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1.
Amino acid residues arginine (R) and lysine (K) have similar physicochemical characteristics and are often mutually substituted
during evolution without affecting protein function. Statistical examinations on human proteins show that more R than K residues
are used in the proximity of R residues, whereas more K than R are used near K residues. This biased use occurs on both a
global and a local scale (shorter than ∼100 residues). Even within a given exon, G + C-rich and A + T-rich short DNA segments
preferentially encode R and K, respectively. The biased use of R and K on a local scale is also seen in Saccharomyces cerevisiae and Caenorhabdidtis elegans, which lack global-scale mosaic structures with varying GC%, or isochores. Besides R and K, several amino acids are also used
with a positive or negative correlation with the local GC% of third codon bases. The local-, or ``within-gene'-, scale heterogeneity
of the DNA sequence may influence the sequence of the encoded protein segment.
Received: 2 March 1998 / Accepted: 23 April 1998 相似文献
2.
Noboru Sueoka 《Journal of molecular evolution》1999,49(1):49-62
The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely
different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average
G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used
to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides
to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon
position from Parity Rule 2 (PR2), where A=T and G=C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority
of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class
of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that
when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation
coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available,
it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition,
PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint.
Received: 5 November 1998 / Accepted: 1 March 1999 相似文献
3.
On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses 总被引:1,自引:0,他引:1
Angelo Pavesi Bettina De Iaco Maria Ilde Granero Alfredo Porati 《Journal of molecular evolution》1997,44(6):625-631
In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region
of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging
to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap
a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the
nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and
plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both
types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation
between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses,
indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage
correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison
of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine,
leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed
as a way with which they may expand their coding ability and gain new, specialized functions.
Received: 28 October 1996 / Accepted: 29 January 1997 相似文献
4.
A Molecular Phylogeny of Lilium in the Internal Transcribed Spacer Region of Nuclear Ribosomal DNA 总被引:4,自引:0,他引:4
Tomotaro Nishikawa Keiichi Okazaki Tae Uchino Katsuro Arakawa Tsukasa Nagamine 《Journal of molecular evolution》1999,49(2):238-249
Phylogenetic relationships among 55 species of Lilium, Cardiocrinum giganteum, and Nomocharis saluenensis were inferred from nucleotide sequence variations in the internal transcribed spacer (ITS) regions of 18S–25S nuclear ribosomal
DNA. The phylogeny derived from ITS sequences estimated using maximum-likelihood methods indicated that (1) most of the species
construct their own clade according to the classification based on morphological features at the section level; (2) section
Daurolirion is not independent of Sinomartagon, and it is appropriate to integrate two sections as Sinomartagon; (3) it is appropriate that L. henryi and L. bulbiferum are classified into subsection 6a and Sinomartagon–Daurolirion, respectively; (4) subsection 6b is much closer to Sinomartagon than subsection 6a and Archelirion, and it arose directly from Sinomartagon; and (5) Lilium is much closer to Nomocharis than Cardiocrinum. Phylogenetic estimation using sequences of the ITS region is suitable at the levels of genus, section, and most of subsection.
Received: 18 December 1998 / Accepted: 14 March 1999 相似文献
5.
A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled
to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general
pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids
from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The
cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic
distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined
as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts.
Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these
high evolutionary rates were significantly higher among geophagine cichlids.
Received: 18 September 1998 / Accepted: 16 December 1998 相似文献
6.
Bacterial family C DNA polymerases (DNA pol IIIs), the major chromosomal replicative enzymes, have been provisionally classified
based on primary sequences and domain structures into three classes: class I (Escherichia coli DNA pol C-type), class II (Bacillus subtilis DNA pol C-type), and class III (cyanobacterial DNA pol C-type), respectively. We have sequenced the structural gene encoding
the DNA pol C catalytic subunit of the thermophilic bacterium Thermus aquaticus. This gene, designated the Taq DNA pol C gene, contains a 3660-bp open reading frame which specifies a polypeptide of molecular
weight of 137,388 daltons. Comparative sequence analyses revealed that Taq DNA pol C is a class I family C DNA polymerase.
The Taq DNA pol C is most closely related to the Deinococcus radiodurans DNA pol C. Although a phylogenetic tree based on the class I family C DNA pols is still in the provisional stage, some important
conclusion can be drawn. First, the high-G+C and the low-G+C Gram-positive bacteria are not monophyletic. Second, the low-G+C
Gram-positive bacteria contain multigenes of family C DNA pols (classes I and II). Third, the cyanobacterial family C DNA
pol, classified as class III because it is encoded by a split gene, forms a group with the high-G+C Gram-positive bacteria.
Received: 7 October 1998 / Accepted: 12 January 1999 相似文献
7.
8.
Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages 总被引:8,自引:0,他引:8
Brian R. Morton 《Journal of molecular evolution》1998,46(4):449-459
In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study
the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each
gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons
based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared
to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias
is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among
the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation
efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities
in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity
among the various genomes are discussed.
Received: 6 June 1997 / Accepted: 24 July 1997 相似文献
9.
Characterization of the Hydra Lamin and Its Gene: A Molecular Phylogeny of Metazoan Lamins 总被引:4,自引:0,他引:4
Andreas Erber Dieter Riemer Helmut Hofemeister Marc Bovenschulte Reimer Stick Georgia Panopoulou Hans Lehrach Klaus Weber 《Journal of molecular evolution》1999,49(2):260-271
We report sequences for nuclear lamins from the teleost fish Danio and six invertebrates. These include two cnidarians (Hydra and Tealia), one priapulid, two echinoderms, and the cephalochordate Branchiostoma. Combining these results with earlier data on Drosophila, Caenorhabditis elegans, and various vertebrates, the following conclusions on lamin evolution can be drawn. First, all invertebrate lamins resemble
in size the vertebrate B-type lamin. Second, all lamins described previously for amphibia, birds and mammals as well as the
first lamin of a fish, characterized here, show a cluster of 7 to 12 acidic residues in the tail domain. Since this acidic
cluster is absent from all invertebrate lamins including that of the cephalochordate Branchiostoma, it was acquired with the vertebrate lineage. The larger A-type lamin of differentiated cells must have arisen subsequently
by gene duplication and insertion of an extra exon. This extra exon of the vertebrate A-lamins is the only major change in
domain organization in metazoan lamin evolution. Third, the three introns of the Hydra and Priapulus genes correspond in position to the last three introns of vertebrate B-type lamin genes. Thus the entirely different gene
organization of the C. elegans and Drosophila Dmo genes seems to reflect evolutionary drift, which probably also accounts for the fact that C. elegans has the most diverse lamin sequence. Finally we discuss the possibility that two lamin types, a constitutively expressed
one and a developmentally regulated one, arose independently on the arthropod and vertebrate lineages.
Received: 4 February 1999 / Accepted: 1 April 1999 相似文献
10.
Pavesi A 《Journal of molecular evolution》2000,50(3):284-295
In viruses an increased coding ability is provided by overlapping genes, in which two alternative open reading frames (ORFs)
may be translated to yield two distinct proteins. The identification of signature sequences in overlapping genes is a topic
of particular interest, since additional out-of-frame coding regions can be nested within known genes. In this work, a novel
feature peculiar to overlapping coding regions is presented. It was detected by analysis of a sample set of 21 virus genomic
sequences and consisted in the repeated occurrence of a cluster of basic amino acid residues, encoded by a frame, combined
to a stretch of acidic residues, encoded by the corresponding overlapping frame. A computer scan of an additional set of virus
sequences demonstrated that this feature is common to several other known overlapping ORFs and led to prediction of a novel
overlapping gene in hepatitis G virus (HGV). The occurrence of a bifunctional coding region in HGV was also supported by its
extremely lower rate of synonymous nucleotide substitutions compared to that observed in the other gene regions of the HGV
genome. Analysis of the amino acid sequence that was deduced from the putative overlapping gene revealed a high content of
basic residues and the presence of a nuclear targeting signal; these characteristics suggest that a core-like protein may
be expressed by this novel ORF.
Received: 21 July 1999 / Accepted: 26 October 1999 相似文献
11.
Michael Kruse Vera Gamulin Helena Cetkovic Zeev Pancer Isabel M. Müller Werner E. G. Müller 《Journal of molecular evolution》1996,43(4):374-383
Protein kinases C (PKCs) comprise closely related Ser/Thr kinases, ubiquitously present in animal tissues; they respond to
second messengers, e.g., Ca2+ and/or diacylglycerol, to express their activities. Two PKCs have been sequenced from Geodia cydonium, a member of the lowest multicellular animals, the sponges (Porifera). One sponge G. cydonium PKC, GCPKC1, belongs to the ``novel' (Ca2+-independent) PKC (nPKC) subfamily while the second one, GCPKC2, has the hallmarks of the ``conventional' (Ca2+-dependent) PKC (cPKC) subfamily. The alignment of the Ser/Thr catalytic kinase domains, of the predicted aa sequences for
these cDNAs with respective segments from previously reported sequences, revealed highest homology to PKCs from animals but
also distant relationships to Ser/Thr kinases from protozoa, plants, and bacteria. However, a comparison of the complete structures
of the sponge PKCs, which are—already—identical to those of nPKCs and cPKCs from higher metazoa, with the structures of protozoan,
plant, and bacterial Ser/Thr kinases indicates that the metazoan PKCs have to be distinguished from the nonmetazoan enzymes.
These data indicate that metazoan PKCs have a universal common ancestor which they share with the nonmetazoan Ser/Thr kinases
with respect to the kinase domain, but they differ from them in overall structural composition.
