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1.
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
2.
The Path from the RNA World 总被引:1,自引:0,他引:1
We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through
to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the
RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome
we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that
incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis
is transferred from RNA → RNP → protein, the first proteins in the ``breakthrough organism' (the first to have encoded protein
synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date
protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular
introns are older than the exons surrounding them, the ``introns-first' theory. Many features of the model for the genome
organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic
genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like' genome
organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism
RNA genome → eukaryotic-like DNA genome → prokaryotic-like DNA genome are all relatively straightforward, whereas the transition
prokaryotic-like genome → eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption
of the transition RNA → RNP → protein. A likely molecular mechanism, ``plasmid transfer,' is available for the origin of
prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and
derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection
for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.
Received: 14 January 1997 / Accepted: 19 May 1997 相似文献
3.
António M. Baptista Per Harald Jonson Edward Hough Steffen B. Petersen 《Journal of molecular evolution》1998,47(3):353-362
The trypsin family of serine proteases is one of the most studied protein families, with a wealth of amino acid sequence
information available in public databases. Since trypsin-like enzymes are widely distributed in living organisms in nature,
likely evolutionary scenarios have been proposed. A novel methodology for Fourier transformation of biological sequences (FOTOBIS)
is presented. The methodology is well suited for the identification of the size and extent of short repeats in protein sequences.
In the present paper the trypsin family of enzymes is analyzed with FOTOBIS and strong evidence for tandem gene duplication
is found. A likely evolutionary path for the development of present-day trypsins involved an intrinsic extensive tandem gene
duplication of a small DNA fragment of 15–18 nucleotides, corresponding to five or six amino acids. This ancestral trypsin
gene was subsequently duplicated, leading to the earliest version of a full-sized trypsin, from which the contemporary trypsins
have developed.
Received: 22 November 1997 / Accepted: 26 January 1998 相似文献
4.
Hiroyuki Satoh Naomi Inokuchi Yasuhiro Nagae Taro Okazaki 《Journal of molecular evolution》1999,49(1):122-129
The β-globin gene cluster of Wistar rat was extensively cloned and the embryonic genes were mapped and sequenced. Four overlapping
λ Dash recombinant clones cover about 31 kb and contain four nonadult β-globin genes, 5′–ε1–γ1–γ2–ψγ3–3′. The ε1 and γ2 are
active genes, since their protein products were detected in the fetal stage of the rat (Iwahara et al., J Biochem 119:360–366,
1996). The γ1 locus might be a pseudogene, since the ATA box in the promoter region is mutated to GTA; however, no other defect
is observed. The ψγ3 locus is a truncated pseudogene because a 19-base deletion, which causes a shift of the reading frame,
is observed between the second nucleotide of the putative codon 68 and codon 76. A sequence comparison suggests that the ψγ3
might be produced by a gene conversion event of the proto-γ-globin gene set. Possible histories of the evolution of rat nonadult
β-globin genes are discussed.
Received: 6 August 1998 / Accepted: 12 February 1999 相似文献
5.
A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA
gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly
within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is
likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA
gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely
to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
Received: 24 November 1997 / Accepted: 14 September 1998 相似文献
6.
Ronald W. DeBry 《Journal of molecular evolution》1998,46(3):355-360
Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published sequence from M. musculus shows that this gene has likely been a pseudogene throughout the evolution of the genus Mus, while the gene from Rattus norvegicus is likely functional. Three large (>20 bp) deletions were found among the Mus pseudogenes, a feature that is very unusual compared to surveys of processed pseudogenes. In addition, there are two single-base
deletions and one 4-bp insertion among the Mus pseudogenes. The species distributions of one of the large deletions and the 4-bp insertion require either independent insertions
of an identical sequence, independent deletions with identical boundaries, or a deletion followed by precise reintegration
of the original sequence. The evidence favors the hypothesis of multiple deletions with identical boundaries. The ``coding'
regions of the Mus pseudogenes show a much reduced level of among-species variability in the 3′ half of the pseudogene, compared both to the
5′ half and to flanking sequences. This supports a hypothesis that the 3′ end of the pseudogene is the target of frequent
gene conversion by functional H2a genes.
