Abstract：
:The trnT-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL intron, a group I intron, and the trnT-trnL and trnL-trnF intergenic spacers. We analyzed the evolution of the region in the three genera of the gymnosperm lineage Gnetales (Gnetum, Welwitschia, and Ephedra), with especially dense sampling in Gnetum for which we sequenced 41 accessions, representing most of the 25-35 species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, while the spacers are so variable in length and composition that homology cannot be found even among the three genera. Palindromic sequences that form hairpin structures were detected in the trnL-trnF spacer, but neither spacer contained promoter elements for the tRNA genes. The absence of promoters, presence of hairpin structures in the trnL-trnF spacer, and high sequence variation in both spacers together suggest that trnT and trnF are independently transcribed. Our model for the expression and processing of the genes tRNA(Thr)(UGU), tRNA(Leu)(UAA), and tRNA(Phe) (GAA) therefore attributes the seemingly neutral evolution of the two spacers to their escape from functional constraints.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Won H,Renner SSdoi
10.1007/s00239-004-0240-3keywords:
subject
Has Abstractpub_date
2005-10-01 00:00:00pages
425-36issue
4eissn
0022-2844issn
1432-1432journal_volume
61pub_type
杂志文章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
doi：10.1007/s00239-004-0324-0
更新日期：2005-10-01 00:00:00
abstract：:Adenosine 5'-phosphoramidates form when solutions containing adenosine 5'-polyphosphates pnA (n greater than or equal to 3) or P1, P2-diadenosine 5'-diphosphate and amines are allowed to dry out. Mg ions catalyze these reactions. We have studied systems containing ammonia, imidazole, glycine, ethylenediamine and hista...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01751807
更新日期：1977-11-25 00:00:00
abstract：:In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myos...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02406723
更新日期：1993-05-01 00:00:00
abstract：:A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9829-9
更新日期：2018-02-01 00:00:00
abstract：:Computational analysis of the hypothetical open reading frame MJ0236 from Methanococcus jannaschii reveals its membership to a family of bacterial and eukaryotic proteins, predicted to be the HMP-P kinases involved in thiamin biosyntheis (ThiD). The eukaryotic members of this family contain a C-terminal extension simi...
journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/pl00013145
更新日期：1997-12-01 00:00:00
abstract：:The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010197
更新日期：2001-08-01 00:00:00
abstract：:We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition-transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applie...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006590
更新日期：1999-11-01 00:00:00
abstract：:Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked seque...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0239-9
更新日期：2005-05-01 00:00:00
abstract：:The 5S ribosomal RNA sequences have been determined for the rhodoplast of the red alga Porphyra umbilicalis and the chloroplast of the conifer Juniperus media. The 5S RNA sequence of the Vicia faba chloroplast is corrected with respect to a previous report. A survey of the known sequences and secondary structures of 5...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02138372
更新日期：1988-01-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9137-x
更新日期：2008-08-01 00:00:00
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
doi：10.1007/s00239-018-9861-9
更新日期：2018-08-01 00:00:00
abstract：:Two families of high-cysteine chorion proteins in Bombyx mori are encoded in 15 tandemly arranged nonidentical gene pairs. It is assumed that this locus arose by duplication with subsequent sequence divergence. We have compared DNA sequences from two such neighboring pairs of genes in an attempt to understand the mann...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02104732
更新日期：1984-01-01 00:00:00
abstract：:TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2352-y
更新日期：2002-11-01 00:00:00
abstract：:A reaction which oligomerizes nucleotides under possible prebiotic conditions has been characterized. Nucleoside monophosphate in the presence of cyanamide at acid pH condenses to form dithymideine pyrophosphate and phosphodiester bonded compounds. Imidazole compounds and activated precursors such as nucleoside tripho...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732356
更新日期：1975-11-04 00:00:00
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
doi：10.1007/BF02100210
更新日期：1989-09-01 00:00:00
abstract：:We outline a method for estimating quantitatively the influence of point mutations and selection on the frequencies of codons and amino acids. We show how the mutation rate, i.e., the rate of amino acid replacement due to point mutation, can be affected by the codon usage as well as by the rates of the involved base e...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102357
