共查询到20条相似文献,搜索用时 15 毫秒
1.
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
2.
Pont-Kingdon G Vassort CG Warrior R Okimoto R Beagley CT Wolstenholme DR 《Journal of molecular evolution》2000,51(4):404-415
The 3231-nucleotide-pair (ntp) sequence of one end of one of the two linear mitochondrial (mt) DNA molecules of Hydra attenuata (phylum Cnidaria, class Hydrozoa, order Anthomedusae) has been determined. This segment contains complete genes for tRNAf-Met, l-rRNA, tRNATrp, subunit 2 of cytochrome c oxidase (COII), subunit 8 of ATP synthetase (ATPase8), and the 5′ 136 ntp of ATPase6. These genes are arranged in the order
given and are transcribed from the same strand of the molecule. As in two other cnidarians, the hexacorallian anthozoan Metridium senile and the octocorallian anthozoan Sarcophyton glaucum, the mt-genetic code of H. attenuata is near standard. The only modification appears to be that TGA specifies tryptophan rather than termination. Also as in M. senile and S. glaucum, the encoded H. attenuata mt-tRNAf-Met has primary and secondary structural features resembling those of Escherichia coli initiator tRNAt-Met. As the encoded mt-tRNATrp cannot be folded into a totally orthodox secondary structure, two alternative forms are suggested. The encoded H. attenuata mt-l-rRNA is 1738 nt, which is 451 nt shorter than the M. senile mt-l-rRNA. Comparisons of secondary structure models of these two mt-l-rRNAs indicate that most of the size difference results
from loss of nucleotides in the H. attenuata molecule at a minimum of 46 locations, which includes elimination of six distinct helical elements.
Received: 9 March 2000 / Accepted: 24 July 2000 相似文献
3.
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
4.
In the course of investigating mitochondrial genome organization in Crypthecodinium cohnii, a non-photosynthetic dinoflagellate, we identified four EcoRI fragments that hybridize to a probe specific for cox1, the gene that encodes subunit 1 of cytochrome oxidase. Cloning and sequence characterization of the four fragments (5.7,
5.1, 4.1, 3.5 kilobase pairs) revealed that cox1 exists in four distinct but related contexts in C. cohnii mtDNA, with a central repeat unit flanked by one of two possible upstream (flanking domain 1 or 2) and downstream (flanking
domain 3 or 4) regions. The majority of the cox1 gene is located within the central repeat; however, the C-terminal portion of the open reading frame extends into flanking
domains 3 and 4, thereby creating two distinct cox1 coding sequences. The 3′-terminal region of one of the cox1 reading frames can assume an elaborate secondary structure, which potentially could act to stabilize the mature mRNA against
nucleolytic degradation. In addition, a high density of small inverted repeats (15–22 base pairs) has been identified at the
5′-end of cox1, further suggesting that hairpin structures could be important for gene regulation. The organization of cox1 in C. cohnii mtDNA appears to reflect homologous recombination events within the central repeat between different cox1 sequence contexts. Such recombining repeats are a characteristic feature of plant (angiosperm) mtDNA, but they have not previously
been described in the mitochondrial genomes of protists.
Received: 21 December 2000 / Accepted: 30 January 2001 相似文献
5.
The complete nucleotide sequence of the mitochondrial genome was determined for a conger eel, Conger myriaster (Elopomorpha: Anguilliformes), using a PCR-based approach that employs a long PCR technique and many fish-versatile primers.
Although the genome [18,705 base pairs (bp)] contained the same set of 37 mitochondrial genes [two ribosomal RNA (rRNA), 22
transfer RNA (tRNA), and 13 protein-coding genes] as found in other vertebrates, the gene order differed from that recorded
for any other vertebrates. In typical vertebrates, the ND6, tRNAGlu, and tRNAPro genes are located between the ND5 gene and the control region, whereas the former three genes, in C. myriaster, have been translocated to a position between the control region and the tRNAPhe gene that are contiguously located at the 5′ end of the 12S rRNA gene in typical vertebrates. This gene order is similar
to the recently reported gene order in four lineages of birds in that the latter lack the ND6, tRNAGlu, and tRNAPro genes between the ND5 gene and the control region; however, the relative position of the tRNAPro to the ND6–tRNAGlu genes in C. myriaster was different from that in the four birds, which presumably resulted from different patterns of tandem duplication of gene
regions followed by gene deletions in two distantly related groups of organisms. Sequencing of the ND5–cyt b region in 11 other anguilliform species, representing 11 families, plus one outgroup species, revealed that the same gene
order as C. myriaster was shared by another 4 families, belonging to the suborder Congroidei. Although the novel gene orders of four lineages of
birds were indicated to have multiple independent origins, phylogenetic analyses using nucleotide sequences from the mitochondrial
12S rRNA and cyt b genes suggested that the novel gene orders of the five anguilliform families had originated in a single ancestral species.
