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1.
Konecny J Schöniger M Hofacker I Weitze MD Hofacker GL 《Journal of molecular evolution》2000,50(3):238-242
Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins.
We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted
to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point
mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one
strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical
properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure.
We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient
search for new variants on the protein level.
Received: 4 June 1999 / Accepted: 12 October 1999 相似文献
2.
Microsatellite DNA sequences have become the dominant source of nuclear genetic markers for most applications. It is important
to investigate the basis of variation between alleles and to know if current assumptions about the mechanisms of microsatellite
mutation (that is to say, variations involving simple changes in the number of repeat) are correct. We have characterized,
by DNA sequencing, the human alleles of a new highly informative (CA)n repeat localized approximately 20 kb centromeric to
the HLA-B gene. Although 12 alleles were identified based on conventional length criteria, sequencing of the alleles demonstrated
that differences between alleles were found to be more complex than previously assumed: A high degree of microsatellite variability
is due to variation in the region immediately flanking the repeat. These data indicate that the mutational process which generates
polymorphism in this region has involved not only simple changes in the number of dinucleotide CA repeats but also perturbations
in the nonrepeated 5′ and 3′ flanking sequences. Three families of alleles (not visible from the overall length of the alleles),
with presumably separate evolutionary histories, exist and can yield to homoplasy of size. Effectively, we can observe alleles
of the same size with different internal structures which are separated by a significant amount of variation. Although allelic
homoplasy for noninterrupted microsatellite loci has been suggested between different species, it has not been unequivocally
demonstrated within species. A strong association is noted between alleles defined at the sequence level and HLA-B alleles.
The observation of several families of alleles at the population level provides information about the evolutionary history
and mutation processes of microsatellites and may have implications for the use of these markers in phylogenetic, linkage
disequilibrium studies, and gene mapping.
Received: 14 May 1996 / Accepted: 9 September 1996 相似文献
3.
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
4.
5.
RNA viruses and retroviruses fix substitutions approximately 1 million-fold faster than their hosts. This diversification
could represent an inevitable drift under purifying selection, the majority of substitutions being phenotypically neutral.
The alternative is to suppose that most fixed mutations are beneficial to the virus, allowing it to keep ahead of the host
and/or host population. Here, relative sequence diversification of different proteins encoded by viral genomes is found to
be linear. The examples encompass a wide variety of retroviruses and RNA viruses. The smoothness of relative divergence spans
quasispeciation following clonal infection, to variation among different isolates of the same virus, to viruses from different
species or those associated with different diseases, indicating that the majority of fixed mutations likely reflects drift.
This held for both mammalian and plant viruses, indicating that adaptive immunity doesn't necessarily shape the relative accumulation
of amino acid substitutions. When compared to their hosts RNA viruses evolution appears conservative.
Received: 16 November 1999 / Accepted: 10 March 2000 相似文献
6.
Moulton V Gardner PP Pointon RF Creamer LK Jameson GB Penny D 《Journal of molecular evolution》2000,51(4):416-421
Opinion is strongly divided on whether life arose on earth under hot or cold conditions, the hot-start and cold-start scenarios,
respectively. The origin of life close to deep thermal vents appears as the majority opinion among biologists, but there is
considerable biochemical evidence that high temperatures are incompatible with an RNA world. To be functional, RNA has to
fold into a three-dimensional structure. We report both theoretical and experimental results on RNA folding and show that
(as expected) hot conditions strongly reduce RNA folding. The theoretical results come from energy-minimization calculations
of the average extent of folding of RNA, mainly from 0–90°C, for both random sequences and tRNA sequences. The experimental
results are from circular-dichroism measurements of tRNA over a similar range of temperatures. The quantitative agreement
between calculations and experiment is remarkable, even to the shape of the curves indicating the cooperative nature of RNA
folding and unfolding. These results provide additional evidence for a lower temperature stage being necessary in the origin
of life.
Received: 1 March 2000 / Accepted: 14 June 2000 相似文献
7.