Received: 1 April 1997 / Accepted: 12 June 1997 相似文献
7.
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
8.
Geneviàve Pont-Kingdon Norichika A. Okada Jane L. Macfarlane C. Timothy Beagley Cristi D. Watkins-Sims Thomas Cavalier-Smith G. Desmond Clark-Walker David R. Wolstenholme 《Journal of molecular evolution》1998,46(4):419-431
The nucleotide sequences of two segments of 6,737 ntp and 258 ntp of the 18.4-kb circular mitochondrial (mt) DNA molecule
of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains
the 3′ 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome
b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5′ terminal 1,124 ntp of the gene for the large subunit rRNA (l-rRNA). These genes are arranged in the order given
and all are transcribed from the same strand of the molecule. The smaller segment contains the 3′ terminal 134 ntp of the
ND4 gene and a complete tRNAf-Met gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify
arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan
rather than termination. Also, as in M. senile the mt-tRNAf-Met gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and TψC loop sequences, and a mismatched nucleotide pair at the top of
the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity
in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast
Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of
the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an
MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.
Received: 13 January 1997 / Accepted: 23 September 1997 相似文献
9.
Peter E.M. Gibbs Werner F. Witke Achilles Dugaiczyk 《Journal of molecular evolution》1998,46(5):552-561
The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor.
From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise
to the vitamin D–binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin
(ALB) gene and a common precursor to α-fetoprotein (AFP) and α-albumin (ALF). This precursor itself duplicated about 250 Myr
ago, giving rise to the youngest family members, AFP and ALF. It should be possible to correlate these dates with the phylogenetic
distribution of members of the gene family among different species. All four genes are found in mammals, but AFP and ALF are
not found in amphibia, which diverged from reptiles about 360 Myr ago, before the divergence of the AFP-ALF progenitor from
albumin.
Although individual family members display an approximate clock-like evolution, there are significant deviations—the rates
of divergence for AFP differ by a factor of 7, the rates for ALB differ by a factor of 2.1. Since the progenitor of this gene
family itself arose by triplication of a smaller gene, the rates of evolution of individual domains were also calculated and
were shown to vary within and between family members. The great variation in the rates of the molecular clock raises questions
concerning whether it can be used to infer evolutionary time from contemporary sequence differences.
Received: 28 February 1995 / Accepted: 6 October 1997 相似文献
10.
Zoltán Szabó Simona A. Levi-Minzi Angela M. Christiano Carole Struminger Mark Stoneking Mark A. Batzer Charles D. Boyd 《Journal of molecular evolution》1999,49(5):664-671
Previous evidence has demonstrated the absence of exons 34 and 35 within the 3′ end of the human tropoelastin (ELN) gene.
These exons encode conserved polypeptide domains within tropoelastin and are found in the ELN gene in vertebrate species ranging
from chickens to rats to cows. We have analyzed the ELN gene in a variety of primate species to determine whether the absence
of exons 34 and 35 in humans either is due to allelic variation within the human population or is a general characteristic
of the Primates order. An analysis of the 3′ end of the ELN gene in several nonhuman primates and in 546 chromosomes from
humans of varying ethnic background demonstrated a sequential loss of exons 34 and 35 during primate evolution. The loss of
exon 35 occurred at least 35–45 million years ago, when Catarrhines diverged from Platyrrhines (New World monkeys). Exon 34 loss, in contrast, occurred only about 6–8 million years ago, when Homo separated from the common ancestor shared with chimpanzees and gorillas. Loss of both exons was probably facilitated by Alu-mediated
recombination events and possibly conferred a functional evolutionary advantage in elastic tissue.
