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1.
2.
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
3.
Characterization of Repetitive DNA Elements in Arabidopsis 总被引:1,自引:0,他引:1
We have applied computational methods to the available database and identified several families of repetitive DNA elements
in the Arabidopsis thaliana genome. While some of the elements have features expected of either miniature inverted-repeat transposable elements (MITEs)
or retrotransposons, the most abundant class of repetitive elements, the AthE1 family, is structurally related to neither. The AthE1 family members are defined by conserved 5′ and 3′ sequences, but these terminal sequences do not represent either inverted
or direct repeats. AthE1 family members with greater than 98% identity are easily identified on different Arabidopsis chromosomes. Similar to nonautonomous DNA-based transposon families, the AthE1 family contains members in which the conserved terminal domains flank unrelated sequences. The primary utility of characterizing
repetitive sequences is in defining, at least in part, the evolutionary architecture of specific Arabidopsis loci. The repetitive elements described here make up approximately 1% of the available Arabidopsis thaliana genomic sequence.
Received: 13 October 1998 / Accepted: 30 December 1998 相似文献
4.
5.
Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances
sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization
protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5′ end of the sperm
bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of
the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates
moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible
to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide
substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald
and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms
observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting
that the polymorphism observed in the 5′ region of S. franciscanus bindin is a result of neutral evolution.
Received: 19 June 1998 / Accepted: 2 August 2000 相似文献
6.
Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine–adenine dinucleotides
(ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we
counted frequencies of ApA dinucleotides at each downstream position within 50 bp from every ApA. We found that the complete
genomes of all three archaebacteria have clear ApA periodicities of about 10 bps. On the other hand, all of the 13 eubacteria
we analyzed were found to have an ApA periodicity of about 11 bp. Similar periodicities exist in the 10 eukaryotes, although
higher organisms such as primates tend to have weaker periodic patterns. None of the mitochondria and chroloplasts we analyzed
showed an evident periodic pattern.
Received: 3 November 1998 / Accepted: 24 March 1999 相似文献
7.
Kazuhiko Takahashi Mutsumi Nishida Masahide Yuma Norihiro Okada 《Journal of molecular evolution》2001,53(4-5):496-507
Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation.
To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed
repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically
inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another
locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with
the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating
that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized
a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna
species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be
occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular
when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.
Received: 15 December 2000 / Accepted: 30 January 2001 相似文献
8.
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
9.
Kazuhisa Tsunoyama Matthew I. Bellgard Takashi Gojobori 《Journal of molecular evolution》2001,53(4-5):456-464
It has been observed that synonymous substitution rates vary among genes in various organisms, although the cause of the
variation is unresolved. At the intragenic level, however, the variation of synonymous substitutions is somewhat controversial.
By developing a rigorous statistical test and applying the test to 418 homologous gene pairs between mouse and rat, we found
that more than 90% of gene pairs showed a statistical significance in intragenic variation of synonymous substitution rates.
Moreover, by examining all conceivable possibilities for the cause of the variation, we successfully found that intragenic
variation of synonymous substitutions in mammalian genes is caused mainly by a nonrandom mutation due to the methylation of
CpG dinucleotides rather than by functional constraints.
Received: 12 January 2001 / Accepted: 28 February 2001 相似文献
10.
Isaäc J. Nijman Patrick van Tessel Johannes A. Lenstra 《Journal of molecular evolution》2002,54(1):9-16
SINE retrotransposition events have proven their value as phylogenetic markers in several eukaryotic taxa at different taxonomic
levels. The genomes of ruminants contain three related SINE elements, Bov-tA, Bov-A2, and Bov-B. To estimate the time points
of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions
in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked
by sequencing whether length variation of the PCR products reflected a SINE retrotransposition. One Bov-B and nine Bov-tA
insertions were shared by cattle, sheep, goat, and giraffe, indicating an early retrotransposition event before the radiation
of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant α-lactalbumine
gene contains a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacement as well as a recent Bov-B insertion.
Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison species, respectively, indicating that most Bov-A2 insertions are relatively recent. The time elapsed since the retrotransposition
was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest that retrotransposition of
SINEs may serve as phylogenetic markers in the ruminant families, subfamilies, and even tribes. In addition, sequencing of
SINE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions
of ruminants.
Received: 19 January 2001 / Accepted: 6 June 2001 相似文献
11.
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
12.
Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one
or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual,
highly conserved, elements of the B1 SINE family were identified from the GenBank nucleotide database using various B1 subfamily
consensus query sequences to determine their integration times into the mouse genome. A comparison of orthologous loci in
various species of the genus Mus demonstrated that four subfamilies of B1 elements have been amplifying within the last 1–3 million years. Therefore, B1 sequences
are generated by coexisting source genes. Additionally, three B1 subfamilies have been concurrently propagated during subspecies
divergence and strain formation in Mus, indicating very recent activity of this retroposon family. The patterns of intra- and interspecies variations of orthologous
loci demonstrate the usefulness of B1 integrations as a phylogenetic tool. A single inconsistency in the phylogenetic trends
was depicted by the presence of a B1 insert in an orthologous locus exclusively in M. musculus and M. pahari. However, DNA sequence analysis revealed that these were independent integrations at the same genomic site. One highly conserved
B1 element that integrated at least 4–6 million years ago suggests the possibility of occasional function for B1 integrations.
