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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.
Shin-ichi Yokobori Tsutomu Suzuki Kimitsuna Watanabe 《Journal of molecular evolution》2001,53(4-5):314-326
Characteristic features of tRNA such as the anticodon sequence and modified nucleotides in the anticodon loop are thought
to be crucial effectors for promoting or restricting codon reassignment. Our recent findings on basepairing rules between
anticodon and codon in various metazoan mitochondria suggest that the complete loss of a codon is not necessarily essential
for codon reassignment to take place. We postulate that a possible competition between two tRNAs with cognate anticodon sequences
towards the relevant codon to be varied has a potential role in codon reassignment. Our proposition can be viewed as an expanded
version of the codon capture theory proposed by Osawa and Jukes (J Mol Evol 28: 271–278, 1989).
Received: 28 December 2000 / Accepted: 12 March 2001 相似文献
3.
Codon Usage Bias and tRNA Abundance in Drosophila 总被引:5,自引:0,他引:5
Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development.
We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the exception
of Asp which had very low contribution to overall bias. Asp was also the only amino acid that did not show a clear preference
for one of its synonymous codons. Synonymous codon usage in Drosophila was consistent with ``optimal' codons deduced from the isoaccepting tRNA availability. Interestingly, amino acids whose
major isoaccepting tRNAs change during development did not show as strong bias as those with developmentally unchanged tRNA
pools. Asp is the only amino acid for which the major isoaccepting tRNAs change between larval and adult stages. We conclude
that synonymous codon usage in Drosophila is well explained by tRNA availability and is probably influenced by developmental changes in relative abundance.
Received: 5 December 1996 / Accepted: 14 June 1997 相似文献
4.
We previously reported the sequence of a 9260-bp fragment of mitochondrial (mt) DNA of the cephalopod Loligo bleekeri [J. Sasuga et al. (1999) J. Mol. Evol. 48:692–702]. To clarify further the characteristics of Loligo mtDNA, we have sequenced an 8148-bp fragment to reveal the complete mt genome sequence. Loligo mtDNA is 17,211 bp long and possesses a standard set of metazoan mt genes. Its gene arrangement is not identical to any other
metazoan mt gene arrangement reported so far. Three of the 19 noncoding regions longer than 10 bp are 515, 507, and 509 bp
long, and their sequences are nearly identical, suggesting that multiplication of these noncoding regions occurred in an ancestral
Loligo mt genome. Comparison of the gene arrangements of Loligo, Katharina tunicata, and Littorina saxatilis mt genomes revealed that 17 tRNA genes of the Loligo mt genome are adjacent to noncoding regions. A majority (15 tRNA genes) of their counterparts is found in two tRNA gene clusters
of the Katharina mt genome. Therefore, the Loligo mt genome (17 tRNA genes) may have spread over the genome, and this may have been coupled with the multiplication of the
noncoding regions. Maximum likelihood analysis of mt protein genes supports the clade Mollusca + Annelida + Brachiopoda but
fails to infer the relationships among Katharina, Loligo, and three gastropod species.
Received: 9 May 2001 / Accepted: 3 October 2001 相似文献
5.
David L. Thurlow Gina M. Pulido Kristen J. Millar 《Journal of molecular evolution》1997,44(6):686-689
The protein sequence of ATP/CTP:tRNA nucleotidyltransferase (cca) from Sulfolobus shibatae was used to search open reading frames in the genome of Methanococcus jannaschii. Translations of two unidentified open reading frames showed significant sequence similarity to portions of the Sulfolobus cca protein. When the two open reading frames were joined together, the expanded open reading frame was similar in sequence to
the entire Sulfolobus cca protein and displayed features of the active site signature sequence proposed for members of class I enzymes within the superfamily
of nucleotidyltransferases (Yue et al., 1996, RNA 2, 895–908). A possible UUG start codon was identified based on significant sequence similarity of the resulting amino-terminal
region to that of Sulfolobus, and on a six-base complementarity between an adjacent upstream sequence and Methanococcus 16S rRNA.
Received: 10 February 1997 相似文献
6.
7.
Satoru Kanai Hiroyuki Toh Toshiya Hayano Masakazu Kikuchi 《Journal of molecular evolution》1998,47(2):200-210
Protein disulfide isomerase (PDI) is an enzyme that promotes protein folding by catalyzing disulfide bridge isomerization.