Received: 6 July 1998 / Accepted: 18 February 1999 相似文献
11.
Mukhopadhyay D 《Journal of molecular evolution》2000,50(3):214-223
A serine protease inhibitor of the Kunitz-STI (soybean trypsin inhibitor) family, isolated from the legume seeds of winged
bean, was found to inhibit chymotrypsin at a 1:2 stoichiometric ratio. When the structure was determined in our laboratory,
it was found to form a characteristic β-trefoil fold, which is also seen in other proteins from distant families and sources.
The folding organization divides the protein into three approximately equal subdomains related by a pseudo-threefold axis
of symmetry passing parallel to the barrel axis of the trefoil. Following the now established idea that the present-day genes
originated from ancestral minigenes through evolution, the origin of the proteins having this β-trefoil organization is scrutinized
using its subdomain motif as the search probe. The results, based mainly on structural analyses, indicate the independent
existence of such a motif, mimicking the unknown ancestral protein(s) that might have been distributed in nature, not only
by gene duplication, but also by insertion and permutation in other folds. The understanding led to a hypothesis for the possible
origin of the Kunitz-STI family. On the basis of this model of evolution, structurally hypervariable regions were located
on the protein where mutations could be designed and a broad range of engineering of the protein's activity could be conceived.
Received: 20 January 1999 / Accepted: 6 October 1999 相似文献
12.
13.
Multiple phospholipase A2 (PLA2) isoenzymes found in a single snake venom induce a variety of pharmacological effects. These multiple forms are formed by
gene duplication and accelerated evolution of exons. We examined the amino acid sequences of 127 snake venom PLA2 enzymes and their homologues to study in which location most natural substitutions occur. Our data show that hot spots of
amino acid substitutions in this group of proteins occur mostly on the surface. A logistic model correlating the substitution
rates of each amino acid residue with their surface accessibility indicates that the probability of natural substitutions
occurring in the fully exposed residue is 2.6–3.5 times greater than that of substitutions occurring in buried residues. These
surface substitutions play a significant role in the evolution of new PLA2 isoenzymes by altering the specificity of targeting to various tissues or cells, resulting in distinct pharmacological effects.
Thus natural substitutions in PLA2 enzymes, in contrast to popular belief, are not random substitutions but appear to be directed toward modifying the molecular
surface.
Received: 11 May 1998 / Accepted: 29 June 1998 相似文献
14.
Calpains, the Ca2+-dependent intracellular proteinases, are involved in the regulation of distinct cellular pathways including signal transduction
and processing, cytoskeleton dynamics, and muscle homeostasis. To investigate the evolutionary origin of diverse calpain subfamilies,
a phylogenetic study was carried out. The topology of the calpain phylogenetic tree has shown that some of the gene duplications
occurred before the divergence of the protostome and deuterostome lineages. Other gene doublings, leading to vertebrate-specific
calpain forms, took place during early chordate evolution and coincided with genome duplications as disclosed by the localization
of calpain genes to paralogous chromosome regions in the human genome. On the basis of the phylogenetic tree, the time of
gene duplications, and the localization of calpain genes, we propose a model of tandem and chromosome duplications for the
evolution of vertebrate-specific calpain forms. The data presented here are consistent with scenarios proposed for the evolution
of other multigene families.
Received: 17 November 1998 / Accepted: 30 April 1999 相似文献
15.
16.
The aldo-keto reductase enzymes comprise a functionally diverse gene family which catalyze the NADPH-dependant reduction
of a variety of carbonyl compounds. The protein sequences of 45 members of this family were aligned and phylogenetic trees
were deduced from this alignment using the neighbor-joining and Fitch algorithms. The branching order of these trees indicates
that the vertebrate enzymes cluster in three groups, which have a monophyletic origin distinct from the bacterial, plant,
and invertebrate enzymes. A high level of conservation was observed between the vertebrate hydroxysteroid dehydrogenase enzymes,
prostaglandin F synthase, and ρ-crystallin of Xenopus laevis. We infer from the phylogenetic analysis that prostaglandin F synthase may represent a recent recruit to the eicosanoid biosynthetic
pathway from the hydroxysteroid dehydrogenase pathway and furthermore that, in the context of gene recruitment, Xenopus laevisρ-crystallin may represent a shared gene.