Received: 10 January 1996 / Accepted: 12 March 1996 相似文献
12.
The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we
report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic
method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array
of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints
of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution
rates was surprisingly narrow for those viruses where a significant relationship between genetic divergence and time was found,
as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis
of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower
substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation
study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected,
provided that sufficiently large data sets are analyzed.
Received: 23 February 2001 / Accepted: 3 July 2001 相似文献
13.
14.
Mutation and Recombination in Cattle Satellite DNA: A Feedback Model for the Evolution of Satellite DNA Repeats 总被引:6,自引:0,他引:6
The cattle genome contains several distinct centromeric satellites with interrelated evolutionary histories. We compared
these satellites in Bovini species that diverged 0.2 to about 5 Myr ago. Quantification of hybridization signals by phosphor imaging revealed a large
variation in the relative amounts of the major satellites. In the genome of water buffalo this has led to the complete deletion
of satellite III. Comparative sequencing and PCR-RFLP analysis of satellites IV, 1.711a, and 1.711b from the related Bos and Bison species revealed heterogeneities in 0.5 to 2% of the positions, again with variations in the relative amounts of sequence
variants. Restriction patterns generated by double digestions suggested a recombination of sequence variants. Our results
are compatible with a model of the life history of satellites during which homogeneity of interacting repeat units is both
cause and consequence of the rapid turnover of satellite DNA. Initially, a positive feedback loop leads to a rapid saltatory
amplification of homogeneous repeat units. In the second phase, mutations inhibit the interaction of repeat units and coexisting
sequence variants amplify independently. Homogenization by the spreading of one of the variants is prevented by recombination
and the satellite is eventually outcompeted by another, more homogeneous tandem repeat sequence.
Received: 21 July 2000 / Accepted: 30 October 2000 相似文献
15.
16.
Jenkins GM Pagel M Gould EA de A Zanotto PM Holmes EC 《Journal of molecular evolution》2001,52(4):383-390
The extent to which base composition and codon usage vary among RNA viruses, and the possible causes of this bias, is undetermined
in most cases. A maximum-likelihood statistical method was used to test whether base composition and codon usage bias covary
with arthropod association in the genus Flavivirus, a major source of disease in humans and animals. Flaviviruses are transmitted by mosquitoes, by ticks, or directly between
vertebrate hosts. Those viruses associated with ticks were found to have a significantly lower G+C content than non-vector-borne
flaviviruses and this difference was present throughout the genome at all amino acids and codon positions. In contrast, mosquito-borne
viruses had an intermediate G+C content which was not significantly different from those of the other two groups. In addition,
biases in dinucleotide and codon usage that were independent of base composition were detected in all flaviviruses, but these
did not covary with arthropod association. However, the overall effect of these biases was slight, suggesting only weak selection
at synonymous sites. A preliminary analysis of base composition, codon usage, and vector specificity in other RNA virus families
also revealed a possible association between base composition and vector specificity, although with biases different from
those seen in the Flavivirus genus.
Received: 29 August 2000 / Accepted: 19 December 2000 相似文献
17.
Albert Jeltsch 《Journal of molecular evolution》1999,49(1):161-164
Circular permutations of genes during molecular evolution often are regarded as elusive, although a simple model can explain
these rearrangements. The model assumes that first a gene duplication of the precursor gene occurs in such a way that both
genes become fused in frame, leading to a tandem protein. After generation of a new start codon within the 5′ part of the
tandem gene and a stop at an equivalent position in the 3′ part of the gene, a protein is encoded that represents a perfect
circular permutation of the precursor gene product. The model is illustrated here by the molecular evolution of adenine-N6 DNA methyltransferases. β- and γ-type enzymes of this family can be interconverted by a single circular permutation event.
Interestingly, tandem proteins, proposed as evolutionary intermediates during circular permutation, can be directly observed
in the case of adenine methyltransferases, because some enzymes belonging to type IIS, like the FokI methyltransferase, are built up by two fused enzymes, both of which are active independently of each other. The mechanism
for circular permutation illustrated here is very easy and applicable to every protein. Thus, circular permutation can be
regarded as a normal process in molecular evolution and a changed order of conserved amino acid motifs should not be interpreted
to argue against divergent evolution.
Received: 17 November 1998 / Accepted: 19 February 1999 相似文献
18.