On the Possibility of Constructive Neutral Evolution 总被引:22,自引:0,他引:22
Arlin Stoltzfus 《Journal of molecular evolution》1999,49(2):169-181
The neutral theory often is presented as a theory of ``noise' or silent changes at an isolated ``molecular level,' relevant
to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless,
precisely these issues can be addressed in neutral models, such as those elaborated here with regard to scrambled ciliate
genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate
genes. All of these are instances of a more general scheme of ``constructive neutral evolution' that invokes biased variation,
epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or
operations. The directional and constructive outcomes of these models are due not to neutral allele fixations per se, but
to these other factors. Neutral models of this type may help to clarify the poorly understood role of nonselective factors
in evolutionary innovation and directionality.
Received: 3 September 1998 / Accepted: 15 February 1999 相似文献
8.
Jennifer M. Seddon Peter R. Baverstock Arthur Georges 《Journal of molecular evolution》1998,46(4):460-464
Assertions that the ``conventional' rate of mitochondrial DNA (mtDNA) evolution is reduced in poikilotherms in general and
turtles in particular were tested for side-necked turtles (Pleurodira: Chelidae). Homologous data sets of mitochondrial 12S
rRNA gene sequences were used to compare the average divergence between the Australian and South American species for two
Gondwanan groups: the chelid turtles and the marsupials. The mean nucleotide divergences between continental groups for both
the turtles and the marsupials are remarkably similar. These data suggest that the rate of evolution of mitochondrial 12S
rRNA gene is not substantially slower in turtles than in the homeothermic marsupials.
Received: 24 February 1997 / Accepted: 30 June 1997 相似文献
9.
We obtained 16 nucleotide sequences (∼1400 bp each) of the first intron of the mitochondrial (mt) gene for NADH subunit 4
(nad4) from 10 species of Brassicaceae. Using these new sequences and five published sequences from GenBank, we constructed
a phylogenetic tree of the Brassicaceae species under study and showed that the rate of nucleotide substitution in the first
intron of nad4 is very low, about 0.16–0.23 × 10−9 substitution per site per year, which is about half of the silent rate in exons of nad4. The ratios of substitution rates
in this intron, ITS, and IGS are approximately 1:23:73, where ITS is the nuclear intergenic spacer between 18S and 25S rRNA
genes and IGS is the intergenic spacer of 5S rRNA genes. A segment (335 bp) in the first intron of nad4 in Brassicaceae species
that is absent in wheat was considered as a nonfunctional sequence and used to estimate the neutral rate (the rate of mutation)
in mtDNA to be 0.5–0.7 × 10−9 substitution per site per year, which is about three times higher than the substitution rate in the rest of the first intron
of nad4. We estimated that the dates of divergence are 170–235 million years (Myr) for the monocot–dicot split, 112–156 Myr
for the Brassicaceae–Lettuce split, 14.5–20.4 Myr for the Brassica–Arabidopsis split, and 14.5–20.4 Myr for the Arabidopsis–Arabideae split.
Received: 14 July 1998 / Accepted: 1 October 1998 相似文献
10.
Tertiary structures of proteins are conserved better than their primary structures during evolution. Quaternary structures
or subunit organizations, however, are not always conserved. A typical case is found in hemoglobin family. Although human,
Scapharca, and Urechis have tetrameric hemoglobins, their subunit contacts are completely different from each other. We report here that only one
or two amino acid replacements are enough to create a new contact between subunits. Such a small number of chance replacements
is expected during the evolution of hemoglobins. This result explains why different modes of subunit interaction evolved in
animal hemoglobins. In contrast, certain interactions between subunits are necessary for cooperative oxygen binding. Cooperative
oxygen binding is observed often in dimeric and tetrameric hemoglobins. Conformational change of a subunit induced by the
first oxygen binding to the heme group is transmitted through the subunit contacts and increases the affinity of the second
oxygen. The tetrameric hemoglobins from humans and Scapharca have cooperativity in spite of their different modes of subunit contact, but the one from Urechis does not. The relationship between cooperativity and the mode of subunit contacts is not clear. We compared the atomic interactions
at the subunit contact surface of cooperative and non-cooperative tetrameric hemoglobins. We show that heme-contact modules
M3–M6 play a key role in the subunit contacts responsible for cooperativity. A module was defined as a contiguous peptide
segment having compact conformation and its average length is about 15 amino acid residues. We show that the cooperative hemoglobins
have interactins involving at least two pairs of modules among the four heme-contact modules at subunit contact.