Received: 26 August 1996 / Accepted: 5 June 1997 相似文献
17.
Bujnicki JM 《Journal of molecular evolution》2000,50(1):39-44
To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments
have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the
first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates
of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic
analyses. It is shown that λ-exonuclease initially diverged from the common ancestor and then two ``endonucleolytic' families
branched out, separating ``blunt end cutters' from ``5′ four-base overhang cutters.' These data may contribute to a better
understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among
extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a
platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational
choice of homology modeling templates, and targets for protein engineering.
Received: 14 June 1999 / Accepted: 11 August 1999 相似文献
18.
The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid
protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this
organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal
genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes
for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI
cDNAs from E. gracilis possess short 5′ and 3′ untranslated transcribed sequences and lack a 3′ poly[A] tail.
The COI gene does not require uridine insertion/deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional,
and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [α-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3′ end structures of mRNAs, phylogenetic
analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes
of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using
nuclear ribosomal RNA sequences.
Received: 5 March 1996 / Accepted: 31 July 1996 相似文献
19.
20.
Emmanuel Mertens Uri S. Ladror Jennifer A. Lee Anya Miretsky Andrea Morris Catherine Rozario Robert G. Kemp Miklós Müller 《Journal of molecular evolution》1998,47(6):739-750
The pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate protist Trichomonas vaginalis has been purified. The enzyme is a homotetramer of about 50 kDa subunits and is not subject to allosteric regulation. The
protein was fragmented and a number of peptides were sequenced. Based on this information a PCR product was obtained from
T. vaginalis gDNA and used to isolate corresponding cDNA and gDNA clones. Southern analysis indicated the presence of five genes. One
open reading frame (ORF) was completely sequenced and for two others the 5′ half of the gene was determined. The sequences
were highly similar. The complete ORF corresponded to a polypeptide of about 46 kDa. All the peptide sequences obtained were
present in the derived sequences. The complete ORF was highly similar to that of other PFKs, primarily in its amino-terminal
half. The T. vaginalis enzyme was most similar to PPi-PFK of the mitochondriate heterolobosean, Naegleria fowleri. Most of the residues shown or assumed to be involved in substrate binding in other PPi-PFKs were conserved in the T. vaginalis enzyme. Direct comparison and phylogenetic reconstruction revealed a significant divergence among PPi-PFKs and related enzymes, which can be assigned to at least four distantly related groups, three of which contain enzymes
of protists. The separation of these groups is supported with a high percentage of bootstrap proportions. The short T. vaginalis PFK shares a most recent common ancestor with the enzyme from N. fowleri. This pair is clearly separated from a group comprising the long (>60-kDa) enzymes from Giardia lamblia, Entamoeba histolytica pfk2, the spirochaetes Borrelia burgdorferi and Trepomena pallidum, as well as the α- and β-subunits of plant PPi-PFKs. The third group (``X') containing protist sequences includes the glycosomal ATP-PFK of Trypanosoma brucei, E. histolytica pfk1, and a second sequence from B. burgdorferi. The fourth group (``Y') comprises cyanobacterial and high-G + C, Gram-positive eubacterial sequences. The well-studied PPi-PFK of Propionibacterium freudenreichii is highly divergent and cannot be assigned to any of these groups. These four groups are well separated from typical ATP-PFKs,
the phylogenetic analysis of which confirmed relationships established earlier. These findings indicate a complex history
of a key step of glycolysis in protists with several early gene duplications and possible horizontal gene transfers.
Received: 5 December 1997 / Accepted: 18 March 1998 相似文献