thermal denaturation.

    abstract::An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was con...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Preisler RS,Thompson WF

    更新日期:1981-01-01 00:00:00

  • Optimization models and the structure of the genetic code.

    abstract::The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving. Here, we review studies of the structure of the genetic code based on optimization models. We also review studies that, from the structure of the cod...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章,评审


    authors: Jestin JL,Kempf A

    更新日期:2009-11-01 00:00:00