Received: 12 January 2001 / Accepted: 3 April 2001 相似文献
11.
Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals 总被引:1,自引:0,他引:1
Relationships among families and suborders of scleractinian corals are poorly understood because of difficulties 1) in making
inferences about the evolution of the morphological characters used in coral taxonomy and 2) in interpreting their 240-million-year
fossil record. Here we describe patterns of molecular evolution in a segment of the mitochondrial (mt) 16S ribosomal gene from taxa of 14 families of corals and the use of this gene segment in a phylogenetic analysis of relationships
within the order. We show that sequences obtained from scleractinians are homologous to other metazoan 16S ribosomal sequences
and fall into two distinct clades defined by size of the amplified gene product. Comparisons of sequences from the two clades
demonstrate that both sets of sequences are evolving under similar evolutionary constraints: they do not differ in nucleotide
composition, numbers of transition and transversion substitutions, spatial patterns of substitutions, or in rates of divergence.
The characteristics and patterns observed in these sequences as well as the secondary structures, are similar to those observed
in mt 16S ribosomal DNA sequences from other taxa. Phylogenetic analysis of these sequences shows that they are useful for evaluating
relationships within the order. The hypothesis generated from this analysis differs from traditional hypotheses for evolutionary
relationships among the Scleractinia and suggests that a reevaluation of evolutionary affinities in the order is needed.
Received: 4 September 1996 / Accepted: 7 April 1997 相似文献
12.
Philippe Castagnone-Sereno Hélène Leroy Jean-Philippe Semblat Frédéric Leroy Pierre Abad Carolien Zijlstra 《Journal of molecular evolution》1998,46(2):225-233
An AluI satellite DNA family has been isolated in the genome of the root-knot nematode Meloidogyne chitwoodi. This repeated sequence was shown to be present at approximately 11,400 copies per haploid genome, and represents about 3.5%
of the total genomic DNA. Nineteen monomers were cloned and sequenced. Their length ranged from 142 to 180 bp, and their A
+ T content was high (from 65.7 to 79.1%), with frequent runs of As and Ts. An unexpected heterogeneity in primary structure
was observed between monomers, and multiple alignment analysis showed that the 19 repeats could be unambiguously clustered
in six subfamilies. A consensus sequence has been deduced for each subfamily, within which the number of positions conserved
is very high, ranging from 86.7% to 98.6%. Even though blocks of conserved regions could be observed, multiple alignment of
the six consensus sequences did not enable the establishment of a general unambiguous consensus sequence. Screening of the
six consensus sequences for evidence of internal repeated subunits revealed a 6-bp motif (AAATTT), present in both direct
and inverted orientation. This motif was found up to nine times in the consensus sequences, also with the occurrence of degenerated
subrepeats. Along with the meiotic parthenogenetic mode of reproduction of this nematode, such structural features may argue
for the evolution of this satellite DNA family either (1) from a common ancestral sequence by amplification followed by mechanisms
of sequence divergence, or (2) through independent mutations of the ancestral sequence in isolated amphimictic nematode populations
and subsequent hybridization events. Overall, our results suggest the ancient origin of this satellite DNA family, and may
reflect for M. chitwoodi a phylogenetic position close to the ancestral amphimictic forms of root-knot nematodes.
Received: 23 April 1997 / Accepted: 9 July 1997 相似文献
13.
Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their ruggedness. Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively flat peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of neighboring RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences increases. The patterns that are generated in the RNA sequences and the RNA secondary structures are not directly selected for and can be regarded as a side effect of the evolutionary dynamics of the system.
Correspondence to: M.A. Huynen 相似文献
14.