PDI and its relatives form a diverse protein family whose members are characterized by thioredoxin-like (TX) domains in the
primary structures. The family was classified into four classes by the number and the relative positions of the TX domains.
To investigate the evolution of the domain structures, we aligned the amino acid sequences of the TX domains, and the molecular
phylogeny was examined by the NJ and ML methods. We found that all of the current members of the PDI family have evolved from
an ancestral enzyme, which has two TX domains in the primary structure. The diverse domain structures of the members have
been generated through domain duplications and deletions. 相似文献
8.
The Molecular Evolution of the Vertebrate Trypsinogens 总被引:1,自引:0,他引:1
We expand the already large number of known trypsinogen nucleotide and amino acid sequences by presenting additional trypsinogen
sequences from the tunicate (Boltenia villosa), the lamprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis). The current array of known trypsinogen sequences now spans the entire vertebrate phylogeny. Phylogenetic analysis is made
difficult by the presence of multiple isozymes within species and rates of evolution that vary highly between both species
and isozymes. We nevertheless present a Fitch-Margoliash phylogeny constructed from pairwise distances. We employ this phylogeny
as a vehicle for speculation on the evolution of the trypsinogen gene family as well as the general modes of evolution of
multigene families. Unique attributes of the lamprey and tunicate trypsinogens are noted.
Received: 12 July 1997 相似文献
9.
Michael S.Y. Lee 《Journal of molecular evolution》1999,49(3):385-391
It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear
genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two ``internal' calibration points were used.
However, only one fossil divergence date (the mammal–bird split) was directly used to calibrate the molecular clock. The second
calibration point (the primate–rodent split) was based on molecular estimates that were ultimately also calibrated by the
same mammal–bird split. However, the first tetrapods that can be assigned with confidence to either the mammal (synapsid)
lineage or the bird (diapsid) lineage are approximately 288 million years old, while the first mammals that can be assigned
with confidence to either the primate or the rodent lineages are 65 million years old, or 85 million years old if ferungulates
are part of the primate lineage and zhelestids are accepted as ferungulate relatives. Recalibration of the protein data using
these fossil dates indicates that metazoans diverged between 791 and 528 million years ago, a result broadly consistent with
the palaeontological documentation of the ``Cambrian explosion.' The third, ``external' calibration point (the metazoan–fungal
divergence) was similarly problematic, since it was based on a controversial molecular study (which in turn used fossil dates
including the mammal–bird split); direct use of fossils for this calibration point gives the absurd dating of 455 million
years for metazoan divergences. Similar calibration problems affect another recent study (Wang et al. 1999), which proposes
divergences for metazoans of 1000 million years or more: recalibrations of their clock again yields much more recent dates,
some consistent with a ``Cambrian explosion' scenario. Molecular clock studies have persuasively argued for the imperfection
of the fossil record but have rarely acknowledged that their inferences are also directly based on this same record.
Received: 26 January 1999 / Accepted: 14 April 1999 相似文献
10.
Thomas D. Kim Seong-Eun Cho Chul-Hak Yang Jongsun Kim 《Journal of molecular evolution》2001,53(1):1-9
Fcγ receptor III (FcγRIII), a low-affinity receptor for the Fc portion of immunoglobulin G (IgG Fc), targets antigen-antibody
complexes in a variety of effector cells of the immune system. We have investigated FcγRIII and IgG Fc polymorphism and made
comparative analysis of the functional and evolutionary implications of the interaction between these two molecules. Sequence
analysis and comparison of the three-dimensional structure suggest that the C-terminal Ig domain of FcγRIII is associated
with the binding of IgG. The polymorphic residues of FcγRIII are mainly located in the region of the C-terminal Ig domain
that might be involved in IgG binding. Therefore, polymorphism and functional binding affinity seems to be related to each
other as has been increasingly implicated in clinical observations. IgG Fcs, the natural ligand of FcγRs, also exhibit significant
polymorphism. Three regions have been identified where polymorphism frequently occurs: the putative FcR binding site, the
linker region, and the intermolecular domain-domain interface of the second Ig domain. The putative FcγR binding sites where
polymorphic, and isotype-specific residues cluster are consistent with the regions that have been identified by mutagenesis
and molecular modeling studies. The polymorphic residues of IgG Fc were mainly located in the molecular surface, which could
be used in the recognition of other binding molecules. These observations suggest that polymorphic and isotype-specific residues
in IgG Fc are closely related to their function and protein-protein interaction. Therefore, the colocalization of the polymorphic
residues of FcγRIII and IgG Fcs at their docking sites implies that the polymorphic residues would affect the IgG-FcγRIII
binding interactions to optimize their signaling through evolution.
