共查询到20条相似文献,搜索用时 15 毫秒
1.
Wallis M 《Journal of molecular evolution》2000,50(5):465-473
Previous studies have shown that pituitary growth hormone displays an episodic pattern of evolution, with a slow underlying
evolutionary rate and occasional sustained bursts of rapid change. The present study establishes that pituitary prolactin
shows a similar pattern. During much of tetrapod evolution the sequence of prolactin has been strongly conserved, showing
a slow basal rate of change (approx 0.27 × 109 substitutions/amino acid site/year). This rate has increased substantially (∼12- to 38-fold) on at least four occasions during
eutherian evolution, during the evolution of primates, artiodactyls, rodents, and elephants. That these increases are real
and not a consequence of inadvertant comparison of paralogous genes is shown (for at least the first three groups) by the
fact that they are confined to mature protein coding sequence and not apparent in sequences coding for signal peptides or
when synonymous substitutions are examined. Sequences of teleost prolactins differ markedly from those of tetrapods and lungfish,
but during the course of teleost evolution the rate of change of prolactin has been less variable than that of growth hormone.
It is concluded that the evolutionary pattern seen for prolactin shows long periods of near-stasis interrupted by occasional
bursts of rapid change, resembling the pattern seen for growth hormone in general but not in detail. The most likely basis
for these bursts appears to be adaptive evolution though the biological changes involved are relatively small.
Received: 31 August 1999 / Accepted: 9 February 2000 相似文献
2.
Michael Wallis 《Journal of molecular evolution》2001,53(1):10-18
Pituitary growth hormone (GH) and prolactin have been shown previously to display a pattern of evolution in which episodes
of rapid change are imposed on a low underlying basal rate (near-stasis). This study was designed to explore whether a similar
pattern is seen in the evolution of other protein hormones in mammals. Seven protein hormones were examined (with the common
α-subunit of the glycoprotein hormones providing an additional polypeptide for analysis)—those for which sequences from at
least four eutherian orders are available with a suitable non-eutherian outgroup. Six of these (GH, prolactin, insulin, parathyroid
hormone, glycoprotein hormone α-subunit, and luteinizing hormone β-subunit) showed markedly variable evolutionary rates in
each case with a pattern of a slow basal rate and bursts of rapid change, the precise positions of the bursts varying from
protein to protein. Two protein hormones (follicle-stimulating hormone β-subunit and thyroid-stimulating hormone β-subunit)
showed no significant rate variation. Based on the sequences currently available, and pooling data from all eight proteins,
the phase of slow basal change occupied about 85% of the sampled evolutionary time, but most evolutionary change (about 62%
of the substitutions accepted) occurred during the episodes of rapid change. It is concluded that, in mammals at least, a
pattern of prolonged periods of near-stasis with occasional episodes of rapid change provides a better model of evolutionary
change for protein hormones than the one of constant evolutionary rates that is commonly favored. The mechanisms underlying
this episodic evolution are not yet clear, and it may be that they vary from one group to another; in some cases, positive
selection appears to underlie bursts of rapid change. Where gene duplication is associated with a period of accelerated evolution
this often occurs at the end rather than the beginning of the episode. To what extent the type of pattern seen for protein
hormones can be extended to other proteins remains to be established.
Received: 10 October 2000 / Accepted: 18 December 2000 相似文献
3.
J. Robert Macey Allan Larson Natalia B. Ananjeva Theodore J. Papenfuss 《Journal of molecular evolution》1997,44(6):660-674
A phylogenetic tree for major lineages of iguanian lizards is estimated from 1,488 aligned base positions (858 informative)
of newly reported mitochondrial DNA sequences representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI.
Two well-supported groups are defined, the Acrodonta and the Iguanidae (sensu lato). This phylogenetic hypothesis is used
to investigate evolutionary shifts in mitochondrial gene order, origin for light-strand replication, and secondary structure
of tRNACys. These three characters shift together on the branch leading to acrodont lizards. Plate tectonics and the fossil record indicate
that these characters changed in the Jurassic. We propose that changes to the secondary structure of tRNACys may destroy function of the origin for light-strand replication which, in turn, may facilitate shifts in gene order.
Received: 28 May 1996 / Accepted: 27 December 1996 相似文献
4.
Martijn A. Huynen 《Journal of molecular evolution》1996,43(3):165-169
RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary
structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many
neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures
that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can
play a role in adaptation.
Received: 23 December 1995 / Accepted: 17 March 1996 相似文献
5.