Exploring Nonnatural Evolutionary Pathways by Saturation Mutagenesis: Rapid Improvement of Protein Function 总被引:1,自引:0,他引:1
Random point mutagenesis does not access a large fraction of protein sequence space corresponding to primarily nonconservative
amino acid substitutions. The cost of this limitation during directed evolution is unknown. Random point mutagenesis over
the entire gene encoding the psychrophilic protease subtilisin S41 identified a pair of residues (Lys211 and Arg212) where
mutations provided significant increases in thermostability. These were subjected to saturation mutagenesis to test whether
the amino acids not easily accessible by point mutagenesis provide even better ``solutions' to the thermostabilization challenge.
A significant fraction of these variants surpassed the stability of the variants with point mutations. DNA sequencing revealed
highly hydrophobic residues in the four most stable variants (Pro/Ala, Pro/Val, Leu/Val, and Trp/Ser). These nonconservative
replacements, accessible only by multiple (two to three) base substitutions in a single codon, would be extremely rare in
a point mutation library. Such replacements are also extremely rare in natural evolution. Saturation mutagenesis may be used
advantageously during directed evolution to explore nonnatural evolution pathways and enable rapid improvement in protein
traits.
Received: 15 March 1999 / Accepted: 28 June 1999 相似文献
15.
Secondary structure is evaluated for determining evolutionary relationships between catalytic RNA molecules that are so distantly
related they are scarcely alignable. The ribonucleoproteins RNase P (P) and RNase MRP (MRP) have been suggested to be evolutionarily
related because of similarities in both function and secondary structure. However, their RNA sequences cannot be aligned with
any confidence, and this leads to uncertainty in any trees inferred from sequences. We report several approaches to using
secondary structures for inferring evolutionary trees and emphasize quantitative tests to demonstrate that evolutionary information
can be recovered. For P and MRP, three hypotheses for the relatedness are considered. The first is that MRP is derived from
P in early eukaryotes. The next is that MRP is derived from P from an early endosymbiont. The third is that both P and MRP
evolved in the RNA-world (and the need for MRP has since been lost in prokaryotes). Quantitative comparisons of the pRNA and
mrpRNA secondary structures have found that the possibility of an organellar origin of MRP is unlikely. In addition, comparison
of secondary structures support the identity of an RNase P–like sequence in the maize chloroplast genome. Overall, it is concluded
that RNA secondary structure is useful for evaluating evolutionary relatedness, even with sequences that cannot be aligned
with confidence.
Received: 19 July 1999 / Accepted: 3 May 2000 相似文献
16.
Following the original idea of Maynard Smith on evolution of the protein sequence space, a novel tool is developed that allows the "space walk", from one sequence to its likely evolutionary relative and further on. At a given threshold of identity between consecutive steps, the walks of many steps are possible. The sequences at the ends of the walks may substantially differ from one another. In a sequence space of randomized (shuffled) sequences the walks are very short. The approach opens new perspectives for protein evolutionary studies and sequence annotation. 相似文献
17.
Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and
the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and
analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, a unicellular red alga (AF022186). The analysis revealed that this genome shows several unusual structural features,
such as a hypothetical hairpin structure in a gene-free region and absence of large repeat units. We provide evidence that
this structural organization of the cp-genome of C. caldarium may be that of the most ancient cp-genome so far described. We also compared the cp-genome of C. caldarium to the other known cp-genomes of the red lineage. The cp-genome of C. caldarium cannot be readily aligned with that of Porphyra purpurea, a multicellular red alga, or Guillardia theta due to a displacement of a region of the cp-genome. The phylogenetic tree reveals that the secondary endosymbiosis, through
which G. theta evolved, took place after the separation of the ancestors of C. caldarium and P. purpurea.
We found several genes unique to the cp-genome of C. caldarium. Five of them seem to be involved in the building of bacterial cell envelopes and may be responsible for the thermotolerance
of the chloroplast of this alga. Two additional genes may play a role in stabilizing the photosynthetic machinery against
salt stress and detoxification of the chloroplast. Thus, these genes may be unique to the cp-genome of C. caldarium and may be required for the endurance of the extreme living conditions of this alga.