Received: 13 July 2000 / Accepted: 30 November 2000 相似文献
6.
Margaret J. Beaton Andrew J. Roger Thomas Cavalier-Smith 《Journal of molecular evolution》1998,47(6):697-708
The nucleotide sequence for an 11,715-bp segment of the mitochondrial genome of the octocoral Sarcophyton glaucum is presented, completing the analysis of the entire genome for this anthozoan member of the phylum Cnidaria. The genome contained
the same 13 protein-coding and 2 ribosomal RNA genes as in other animals. However, it also included an unusual mismatch repair
gene homologue reported previously and codes for only a single tRNA gene. Intermediate in length compared to two other cnidarians
(17,443 and 18,911 bp), this organellar genome contained the smallest amount of noncoding DNA (428, compared to 1283 and 781
nt, respectively), making it the most compact one found for the phylum to date. The mitochondrial genes of S. glaucum exhibited an identical arrangement to that found in another octocoral, Renilla kolikeri, with five protein-coding genes in the same order as has been found in insect and vertebrate mitochondrial genomes. Although
gene order appears to be highly conserved among octocorals, compared to the hexacoral, Metridium senile, few similarities were found. Like other metazoan mitochondrial genomes, the A + T composition was elevated and a general
bias against codons ending in G or C was observed. However, an exception to this was the infrequent use of TGA compared to
TGG to code for tryptophan. This divergent codon bias is unusual but appears to be a conserved feature among two rather distantly
related anthozoans.
Received: 27 January 1998 / Accepted: 25 May 1998 相似文献
7.
A 8022 base pair fragment from the mitochondrial DNA of the prosobranch gastropod Littorina saxatilis has been sequenced and shown to contain the complete genes for 12 transfer RNAs and five protein genes (CoII, ATPase 6, ATPase
8, ND1, ND6), two partial protein genes (CoI and cyt b), and two ribosomal RNAs (small and large subunits). The order of these constituent genes differs from those of other molluscan
mitochondrial gene arrangements. Only a single rearrangement involving a block of protein coding genes and three tRNA translocations
are necessary to produce identical gene orders between L. saxatilis and K. tunicata. However, only one gene boundary is shared between the L. saxatilis gene order and that of the pulmonate gastropod Cepaea nemoralis. This extends the observation that there is little conservation of mitochrondrial gene order amongst the Mollusca and suggests
that radical mitochondrial DNA gene rearrangement has occurred on the branch leading to the pulmonates.
Received: 4 June 1998 / Accepted: 20 August 1998 相似文献
8.
Héctor Musto Héctor Romero Alejandro Zavala Giorgio Bernardi 《Journal of molecular evolution》1999,49(3):325-329
This paper analyses the compositional correlations that hold in the chicken genome. Significant linear correlations were
found among the regions studied—coding sequences (and their first, second, and third codon positions), flanking regions (5′
and 3′), and introns—as is the case in the human genome. We found that these compositional correlations are not limited to
global GC levels but even extend to individual bases. Furthermore, an analysis of 1037 coding sequences has confirmed a correlation
among GC3, GC2, and GC1. The implications of these results are discussed.
Received: 9 December 1998 / Accepted: 18 April 1999 相似文献
9.