A Phylogenetic Study of the Origin of the Domestic Pig Estimated from the Near-Complete mtDNA Genome 总被引:18,自引:0,他引:18
The near-complete pig mtDNA genome sequence (15,997 bp) was determined from two domestic pigs (one Chinese Meishan and one
Swedish Landrace) and two European wild boars. The sequences were analyzed together with a previously published sequence representing
a Swedish domestic pig. The sequences formed three distinct clades, denoted A, E1, and E2, with considerable sequence divergence
between them (0.8–1.2%). The results confirm our previous study (based on the sequence of the cytochrome B gene and the control
region only) and provide compelling evidence that domestication of pigs must have occurred from both an Asian and a European
subspecies of the wild boar. We estimated the time since the divergence of clade A (found in Chinese Meishan pigs) and E1
(found in European domestic pigs) at about 900,000 years before present, long before domestication about 9000 years ago. The
pattern of nucleotide substitutions among the sequences was in good agreement with previous interspecific comparisons of mammalian
mtDNA; the lowest substitution rates were observed at nonsynonymous sites in protein-coding genes, in the tRNA and rRNA genes,
while the highest rates were observed at synonymous sites and in the control region. The presence of Asian clade A in some
major European breeds (Large White and Landrace) most likely reflects the documented introgression of Asian germplasm into
European stocks during the 18th and 19th centuries. The coexistence of such divergent mtDNA haplotypes for 100+ generations
is expected to lead to the presence of recombinant haplotypes if paternal transmission and recombination occur at a low frequency.
We found no evidence of such recombination events in the limited sample studied so far.
Received: 19 April 2000; Accepted: 15 November 2000 相似文献
19.
Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection 总被引:7,自引:0,他引:7
Héctor Musto Héctor Romero Alejandro Zavala Kamel Jabbari Giorgio Bernardi 《Journal of molecular evolution》1999,49(1):27-35
We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly
biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among
genes. At one end genes display codon choices determined mainly by the extreme genome composition of this parasite, and very
probably their expression level is low. At the other end a few genes exhibit an increased relative usage of a particular subset
of codons, many of which are C-ending. Since the majority of these few genes is putatively highly expressed, we postulate
that the increased C-ending codons are translationally optimal. In conclusion, while codon usage of the majority of P. falciparum genes is determined mainly by compositional constraints, a small number of genes exhibit translational selection.
Received: 10 November 1998 / Accepted: 28 January 1999 相似文献
20.
Y.-H. Tai J. Flick S.A. Levine J.L. Madara G.W.G. Sharp M. Donowitz 《The Journal of membrane biology》1996,149(1):71-79
Elevation in intracellular Ca2+ acting via protein kinase C (PKC) is shown to regulate tight junction resistance in T84 cells, a human colon cancer line and a model Cl− secretory epithelial cell. The Ca2+ ionophore A23187, which was used to increase the intracellular Ca2+ concentration, caused a decrease in tight junction resistance in a concentration- and time-dependent manner. Dual Na+/mannitol serosal-to-mucosal flux analysis performed across the T84 monolayers treated with 2 μm A23187 revealed that A23187 increased both fluxes and that in the presence of ionophore there was a linear relationship between
the Na+ and mannitol fluxes with a slope of 56.4, indicating that the decrease in transepithelial resistance was due to a decrease
in tight junction resistance. Whereas there was no effect of 0.1 μm A23187, 1 or 2 μm produced a 55% decrease in baseline resistance in 1 hr and 10 μm decreased resistance more than 80%. The A23187-induced decrease in tight junction resistance was partially reversible by
washing 3 times with a Ringer's-HCO3 solution containing 1% BSA. The A23187 effect on resistance was dependent on intracellular Ca2+; loading the T84 cells with the intracellular Ca2+ chelator BAPTA significantly reduced the decrease in tight junction resistance caused by A23187. This intracellular Ca2+ effect was mediated by protein kinase C and not calmodulin. While the protein kinase C antagonist H-7 totally prevented the
action of A23187 on tight junction resistance, the Ca2+/calmodulin inhibitor W13 did not have any effect. Sphingosine, another inhibitor of PKC, partially reduced the A23187-induced
decline in tight junction resistance. The PKC agonist PMA mimicked the A23187 effect on resistance, although the effect was
delayed up to 1 hr after exposure. In addition, however, PMA also caused an earlier increase in resistance, indicating it
had an additional effect in addition to mimicking the effect of elevating Ca2+. The effects of a phospholipase inhibitor (mepacrine) and of inhibitors of arachidonic acid metabolism (indomethacin for
the cyclooxygenase pathway, NDGA for the lipoxygenase pathway, and SKF 525A for the epoxygenase pathway) on the A23187 action
were also examined. None of these agents altered the A23187-induced decrease in resistance. Monolayers exposed to 2 μm A23187 for 1 hr were stained with fluorescein conjugated phalloidin, revealing that neighboring cells did not part one from
another and that A23187 did not have a detectable effect on distribution of F-actin in the perijunctional actomyosin ring.
The results indicate that elevation in intracellular Ca2+ decreases tight junction resistance in the T84 monolayer, acting through protein kinase C by a mechanism which does not involve visible changes in the perijunctional actomyosin
ring.
Received: 14 July 1995/Revised: 25 September 1995 相似文献