Received: 9 December 1999 / Accepted: 15 February 2001 相似文献
11.
Molecular Evidence on the Evolutionary and Biogeographical Patterns of European Cyprinids 总被引:21,自引:0,他引:21
The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140
bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the
phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss
alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids
was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover,
the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa
(e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic
relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the
cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close
phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead,
the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence.
It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals
with low dispersal abilities, including fish, amphibians, and invertebrates.
Received: 2 February 1999 / Accepted: 16 March 1999 相似文献
12.
The chaetognaths are an extraordinarily homogeneous phylum of animals at the morphological level, with a bauplan that can
be traced back to the Cambrian. Despite the attention of zoologists for over two centuries, there is little agreement on classification
within the phylum. We have used a molecular biological approach to investigate the phylogeny of extant chaetognaths. A rapidly
evolving expansion segment toward the 5′ end of 28S ribosomal DNA (rDNA) was amplified using the polymerase chain reaction
(PCR), cloned, and sequenced from 26 chaetognath samples representing 18 species. An unusual finding was the presence of two
distinct classes of 28S rDNA gene in chaetognaths; our analyses suggest these arose by a gene (or gene cluster) duplication
in a common ancestor of extant chaetognaths. The two classes of chaetognath 28S rDNA have been subject to different rates
of molecular evolution; we present evidence that both are expressed and functional. In phylogenetic reconstructions, the two
classes of 28S rDNA yield trees that root each other; these clearly demonstrate that the Aphragmophora and Phragmophora are
natural groups. Within the Aphragmophora, we find good support for the groupings denoted Solidosagitta, Parasagitta, and Pseudosagitta. The relationships between several well-supported groups within the Aphragmophora are uncertain; we suggest this reflects
rapid, recent radiation during chaetognath evolution.
Received: 19 March 1996 / Accepted: 5 August 1996 相似文献
13.
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
14.
A heuristic approach to search for the maximum-likelihood (ML) phylogenetic tree based on a genetic algorithm (GA) has been
developed. It outputs the best tree as well as multiple alternative trees that are not significantly worse than the best one
on the basis of the likelihood criterion. These near-optimum trees are subjected to further statistical tests. This approach
enables ones to infer phylogenetic trees of over 20 taxa taking account of the rate heterogeneity among sites on practical
time scales on a PC cluster. Computer simulations were conducted to compare the efficiency of the present approach with that
of several likelihood-based methods and distance-based methods, using amino acid sequence data of relatively large (5–24)
taxa. The superiority of the ML method over distance-based methods increases as the condition of simulations becomes more
realistic (an incorrect model is assumed or many taxa are involved). This approach was applied to the inference of the universal
tree based on the concatenated amino acid sequences of vertically descendent genes that are shared among all genomes whose
complete sequences have been reported. The inferred tree strongly supports that Archaea is paraphyletic and Eukarya is specifically
related to Crenarchaeota. Apart from the paraphyly of Archaea and some minor disagreements, the universal tree based on these
genes is largely consistent with the universal tree based on SSU rRNA.
Received: 4 January 2001 / Accepted: 16 May 2001 相似文献
15.
16.
Ayako Yamamoto Tetsuo Hashimoto Emiko Asaga Masami Hasegawa Nobuichi Goto 《Journal of molecular evolution》1997,44(1):98-105
Major parts of amino-acid-coding regions of elongation factor (EF)-1α and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones
from each of the products of the EF-1α and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1α
coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of
the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long,
and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1α and EF-2 gene per chromosome were
estimated as four and two, respectively.
The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1α and 761 and 762 residues
from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1αs and EF-2s, respectively.
The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1α and EF-2 data sets. The EF-1α analysis suggested that
three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the
divergence of T. tenax to be immediately next to G. lamblia.
Received: 15 February 1996 / Accepted: 28 June 1996 相似文献
17.
