Abstract：
:Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chemical properties very similar to those of the one that would have been present had the error not occurred. This work has suggested that the second base of codons is less efficient in this respect, by about three orders of magnitude, than the first and third bases. These results are based on the assumption that all forms of error at all bases are equally likely. We extend this work to investigate (1) the effect of weighting transition errors differently from transversion errors and (2) the effect of weighting each base differently, depending on reported mistranslation biases. We find that if the bias affects all codon positions equally, as might be expected were the code adapted to a mutational environment with transition/transversion bias, then any reasonable transition/transversion bias increases the relative efficiency of the second base by an order of magnitude. In addition, if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Freeland SJ,Hurst LDdoi
10.1007/pl00006381subject
Has Abstractpub_date
1998-09-01 00:00:00pages
238-48issue
3eissn
0022-2844issn
1432-1432journal_volume
47pub_type
杂志文章abstract：:The symbiotic protists of the lower termite have been regarded as a model of early-branched eukaryotes because of their simple cellular systems and morphological features. However, cultivation of these symbiotic protists is very difficult. For this reason, these interesting protists have not been well characterized in...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010129
更新日期：2001-01-01 00:00:00
abstract：:Mitochondrial DNA (mtDNA) restriction site maps for nine species of the Drosophila obscura subgroup and for Drosophila melanogaster were established. Taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02109481
更新日期：1990-08-01 00:00:00
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
doi：10.1007/s00239-019-09889-1
更新日期：2019-04-01 00:00:00
abstract：:RNA editing affecting chloroplast and mitochondrial genomes has been identified in all major clades of land plants. The frequency of edited sites varies greatly between lineages but hornworts represent an extreme in propensity for editing in both their chloroplast and mitochondrial genomes. cDNA sequences from seven t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0146-0
更新日期：2005-11-01 00:00:00
abstract：:The kinetics of synonymous codon change and species divergence is described in a matrix formalism that is equally applicable to all levels of codon degeneracy and all levels of codon or nucleotide bias. Based on the formalism it is possible to calculate the sum of all synonymous substitution rate constants from the ob...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00186546
更新日期：1995-09-01 00:00:00
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
doi：10.1007/pl00006194
更新日期：1997-07-01 00:00:00
abstract：:This study dealt with the ability of non-denaturing gel electrophoresis to separate iso-1-cytochrome c with single amino acid replacements isolated from revertants of various cyc1 nonsense mutants of the yeast Saccharomyces cerevisiae. A total of 28 different iso-1-cytochromes c with single amino acid substitutions of...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102869
更新日期：1991-10-01 00:00:00
abstract：:We describe the complete mitochondrial genome of the house centipede Scutigera coleoptrata. Its gene order is unique among characterized arthropod mitochondrial genomes. Comparison to the gene order in the horseshoe crab mtDNA implies 10 or more translocations. By extending comparisons to 30 arthropod mitochondrial ge...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2563-x
更新日期：2004-04-01 00:00:00
abstract：:We describe the structure of a gene expressed in the salivary gland cells of the dipteran Chironomus tentans and show that it encodes 1 of the approximately 15 secretory proteins exported by the gland cells. This sp115,140 gene consists of approximately 65 copies of a 42-bp sequence in a central uninterrupted core blo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101791
更新日期：1990-07-01 00:00:00
abstract：:While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9149-6
更新日期：2008-12-01 00:00:00
abstract：:A comparison of mitochondrial DNA sequences was undertaken for two genes among orangutans from Borneo and Sumatra. The distribution of haplotypes among 42 individuals for NADH dehydrogenease subunit 3 and 39 individuals for cytochrome B was used to infer population structure. The haplotypes among all Bornean orangutan...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010110
更新日期：2000-11-01 00:00:00
abstract：:Cot and chemical analysis show that the haploid genome size of Thermobia domestica is 3-4x10(9) nucleotide pairs. Of this DNA 33% is single copy sequences and 67% is repetitive sequences. The repetitive sequences are predominantly 300 nucleotides in length and are interspersed among the single copy sequences in a shor...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01733135
更新日期：1980-08-01 00:00:00
abstract：:Life is based on biopolymers that have the ability to replicate themselves. Here we consider how a self-replicating RNA system may have originated. We consider a reaction system in which polymerization is possible by the addition of an activated monomer to the end of a chain. We suppose that a small fraction of polyme...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9276-8
更新日期：2009-11-01 00:00:00