Received: 3 June 2000 / Accepted: 18 July 2000 相似文献
18.
The sequence of the mu opioid receptor is highly conserved among human, rat, and mouse. In order to gain insights into the
evolution of the mu opioid receptor, polymerase chain reaction (PCR) was used to screen genomic DNA from a number of different
species using degenerate oligonucleotides which recognize a highly conserved region. DNA was assayed from representative species
of both the protostome and deuterostome branches of the metazoan phylogenetic tree. Mu opioid receptor-like sequences were
found in all vertebrate species that were analyzed. These species included bovine, chicken, bullfrog, striped bass, thresher
shark, and Pacific hagfish. However, no mu opioid receptor-like sequences were detected from protostomes or from any invertebrates.
The PCR results demonstrate that the region of the mu opioid receptor gene between the first intracellular loop and the third
transmembrane domain (TM3) has been highly conserved during evolution and that mu opioid receptor-like sequences are present
in the earliest stages of vertebrate evolution. Additional opioid receptor-like sequence was obtained from mRNA isolated from
Pacific hagfish brain using rapid amplification of cDNA ends (RACE). The sequence of the Pacific hagfish was most homologous
with the human mu opioid receptor (72% at the amino acid level between intracellular loop 1 and transmembrane domain 6) although
over the same region high homology was also observed with the delta opioid receptor (69%), the kappa receptor (63%), and opioid
receptor-like (ORL1) (59%). The hagfish sequence showed low conservation with the mammalian opioid receptors in the first
and second extracellular loops but high conservation in the transmembrane and intracellular domains.
Received: 5 January 1996 / Accepted: 7 March 1996 相似文献
19.
Benoit Cousineau Fabrice Leclerc Robert Cedergren 《Journal of molecular evolution》1997,45(6):661-670
Sequence similarity has given rise to the proposal that IF-2, EF-G, and EF-Tu are related through a common ancestor. We evaluate
this proposition and whether the relationship can be extended to other factors of protein synthesis. Analysis of amino acid
sequence similarity gives statistical support for an evolutionary affiliation among IF-1, IF-2, IF-3, EF-Tu, EF-Ts, and EF-G
and suggests further that this association is a result of gene duplication/fusion events. In support of this mechanism, the
three-dimensional structures of IF-3, EF-Tu, and EF-G display a predictable domain structure and overall conformational similarity.
The model that we propose consists of three consecutives duplication/fusion events which would have taken place before the
divergence of the three superkingdoms: eubacteria, archaea, and eukaryotes. The root of this protein superfamily tree would
be an ancestor of the modern IF-1 gene sequence. The repeated fundamental motif of this protein superfamily is a small RNA
binding domain composed of two α-helices packed along side of an antiparallel β-sheet.
Received: 17 October 1996 / Accepted: 10 June 1997 相似文献
20.
Ballard JW 《Journal of molecular evolution》2000,51(1):64-75
The current study compares the nucleotide variation among 22 complete mitochondrial genomes of the three distinct Drosophila simulans haplotypes with intron 1 of the alcohol dehydrogenase-related locus. This is the first study to investigate the sequence variation of multiple complete mitochondrial genomes within distinct
mitochondrial haplotypes of a single species. Patterns of variation suggest distinct forces are influencing the evolution
of mitochondrial DNA (mtDNA) and autosomal DNA in D. simulans. First, there is little variation within each mtDNA haplotype but strong differentiation among them. In contrast, there is
no support for differentiation of the mitochondrial haplotypes at the autosomal locus. Second, there is a significant deficiency
of mitochondrial variation in each haplotype relative to the autosomal locus. Third, the ratio of nonsynonymous to synonymous
substitutions is not equal in all branches of the well-resolved phylogeny. There is an excess of nonsynonymous substitutions
relative to synonymous substitutions within each D. simulans haplotype. This result is similar to that previously observed within the mtDNA of distinct species. A single evolutionary
force may be causally linked to the observed patterns of mtDNA variation—a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci.
Received: 16 September 1999 / Accepted: 14 March 2000 相似文献