A. Wiese M. Münstermann T. Gutsmann B. Lindner K. Kawahara U. Zähringer U. Seydel 《The Journal of membrane biology》1998,162(2):127-138
We have studied the interaction of the polycationic peptide antibiotic polymyxin B (PMB) with asymmetric planar bilayer membranes
via electrical measurements. The bilayers were of different compositions, including those of the lipid matrices of the outer
membranes of various species of Gram-negative bacteria. One leaflet, representing the bacterial inner leaflet, consisted of
a phospholipid mixture (PL; phosphatidylethanolamine, -glycerol, and diphosphatidylglycerol in a molar ratio of 81:17:2).
The other (outer) leaflet consisted either of lipopolysaccharide (LPS) from deep rough mutants of PMB-sensitive (Escherichia coli F515) or -resistant strains (Proteus mirabilis R45), glycosphingolipid (GSL-1) from Sphingomonas paucimobilis IAM 12576, or phospholipids (phosphatidylglycerol, diphytanoylphosphatidylcholine). In all membrane systems, the addition
of PMB to the outer leaflet led to the induction of current fluctuations due to transient membrane lesions. The minimal PMB
concentration required for the induction of the lesions and their size correlated with the charge of the lipid molecules.
In the membrane system resembling the lipid matrix of a PMB-sensitive strain (F515 LPS/PL), the diameters of the lesions were
large enough (d= 2.4 nm ± 8%) to allow PMB molecules to permeate (self-promoted transport), but in all other systems they were too small.
A comparison of these phenomena with membrane effects induced by detergents (dodecyltriphenylphosphonium bromide, dodecyltrimethylammonium
bromide, sodiumdodecylsulfate) revealed a detergent-like mechanism of the PMB-membrane interaction.
Received: 16 September 1997/Revised: 25 November 1997 相似文献
18.
19.
We have investigated the phylogenetic relationships of monotremes and marsupials using nucleotide sequence data from the
neurotrophins; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3). The study included
species representing monotremes, Australasian marsupials and placentals, as well as species representing birds, reptiles,
and fish. PCR was used to amplify fragments encoding parts of the neurotrophin genes from echidna, platypus, and eight marsupials
from four different orders. Phylogenetic trees were generated using parsimony analysis, and support for the different tree
structures was evaluated by bootstrapping. The analysis was performed with NGF, BDNF, or NT-3 sequence data used individually
as well as with the three neurotrophins in a combined matrix, thereby simultaneously considering phylogenetic information
from three separate genes. The results showed that the monotreme neurotrophin sequences associate to either therian or bird
neurotrophin sequences and suggests that the monotremes are not necessarily related closer to therians than to birds. Furthermore,
the results confirmed the present classification of four Australasian marsupial orders based on morphological characters,
and suggested a phylogenetic relationship where Dasyuromorphia is related closest to Peramelemorphia followed by Notoryctemorphia
and Diprotodontia. These studies show that sequence data from neurotrophins are well suited for phylogenetic analysis of mammals
and that neurotrophins can resolve basal relationships in the evolutionary tree.
Received: 27 January 1997 / Accepted: 20 March 1997 相似文献
20.
Madern D 《Journal of molecular evolution》2002,54(6):825-840
The NAD(P)-dependent malate (L-MalDH) and NAD-dependent lactate (L-LDH) form a large super-family that has been characterized
in organisms belonging to the three domains of life. In the first part of this study, the group of [LDH-like] L-MalDH, which
are malate dehydrogenases resembling lactate dehydrogenase, were analyzed and clearly defined with respect to the other enzymes.
In the second part, the phylogenetic relationships of the whole super-family were presented by taking into account the [LDH-like]
L-MalDH. The inferred tree unambiguously shows that two ancestral genes duplications, and not one as generally thought, are
needed to explain both the distribution into two enzymatic functions and the observation of three main groups within the super-family:
L-LDH, [LDH-like] L-MalDH, and dimeric L-MalDH. In addition, various cases of functional changes within each group were observed
and analyzed. The direction of evolution was found to always be polarized: from enzymes with a high stringency of substrate
recognition to enzymes with a broad substrate specificity. A specific phyletic distribution of the L-LDH, [LDH-like] L-MalDH,
and dimeric L-MalDH over the Archaeal, Bacterial, and Eukaryal domains was observed. This was analyzed in the light of biochemical,
structural, and genomic data available for the L-LDH, [LDH-like] L-MalDH, and dimeric L-MalDH. This analysis led to the elaboration
of a refined evolutionary scenario of the super-family, in which the selection of L-LDH and the fate of L-MalDH during mitochrondrial
genesis are presented. 相似文献