The complete macronuclear DNA polymerase α gene, previously sequenced in Oxytricha nova, has been cloned from a genomic macronuclear library and sequenced for the hypotrich O. trifallax. Macronuclear DNA clones of DNA polymerase α encoding ∼1000 amino acids, or approximately two-thirds of the open reading frame,
have been obtained by PCR and sequenced for Halteria grandinella, Holosticha species, Paraurostyla viridis, Pleurotricha lanceolata, Stylonychia lemnae Teller, Sty. mytilus, Uroleptus gallina, and Urostyla grandis. Phylogenetic relationships inferred from DNA polymerase α amino acid sequences have been used to clarify taxonomic relationships
previously determined by morphology of the cell cortex. Hypotrich phylogenies based on DNA polymerase α amino acid sequences
are incongruent with morphological and other molecular phylogenies. Based upon these data, we assert that, contrary to morphological
data, O. nova and O. trifallax are different species, and we propose that the oligotrich Halteria grandinella be reclassified as a hypotrich. This work also extends the available data base of eukaryotic DNA polymerase α sequences,
and suggests new amino acid sequence targets for mutagenesis experiments to continue the functional dissection of DNA pol
α biochemistry at the molecular level.
Received: 7 January 1997 / Accepted: 7 April 1997 相似文献
10.
Sun L Li Y McCullough AK Wood TG Lloyd RS Adams B Gurnon JR Van Etten JL 《Journal of molecular evolution》2000,50(1):82-92
Large dsDNA-containing chlorella viruses encode a pyrimidine dimer-specific glycosylase (PDG) that initiates repair of UV-induced
pyrimidine dimers. The PDG enzyme is a homologue of the bacteriophage T4-encoded endonuclease V. The pdg gene was cloned and sequenced from 42 chlorella viruses isolated over a 12-year period from diverse geographic regions. Surprisingly,
the pdg gene from 15 of these 42 viruses contain a 98-nucleotide intron that is 100% conserved among the viruses and another 4 viruses
contain an 81-nucleotide intron, in the same position, that is nearly 100% identical (one virus differed by one base). In
contrast, the nucleotides in the pdg coding regions (exons) from the intron-containing viruses are 84 to 100% identical. The introns in the pdg gene have 5′-AG/GTATGT and 3′-TTGCAG/AA splice site sequences which are characteristic of nuclear-located, spliceosomal processed
pre-mRNA introns. The 100% identity of the 98-nucleotide intron sequence in the 15 viruses and the near-perfect identity of
an 81-nucleotide intron sequence in another 4 viruses imply strong selective pressure to maintain the DNA sequence of the
intron when it is in the pdg gene. However, the ability of intron-plus and intron-minus viruses to repair UV-damaged DNA in the dark was nearly identical.
These findings contradict the widely accepted dogma that intron sequences are more variable than exon sequences.
Received: 13 May 1999 / Accepted: 20 August 1999 相似文献
11.
The nearly complete nuclear large subunit ribosomal RNA (LSU rRNA) gene in corals was amplified by primers designed from
polymerase chain reaction (PCR) strategies. The motif of the putative 3′-terminus of the LSU rRNA gene was sequenced and identified
from intergenic spacer (IGS) clones obtained by PCR using universal primers designed for corals. The 3′-end primer was constructed
in tandem with the universal 5′-end primer for the LSU rRNA gene. PCR fragments of 3500 bp were amplified for octocorals and
non-Acropora scleractinian corals. More than 80% of the Acropora LSU rRNA gene (3000 bp) was successfully amplified by modification of the 5′-end of the IGS primer. Analysis of the 5′-end
of LSU rDNA sequences, including the D1 and D2 divergent domains, indicates that the evolutionary rate of the LSU rDNA differs
among these taxonomic groups of corals. The genus Acropora showed the highest divergence pattern in the LSU rRNA gene, and the presence of a long branch of the Acropora clade from the other scleractinian corals in the phylogenetic tree indicates that the evolutionary rate of Acropora LSU rDNA might have accelerated after divergence from the common ancestor of scleractinian corals.
Received February 17, 2000; accepted June 12, 2000. 相似文献
12.