abstract：:Oligonucleotide cataloguing has been used to characterize a number of 5S RNA species from various Procaryotes. Such catalogs can be used to establish certain and detailed phylogenetic relationships among organisms. Confining attention at present to four Families of Procaryotes, theEnterobacteriaceae, theBacillaceae, t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01659163
更新日期：1972-06-01 00:00:00
abstract：:The 70-kDa heat-shock protein (HSP70) constitutes the most conserved protein present in all organisms that is known to date. Based on global alignment of HSP70 sequences from organisms representing all three domains, numerous sequence signatures that are specific for prokaryotic and eukaryotic homologs have been ident...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00182743
更新日期：1993-12-01 00:00:00
abstract：:Abortive cycling features transcription initiation by RNA polymerase in both prokaryote and eukaryote. It is known that T7 RNA polymerase produces abortive transcripts up to eight ribonucleotides in length depending on the initial sequence of the DNA message. On the other hand, T7 RNA polymerase initiates DNA replicat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160407
更新日期：1994-12-01 00:00:00
abstract：:Microsporidia are a group of obligate intracellular eukaryotic parasites with small genomes. They infect animals from a wide variety of phyla, including humans. Two manganese superoxide dismutase (MnSOD) genes, designated NbMnSOD1 and NbMnSOD2, were found to be organized in a tandem array within the Nosema bombycis ge...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9394-3
更新日期：2010-12-01 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：:The efficiency of obtaining the correct tree by the maximum likelihood method (Felsenstein 1981) for inferring trees from DNA sequence data was compared with trees obtained by distance methods. It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolu...
journal_title：Journal of molecular evolution
pub_type： 评论,杂志文章
doi：10.1007/BF02101285
更新日期：1991-05-01 00:00:00
abstract：:Scorpion venom toxins were systematically classified according to amino acid composition, insertion/deletion events and sequence. The significance of each comparison method and its outcome is discussed in relation to known immunological and structural properties. A general classification of the toxins is proposed that...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02257372
更新日期：1984-01-01 00:00:00
abstract：:Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9348-9
更新日期：2010-05-01 00:00:00
abstract：:The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of biological entities. We investigated the amount and nature of this variation for the lichenized fun...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-013-9603-y
更新日期：2014-02-01 00:00:00
abstract：:There has been considerable discussion in recent years on the evolution of the tandemly repeated multigene families, since some organisms show a concerted model whereas others show a birth-and-death model. This controversial subject extends to several species of fish. In this study, three species of the Sparidae famil...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-013-9541-8
更新日期：2013-03-01 00:00:00
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
doi：10.1007/s00239-005-0292-z
更新日期：2006-10-01 00:00:00
abstract：:The evolutionary speed and the consequent immune escape of H3N2 influenza A virus make it an interesting evolutionary system. Charged amino acid residues are often significant contributors to the free energy of binding for protein-protein interactions, including antibody-antigen binding and ligand-receptor binding. We...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9405-4
更新日期：2011-01-01 00:00:00
abstract：:To get a better understanding of the effect of interelement selection on the variation of long terminal repeat retrotransposon families, we have investigated the evolutionary history of blood in the Drosophila melanogaster species complex. We carried out a PCR approach to amplify the 5' untranslated region from blood ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010164
更新日期：2001-04-01 00:00:00
abstract：:Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much contro...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163149
更新日期：1994-04-01 00:00:00
abstract：:Fox and Woese (1975a) have shown that a model of 5S RNA secondary structure similar to the one originally derived for Chlorella 5S RNA can be generalized with relatively minor variations to all sequenced 5S RNA molecules, i.e. that corresponding base paired regions can be formed at approximately the same positions. We...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01796136
更新日期：1977-09-20 00:00:00
abstract：:Barnacles (Cirripedia) are a subclass of Crustacea. Their peculiar segmentation pattern (few segments, absence of abdominal segments, and, in the parasitic rhizocephalan, loss of segmentation at the adult stage) prompted us to study the engrailed gene, which encodes a homeodomain transcription factor and is expressed ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006181
更新日期：1997-06-01 00:00:00
abstract：:Factors involved in the selection of the 20 protein L-alpha-amino acids during chemical evolution and the early stages of Darwinian evolution are discussed. The selection is considered on the basis of the availability in the primitive ocean, function in proteins, the stability of the amino acid and its peptides, stabi...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01795749
更新日期：1981-01-01 00:00:00