更新日期：1984-01-01 00:00:00
abstract：:The present work represents the first attempt to study in greater detail previously proposed compositional correlations in genomes, based on a body of additional data relating to gene localizations as well as to extended flanking sequences extracted from gene banks. We have investigated the correlations that exist bet...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102651
更新日期：1991-06-01 00:00:00
abstract：:Two competing effects at two vastly different scales may explain collagen's current translation length. The necessity to have long molecules for maintaining mechanical integrity at the organism and supraorganism scales may be limited by the need to have small molecules capable of robust self-assembly at the nanoscale....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9111-7
更新日期：2008-06-01 00:00:00
abstract：:A new type of repeat unit was isolated from Balbiani ring 1 of Chironomus pallidivittatus and designated BR1 beta repeat. It consists of a constant and a subrepeated part, like previously described units belonging to the core blocks of the BR genes. The subrepeated part contains 10-codon subrepeats with an arrangement...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101191
更新日期：1988-01-01 00:00:00
abstract：:The relaxin (RLN) and insulin-like (INSL) gene family is a group of genes involved in a variety of physiological roles that includes bone formation, testicular descent, trophoblast development, and cell differentiation. This family appears to have expanded in vertebrates relative to non-vertebrate chordates, but the r...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9403-6
更新日期：2011-01-01 00:00:00
abstract：:Cytochrome proteins perform a broad spectrum of biological functions ranging from oxidative metabolism to electron transport and are thus essential to all organisms. The b-type cytochrome proteins bind heme noncovalently, are expressed in many different forms and are localized to various cellular compartments. We repo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160314
更新日期：1995-10-01 00:00:00
abstract：:This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential p...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160324
更新日期：1995-10-01 00:00:00
abstract：:To get deeper insight into the evolution of phosphoenolpyruvate carboxylase we have identified PEPC fragments (about 1,100 bp) of another 12 plants species not yet investigated in this context. The selected plants include one Chlorophyta, two Bryophyta, four Pteridophyta, and five Spermatophyta species. The obtained p...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006277
更新日期：1998-01-01 00:00:00
abstract：:Since the discovery of the coelacanth, Latimeria chalumnae, more than 50 years ago, paleontologists and comparative morphologists have debated whether coelacanths or lungfishes, two groups of lobe-finned fishes, are the closest living relatives of land vertebrates (Tetrapoda). Previously, Meyer and Wilson (1990) deter...
journal_title：Journal of molecular evolution
pub_type： 杂志文章,评审
doi：10.1007/BF00183221
更新日期：1992-08-01 00:00:00
abstract：:The early evolution of life is a period with many important events with a lot of big and open questions. One of them is the evolution of metabolic pathways, which means the origin and assembly of enzymes that act together. The retrograde hypothesis was the first attempt to explain the origin and evolutionary history o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-021-09994-0
更新日期：2021-01-28 00:00:00
abstract：:Exon-shuffling is an important mechanism accounting for the origin of many new proteins in eukaryotes. However, its role in the creation of proteins in the ancestor of prokaryotes and eukaryotes is still debatable. Excess of symmetric exons is thought to represent evidence for exon-shuffling since the exchange of exon...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0318-y
更新日期：2005-09-01 00:00:00
abstract：:The glycosylation characteristics of the digestive enzyme ribonuclease are summarized. The evolutionary role of this posttranslational modification is discussed and evidence is presented that selection has much influence on the presence or absence of carbohydrate in glycoproteins and on the positions of the carbohydra...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099959
更新日期：1986-01-01 00:00:00
abstract：:Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Pr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006160
更新日期：1997-04-01 00:00:00
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
doi：10.1007/s00239-001-0049-2
更新日期：2002-03-01 00:00:00
abstract：:Energised by the protonmotive force and with the intervention of inorganic catalysts, at base Life reacts hydrogen from a variety of sources with atmospheric carbon dioxide. It seems inescapable that life emerged to fulfil the same role (i.e., to hydrogenate CO(2)) on the early Earth, thus outcompeting the slow geoche...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9289-3
更新日期：2009-11-01 00:00:00