6.
Sequence differences in the tRNA-proline (tRNApro) end of the mitochondrial control-region of three species of Pacific butterflyfishes accumulated 33–43 times more rapidly
than did changes within the mitochondrial cytochrome b gene (cytb). Rapid evolution in this region was accompanied by strong
transition/transversion bias and large variation in the probability of a DNA substitution among sites. These substitution
constraints placed an absolute ceiling on the magnitude of sequence divergence that could be detected between individuals.
This divergence ``ceiling' was reached rapidly and led to a decay in the relative rate of control-region/cytb b evolution.
A high rate of evolution in this section of the control-region of butterflyfishes stands in marked contrast to the patterns
reported in some other fish lineages. Although the mechanism underlying rate variation remains unclear, all taxa with rapid
evolution in the 5′-end of the control-region showed extreme transition biases. By contrast, in taxa with slower control-region
evolution, transitions accumulated at nearly the same rate as transversions. More information is needed to understand the
relationship between nucleotide bias and the rate of evolution in the 5′-end of the control-region.
Despite strong constraints on sequence change, phylogenetic information was preserved in the group of recently differentiated
species and supported the clustering of sequences into three major mtDNA groupings. Within these groups, very similar control-region
sequences were widely distributed across the Pacific Ocean and were shared between recognized species, indicating a lack of
mitochondrial sequence monophyly among species.
Received: 30 June 1996 / Accepted: 15 May 1997 相似文献
7.
To evaluate the relative importance of positive selection and neutral drift from the nucleotide base changes observed in
the homologous alignment of genes, a theoretical equation of base changes is formulated by including both the influence of
selection and the base substitutions due to mutations. Under the assumption that the average rate of base substitutions estimated
from synonymous changes is the ``true' mutation rate applicable at all positions, this method is applied to the vertebrate
globin gene family, and evaluates the departures of base change rates from the ``true' mutation rate at the first and second
codon positions as a consequence of preferential selection for the conservation of important function. In addition to the
strong effect of selection on the amino acid residues in the internal region mostly common to myoglobin and hemoglobin chains,
the distinctive directions of selective parameter values are seen at sites on the globin surface, distinguishing the subunit
contact residues of hemoglobins from the polar residues on the surface of myoglobins. Moreover, this effect of selection distinguishing
between the myoglobin and hemoglobin chain genes becomes weaker in cold-blooded vertebrates, especially in fish, strongly
suggesting the possibility that the clear distinction between these globins is a result of selection out of the changes regarded
as neutral ones in an ancestor of vertebrates. Thus, the present method may also serve to investigate the homology of many
other proteins from the aspect of molecular evolution, mainly focusing on the evolution of their biological functions.
Received: 2 January 1996 / Accepted: 20 February 1997 相似文献
8.
Martínez-Pérez F Becerra A Valdés J Zinker S Aréchiga H 《Journal of molecular evolution》2002,54(6):703-714
Precursor structures of various members of the neuropeptide family adipokinetic hormone/red pigment concentrating hormone
(AKH/RPCH) of mandibular arthropods and the APGWamide family of mollusks were compared. Amino acid alignments showed a common
overall architecture (signal peptide, active peptide, related peptide), with a similar α helix–random coil secondary structure.
DNA sequence alignments revealed close similarities between the genes encoding for the peptides of the two families. The APGWamide
genes are larger than the AKH/RPCH genes. The sequence environment occupied by introns is similar in AKH/RPCH and APGWamide
genes. Such similarities suggest that these peptide families might have been originated by gene rearrangements from a common
ancestor having either an AKH/RPCH/APGWamide-like structure or both an AKH/RPCH-like and an APGWamide-like structures. In
the former model, DNA fragments could have been gained when the ancestor evolved to mollusks and it could have lost nucleotides
when the progression to mandibular arthropods took place. In the second model, AKH/RPCH-like structures could have been fused
during evolution toward mandibular arthropods, whereas in mollusks they could have been lost with the possible amplification
of the APGWamide-like structure. Loss of domains in exon 1 may have originated the signal peptide and the first codon of the
active RPCH. In exon 2, loss of domains possibly determined the junctions of codons 2 to 5 with the loss of a APGWamide copy;
exon 3 underwent fewer variations. The similarity of the mollusk APGWamide precursors is closer to that of the RPCH family
than the insect AKH family, indicating an earlier evolutionary departure. 相似文献
9.
10.