The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs 总被引:7,自引:0,他引:7
The nucleotide sequence of the complete mitochondrial genome of the donkey, Equus asinus, was determined. The length of the molecule is 16,670 bp. The length, however, is not absolute due to pronounced heteroplasmy
caused by variable numbers of two types of repetitive motifs in the control region. The sequence of the repeats is (a) 5′-CACACCCA
and (b) 5′-TGCGCGCA, respectively. The order of (a) and (b) can be expressed as {n[2(a)+(b)]+m(a)}. In 32 different clones analyzed the number of n and m ranged from 0 to 9 and 1 to 7. The two rRNA genes, the 13 peptide-coding genes, and the 22 tRNA genes of the donkey and the
horse, Equus caballus, were compared in detail. Total nucleotide difference outside the control region was 6.9%. Nucleotide difference between peptide-coding
genes ranged from 6.4% to 9.4% with a mean of 8.0%. In the inferred protein sequences of the 13 peptide-coding genes the amino
acid difference was 0.2–8.8%, and the mean for the 13 concatenated amino acid sequences was 1.9%. In the 22 tRNA genes, the
mean difference was 3.5%, and that in the two rRNA genes was 4.1%. The mtDNA differences between the donkey and the horse
suggest that the evolutionary separation of the two species occurred ≈9 million years ago. Analyses of differences among the
mtDNAs of three other species-pairs, harbor seal/grey seal, fin whale/blue whale, and Homo/common chimpanzee, showed that the relative evolutionary rate of individual peptide-coding genes varies among different species-pairs
and modes of comparison. The findings show that the superimposition of sequence data of one lineage for resolving and dating
evolutionary divergences of other lineages should be performed with caution unless based on comprehensive data.
Received: 15 October 1995 / Accepted: 15 April 1996 相似文献
13.
Edward N. Trifonov Alla Kirzhner Valery M. Kirzhner Igor N. Berezovsky 《Journal of molecular evolution》2001,53(4-5):394-401
Evolution of proteins encoded in nucleotide sequences began with the advent of the triplet code. The chronological order
of the appearance of amino acids on the evolution scene and the steps in the evolution of the triplet code have been recently
reconstructed (Trifonov, 2000b) on the basis of 40 different ranking criteria and hypotheses. According to the consensus chronology,
the pair of complementary GGC and GCC codons for the amino acids alanine and glycine appeared first. Other codons appeared
as complementary pairs as well, which divided their respective amino acids into two alphabets, encoded by triplets with either
central purines or central pyrimidines: G, D, S, E, N, R, K, Q, C, H, Y, and W (Glycine alphabet G) and A, V, P, S, L, T, I, F, and M (Alanine alphabet A). It is speculated that the earliest polypeptide chains were very short, presumably of uniform length, belonging to two alphabet
types encoded in the two complementary strands of the earliest mRNA duplexes. After the fusion of the minigenes, a mosaic
of the alphabets would form. Traces of the predicted mosaic structure have been, indeed, detected in the protein sequences
of complete prokaryotic genomes in the form of weak oscillations with the period 12 residues in the form of alteration of
two types of 6 residue long units. The next stage of protein evolution corresponded to the closure of the chains in the loops
of the size 25–30 residues (Berezovsky et al., 2000). Autocorrelation analysis of proteins of 23 complete archaebacterial
and eubacterial genomes revealed that the preferred distances between valine, alanine, glycine, leucine, and isoleucine along
the sequences are in the same range of 25–30 residues, indicating that the loops are primarily closed by hydrophobic interactions
between the ends of the loops. The loop closure stage is followed by the formation of typical folds of 100–200 amino acids,
via end-to-end fusion of the genes encoding the loop-size chains. This size was apparently dictated by the optimal ring closure
for DNA. In both cases the closure into the ring (loop) rendered evolutionarily advantageous stability to the respective structures.
Further gene fusions lead to the formation of modern multidomain proteins. Recombinational gene splicing is likely to have
appeared after the DNA circularization stage.
Received: 21 December 2000 / Accepted: 28 February 2001 相似文献
14.
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
15.
The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering
based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of
the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were
exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology
to the cAMP-binding domains, and subsequently to the region delimited by β-strands 6 and 7 of the crystal structures of bovine
RIα and rat RIIβ (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally
the members of the PKA-R family. A single signature sequence, F–G–E–[LIV]–A–L–[LIMV]–x(3)–[PV]–R–[ANQV]–A, corresponding to
the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members
of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type
were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning
the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved
and are mostly located on the loop that connects α-helix B′ and β strand 7.
Received: 2 November 2000/Accepted: 14 June 2001 相似文献
16.
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
17.