The actin–cross-linking protein spectrin is a prominent component of the membrane cytoskeleton. Spectrin is a tetramer of
two antiparallel αβ-dimers which share a unique and ancient gene structure. The α-spectrin and β-spectrin genes are composed
primarily of tandemly repeated 106-amino-acid segments, each of which forms a triple α-helical coiled coil. Both the genes
and the repeats themselves are homologous. The two genes are thought to be the result of a gene duplication event, and each
gene is the product of duplications of the 106-amino-acid repeats. In this work we compare the process of molecular evolution
across the repeated segments of the α- and β-spectrin genes. We find that the α-spectrin segments have, for the most part,
evolved in a homogeneous fashion, while considerable heterogeneity is found among β-spectrin segments. Several segments with
unique known functions are found to have evolved differently than the others. On the basis of heterogeneity of the evolutionary
process, we suggest that at least one repeat has a unique function that has yet to be documented. We also present new statistical
methods for comparing the evolutionary process between different regions of DNA sequences.
Received: 27 March 1996 / Accepted: 21 October 1996 相似文献
11.
The mammalian defensin molecule is a short, highly cationic peptide cytotoxic to both microbial and mammalian cells which
is cleaved from a precursor including a signal peptide and a highly anionic propiece. A phylogenetic analysis of 28 complete
sequences from five mammalian species (mouse, rat, guinea pig, rabbit, and human) showed species-specific clusters of sequences,
indicating that the genes duplicated after divergence of these species. Comparison of rates of synonymous and nonsynonymous
nucleotide substitution suggested that gene duplication has often been followed by a period in which diversification of the
mature defensins at the amino acid level has been selectively favored. In some comparisons, it appeared that amino acid differences
in this region have appeared in a nonrandom fashion so as to change the pattern of residue charges. Because it has been hypothesized
that the negative charge in the propiece serves to balance the positive charge in the mature defensin and thus to prevent
cytotoxicity prior to cleavage, we used a maximum likelihood method of reconstructing ancestral states in order to test whether
this balance has been maintained over evolutionary time in spite of rapid diversification of the mature defensin at the amino
acid level. Reconstructed ancestral sequences always maintained a charge balance between mature defensin and propiece, and
changes in the net positive charge of the mature defensin were balanced by corresponding changes in the propiece. The results
support the hypothesis that, in the evolution of these proteins, amino acid changes have occurred in a coordinated fashion
so as to preserve an adaptive phenotype.
Received: 23 October 1996 / Accepted: 7 January 1997 相似文献
12.
Maria Manuela M. Caniça Chang Y. Lu Rajagopal Krishnamoorthy Gérard C. Paul 《Journal of molecular evolution》1997,44(1):57-65
The molecular diversity of inhibitor-resistant TEM (IRT) enzymes was explored using a strategy which involved DNA amplification
by polymerase chain reaction (PCR), analysis of restriction fragment length polymorphism (RFLP), and direct nucleotide sequencing.
The study of plasmid-borne genes from 27 strains, resistant to amoxicillin and β-lactamase-inhibitor combinations, identified
mutations resulting in amino acid change at positions 69, 244, 275, and 276 known to be associated with the IRT phenotype
and a mutation at nucleotide position 162 in the promoter region. These mutations were found to lie on two different gene
sequences, described here as ``TEM-1B like' and ``TEM-2 like' restriction linkage groups. Further analysis, of nucleotide
sequences of promoter and coding regions of the β-lactamases, confirmed that a given mutation causing IRT phenotype could
be associated with two different gene sequence frameworks and two different causal mutations could lie on identical gene sequence
framework. These data argue in favor of convergent phenotypic evolution of IRT enzymes under the selective pressure imposed
by the intensive clinical use of β-lactam–β-lactamase inhibitor combinations.
Received: 18 March 1996 / Accepted: 15 July 1996 相似文献
13.
Jih-Shiou Liu Yau-Heiu Hsu Tzu-Yu Huang Na-Sheng Lin 《Journal of molecular evolution》1997,44(2):207-213
Satellite RNA of bamboo mosaic potexvirus (satBaMV) is a linear RNA molecule which encodes a 20-kDa nonstructural protein.
Sequences of seven different satBaMV isolates from bamboo hosts in three genera showed 0.7% to 7.5% base variation which spanned
the whole RNA molecule. However, the putative 20-kDa open reading frame was all preserved in these isolates. The phylogenetic
relationship based on the nucleotide sequence did not show particular grouping of satBaMV from the host in one genus; neither
was the grouping of satBaMV evident by location of sampling. Putative secondary structures of the 3′ untranslated regions
showed a basic pattern with conserved hexanucleotides (ACCUAA) and polyadenylation signal (AAUAAA) located in the loop regions.
Although the satBaMV-encoded 20-kDa protein is a nonstructural protein, its predicted secondary structure contains eight-stranded
β-sheets which may form ``jelly-roll' structure similar to that found in capsid protein encoded by satellite virus of panicum
mosaic virus.
Received: 26 June 1996 / Accepted: 9 September 1996 相似文献
14.
An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as
functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral
populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space
during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all
sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs
of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious
paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six
potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid.
As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted
of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not
be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA
sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded
as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement
and that, in at least limited cases, this conjecture can be tested experimentally.
Received: 27 August 1996 / Accepted: 14 April 1997 相似文献
15.
We examined the evolution of the repeat regions of three noncoding microsatellite loci in 58 species of the Polistinae, a
subfamily of wasps that diverged over 140 million years ago. A phylogenetic approach allows two new kinds of approaches to
studying microsatellite evolution: character mapping and comparative analysis. The basic repeat structure of the loci was
highly conserved, but was often punctuated with imperfections that appear to be phylogenetically informative. Repeat numbers
evolved more rapidly than other changes in the repeat region. Changes in number of repeats among species seem consistent with
the stepwise mutation model, which is based on slippage during replication as the main source of mutations. Changes in repeat
numbers can occur even when there are very few tandem repeats but longer repeats, especially perfect repeats led to greater
rates of evolutionary change. Species phylogenetically closer to the one from which we identified the loci had longer stretches
of uninterrupted repeats and more different motifs, but not longer total repeat regions. The number of perfect repeats increased
more often than it decreased. However, there was no evidence that some species have consistently greater numbers of repeats
across loci than other species have, once ascertainment bias is eliminated. We also found no evidence for a population size
effect posited by one form of the directionality hypothesis. Overall, phylogenetic variation in repeat regions can be explained
by adding neutral evolution to what is already known about the mutation process. The life cycle of microsatellites appears
to reflect a balance between growth by slippage and degradation by an essentially irreversible accumulation of imperfections.
Received: 13 April 1999 / Accepted: 8 September 1999 相似文献
16.
Characteristics of Nucleotide Substitution in the Hepatitis C Virus Genome: Constraints on Sequence Change in Coding Regions at Both Ends of the Genome 总被引:19,自引:0,他引:19
Comparison of complete genome sequences for different variants of hepatitis C virus (HCV) reveals several different constraints
on sequence change. Synonymous changes are suppressed in coding regions at both 5′ and 3′ ends of the genome. No evidence
was found for the existence of alternative reading frames or for a lower mutation frequency in these regions. Instead, suppression
may be due to constraints imposed by RNA secondary structures identified within the core and NS5b genes. Nonsynonymous substitutions
are less frequent than synonymous ones except in the hypervariable region of E2 and, to a lesser extent, in E1, NS2, and NS5b.
Transitions are more frequent than transversions, particularly at the third position of codons where the bias is 16:1. In
addition, nucleotide substitutions may not occur symmetrically since there is a bias toward G or C at the third position of
codons, while T ↔ C transitions were twice as frequent as A ↔ G transitions. These different biases do not affect the phylogenetic
analysis of HCV variants but need to be taken into account in interpreting sequence change in longitudinal studies.
Received: 9 September 1996 / Accepted: 20 April 1997 相似文献
17.
Suga H Koyanagi M Hoshiyama D Ono K Iwabe N Kuma K Miyata T 《Journal of molecular evolution》1999,48(6):646-653
To know whether genes involved in cell–cell communication typical of multicellular animals dramatically increased in concert
with the Cambrian explosion, the rapid evolutionary burst in the major groups of animals, and whether these genes exist in
the sponge lacking cell cohesiveness and coordination typical of eumetazoans, we have carried out cloning of the G-protein
α subunit (Gα) and the protein tyrosine kinase (PTK) cDNAs from Ephydatia fluviatilis (freshwater sponge) and Hydra magnipapillata strain 105 (hydra). We obtained 13 Gα and 20 PTK cDNAs. Generally animal gene families diverged first by gene duplication
(subtype duplication) that gave rise to diverse subtypes with different primary functions, followed by further gene duplication
in the same subtype (isoform duplication) that gave rise to isoform genes with virtually identical function. Phylogenetic
trees of Gα and PTK families including cDNAs from sponge and hydra revealed that most of the present-day subtypes had been
established in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among the
extant animal phyla, by extensive subtype duplication: for PTK and Gα families, 23 and 9 subtype duplications were observed
in the early stage before the parazoan–eumetazoan split, respectively, and after that split, only 2 and 1 subtype duplications
were found, respectively. After the separation from arthropods, vertebrates underwent frequent isoform duplications before
the fish–tetrapod split. Furthermore, rapid amino acid changes appear to have occurred in concert with the extensive subtype
duplication and isoform duplication. Thus the pattern of gene diversification during animal evolution might be characterized
by bursts of gene duplication interrupted by considerably long periods of silence, instead of proceeding gradually, and there
might be no direct link between the Cambrian explosion and the extensive gene duplication that generated diverse functions
(subtypes) of these families.