Bocchetta M Gribaldo S Sanangelantoni A Cammarano P 《Journal of molecular evolution》2000,50(4):366-380
The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in
the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1α) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase β- and β′-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade
in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum
parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1α) and EF-G(2) data sets, which lack both resolution
and statistical robustness. In the EF analysis MP outperforms ML in discriminating (at the 0.05 level) trees having A. pyrophilus and T. maritima as the most basal lineages from competing alternatives that have (i) mesophiles, or the Thermus genus, as the deepest bacterial radiation and (ii) a monophyletic A. pyrophilus–T. maritima cluster situated at the base of the bacterial clade. RNAP-based phylogenies are equivocal with respect to the Aquifex and Thermotoga placements. The two hyperthermophiles fall basal to all other bacterial phyla when potential artifacts contributed by the
compositionally biased and fast-evolving Mycoplasma genitalium and Mycoplasma pneumoniae sequences are eschewed. However, the branching order of the phyla is tenuously supported in ML trees inferred by the exhaustive
search method and is unresolved in ML trees inferred by the quartet puzzling algorithm. A rooting of the RNA polymerase-subunit
tree at the mycoplasma level seen in both the MP trees and the ML trees reconstructed with suboptimal amino acid substitution
models is not supported by the EF-based phylogenies which robustly affiliate mycoplasmas with low-G+C gram-positives and,
most probably, reflects a ``long branch attraction' artifact.
Received: 22 September 1999 / Accepted: 11 January 2000 相似文献
18.
We conducted comprehensive sequence analysis of 5′ flanking regions of primate Alu elements. Information contents were computed and frequencies of 1024 pentanucleotides were measured to approximate the location
of a characteristic sequence and to specify its pattern(s), which may be involved in the integration of Alu elements into their host genomes. A large number of samples was used, the wide region of the 5′ end of Alu elements was analyzed, and comparisons were made among different subfamilies. Through our analyses, ``TTTTAAAAA' or ``(T)
m
(A)
n
' can be stated as a candidate for the characteristic sequence pattern, which resides around the region 5 to 20 base pairs
upstream of the 5′ end of Alu elements. This characteristic sequence pattern was more prominent in the sequences of younger Alus, which is a strong indication that the sequence pattern has a role at the time of Alu integration.
Received: 10 May 1999 / Accepted: 1 October 1999 相似文献
19.
We recently reported that ATP is released from Necturus erythrocytes via a conductive pathway during hypotonic swelling and that extracellular ATP potentiates regulatory volume
decrease (RVD). This study was designed to determine whether extracellular ATP exerts its effect via a purinoceptor. This
was accomplished using three different experimental approaches: 1) hemolysis studies to examine osmotic fragility, 2) a Coulter
counter to assess RVD, and 3) the whole-cell patch-clamp technique to measure membrane currents. We found extracellular ATP
and ATPγS, two P2 agonists, decreased osmotic fragility, enhanced cell volume recovery in response to hypotonic shock, and
increased whole-cell currents. In addition, 2-methylthio-ATP potentiated RVD. In contrast, UTP, α,β-methylene-ATP, and 2′-&
3′-O-(4-benzoyl-benzoyl) adenosine 5′-triphosphate and the P1 agonist adenosine had no effect regardless of experimental approach.
Furthermore, the P2 antagonist suramin increased osmotic fragility, inhibited RVD, and reduced whole-cell conductance in swollen
cells. Consistent with a previous study that indicated cell swelling activates a K+ conductance, suramin had no effect in the presence of gramicidin (a cationophore used to maintain a high K+ permeability). We also found the P2 antagonist pyridoxal-5-phosphate-6-azophenyl-2′4-disulfonic acid (PPADS) increased osmotic
fragility; however, reactive blue 2 and the P1 antagonists caffeine and theophylline had no effect. Our results show that
extracellular ATP activated a P2 receptor in Necturus erythrocytes during hypotonic swelling, which in turn potentiated RVD by stimulating K+ efflux. Pharmacological evidence suggested the presence of a P2X receptor subtype.
Received: 6 January 2001/Revised: 17 April 2001 相似文献
20.
Yuji Inagaki Yasuko Hayashi-Ishimaru Megumi Ehara Ikuo Igarashi Takeshi Ohama 《Journal of molecular evolution》1997,45(3):295-300
The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired
during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have
been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase
subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan
protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and
algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The
COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes,
but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes
and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host
cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts
are remnants of endosymbiotic algae.
Received: 24 March 1997 / Accepted: 21 April 1997 相似文献