Received: 4 November 1998 / Accepted: 17 November 1998 相似文献
18.
Yu. A. Ivashchuk-Kienbaum 《The Journal of membrane biology》1996,151(3):247-259
A method has been developed to monitor changes of the membrane potential across vesicle membranes in real time. Using the
potential-sensitive fluorescent dye indocyanine and on the basis of a water/lipid redistribution model, a calculation procedure
has been introduced to estimate the membrane potential in vesicles with incorporated cytochrome-c oxidase. Physical parameters,
such as vesicle size distribution and density of the lipid bilayer were estimated and used as calculation parameters. By extrapolation
of the transient potential change to zero time, the initial rate of the potential change (dU/dt) could be calculated. It is also shown, that the initial potential change (dU/dt) may be used to study the proton/electron stoichiometry of cytochrome-c oxidase incorporated in the vesicles.
Received: 28 September 1995/Revised: 6 February 1996 相似文献
19.
Caetano-Anollés G 《Journal of molecular evolution》2002,54(3):333-345
The origin and diversification of RNA secondary structure were traced using cladistic methods. Structural components were
coded as polarized and ordered multi-state characters, following a model of character state transformation outlined by considerations
in statistical mechanics. Several classes of functional RNA were analyzed, including ribosomal RNA (rRNA). Considerable phylogenetic
signal was present in their secondary structure. The intrinsically rooted phylogenies reconstructed from evolved RNA structure
depicted those derived from nucleic acid sequence at all taxonomical levels, and grouped organisms in concordance with traditional
classification, especially in the archaeal and eukaryal domains. Natural selection appears therefore to operate early in the
information flow that originates in sequence and ends in an adapted phenotype. When examining the hierarchical classification
of the living world, phylogenetic analysis of secondary structure of the small and large rRNA subunits reconstructed a universal
tree of life that branched in three monophyletic groups corresponding to Eucarya, Archaea, and Bacteria, and was rooted in
the eukaryotic branch. Ribosomal characters involved in the translational cycle could be easily traced and showed that transfer
RNA (tRNA) binding domains in the large rRNA subunit evolved concurrently with the rest of the rRNA molecule. Results suggest
it is equally parsimonious to consider that ancestral unicellular eukaryotes or prokaryotes gave rise to all extant life forms
and provide a rare insight into the early evolution of nucleic acid and protein biosynthesis.
Received: 13 September 2000 / Accepted: 27 August 2001 相似文献
20.
Evolutionary Comparisons of RecA-Like Proteins Across All Major Kingdoms of Living Organisms 总被引:17,自引:0,他引:17
Volker Brendel Luciano Brocchieri Steven J. Sandler Alvin J. Clark Samuel Karlin 《Journal of molecular evolution》1997,44(5):528-541
Protein sequences with similarities to Escherichia coli RecA were compared across the major kingdoms of eubacteria, archaebacteria, and eukaryotes. The archaeal sequences branch
monophyletically and are most closely related to the eukaryotic paralogous Rad51 and Dmc1 groups. A multiple alignment of
the sequences suggests a modular structure of RecA-like proteins consisting of distinct segments, some of which are conserved
only within subgroups of sequences. The eukaryotic and archaeal sequences share an N-terminal domain which may play a role
in interactions with other factors and nucleic acids. Several positions in the alignment blocks are highly conserved within
the eubacteria as one group and within the eukaryotes and archaebacteria as a second group, but compared between the groups
these positions display nonconservative amino acid substitutions. Conservation within the RecA-like core domain identifies
possible key residues involved in ATP-induced conformational changes. We propose that RecA-like proteins derive evolutionarily
from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like
proteins acting in series or cooperatively.
Received: 25 October 1996 / Accepted: 31 December 1996 相似文献