Received: 25 February 2000 / Accepted: 5 June 2000 相似文献
13.
How thyroid hormones move across biological or model membranes is a subject of controversy. The passage of the 3,5,3′triiodo
l-thyronine and 3,5,3′,5′ tetraiodo l-thyronine across model membranes was evaluated by the addition of the hormones to liposomes containing 2,4,6-trinitrobenzene
sulfonic acid. Results indicate that hormones can react with an amino-reactive compound pre-encapsulated into phosphatidylcholine
liposomes. The transversal motions of thyroid hormones were characterized by using physiological concentration levels of (125I) 3,5,3′triiodo l-thyronine and (125I) 3,5,3′,5′ tetraiodo l-thyronine. The hormone distribution between the two monolayers was time-dependent and kinetic data were fitted to a single
exponential. Results obtained show that 3,5,3′ triiodo l-thyronine can permeate phospholipid membranes and the diffusion time increases in the gel and liquid-ordered phase. On the
contrary, 3,5,3′, 5′ tetraiodo l-thyronine could not diffuse the liposomal membrane from dimyristoyl and dipalmitoyl phosphatidylcholine in gel phase and
egg yolk phosphatidylcholine:cholesterol in the liquid-ordered phase. Our results in the liquid-ordered phase suggest that
diffusion movement of thyroid hormones across cell membranes depends on the amount of cholesterol in the bilayer.
Received: 1 June 1998/Revised: 14 October 1998 相似文献
14.
15.
Boris V. Skryabin Joachim Kremerskothen Dido Vassilacopoulou Todd R. Disotell Vladimir V. Kapitonov Jerzy Jurka Jürgen Brosius 《Journal of molecular evolution》1998,47(6):677-685
The gene encoding BC200 RNA arose from a monomeric Alu element. Subsequently, the RNA had been recruited or exapted into
a function of the nervous system. Here we confirm the presence of the BC200 gene in several primate species among the Anthropoidea.
The period following the divergence of New World monkeys and Old World monkeys from their common ancestor is characterized
by a significantly higher substitution rate in the examined 5′ flanking region than in the BC200 RNA coding region itself.
Furthermore, the conservation of CpG dimers in the RNA coding region (200 bp) is drastically increased compared to the 5′
flanking region (∼400 bp) over all 12 species examined. Finally, the brain-specific expression pattern of BC200 RNA and its
presence as a ribonucleoprotein particle (RNP) are conserved in Old World and New World monkeys. Our studies indicate that
the gene encoding BC200 RNA was created at least 35–55 million years ago and its presence, mode of expression, and association
with protein(s) as an RNP are under selective pressure.
Received: 1 December 1997 / Accepted: 3 June 1998 相似文献
16.
Quantitative analyses were carried out on a large number of proteins that contain the highly conserved basic helix–loop–helix
domain. Measures derived from information theory were used to examine the extent of conservation at amino acid sites within
the bHLH domain as well as the extent of mutual information among sites within the domain. Using the Boltzmann entropy measure,
we described the extent of amino acid conservation throughout the bHLH domain. We used position association (pa) statistics that reflect the joint probability of occurrence of events to estimate the ``mutual information content' among
distinct amino acid sites. Further, we used pa statistics to estimate the extent of association in amino acid composition at each site in the domain and between amino acid
composition and variables reflecting clade and group membership, loop length, and the presence of a leucine zipper. The pa values were also used to describe groups of amino acid sites called ``cliques' that were highly associated with each other.
Finally, a predictive motif was constructed that accurately identifies bHLH domain-containing proteins that belong to Groups
A and B.
Received: 15 December 1997 / Accepted: 1 October 1998 相似文献
17.
J. Hinrich G.v.d. Schulenburg Ulrike Englisch J.-Wolfgang Wägele 《Journal of molecular evolution》1999,48(1):2-12
A comparison of ribosomal internal transcribed spacer 1 (ITS1) elements of digenetic trematodes (Platyhelminthes) including
unidentified digeneans isolated from Cyathura carinata (Crustacea: Isopoda) revealed DNA sequence similarities at more than half of the spacer at its 3′ end. Primary sequence similarity
was shown to be associated with secondary structure conservation, which suggested that similarity is due to identity by descent
and not chance. Using an analysis of apomorphies, the sequence data were shown to produce a distinct phylogenetic signal.
This was confirmed by the consistency of results of different tree reconstruction methods such as distance approaches, maximum
parsimony, and maximum likelihood. Morphological evidence additionally supported the phylogenetic tree based on ITS1 data
and the inferred phylogenetic position of the unidentified digeneans of C. carinata met the expectations from known trematode life-cycle patterns. Although ribosomal ITS1 elements are generally believed to
be too variable for phylogenetic analysis above the species or genus level, the overall consistency of the results of this
study strongly suggests that this is not the case in digenetic trematodes. Here, 3′ end ITS1 sequence data seem to provide
a valuable tool for elucidating phylogenetic relationships of a broad range of phylogenetically distinct taxa.
Received: 20 October 1997 / Accepted: 24 March 1998 相似文献
18.
The dependence of currents through the cyclic nucleotide-gated (CNG) channels of mammalian olfactory receptor neurons (ORNs)
on the concentration of NaCl was studied in excised inside-out patches from their dendritic knobs using the patch-clamp technique.
With a saturating concentration (100 μm) of adenosine 3′, 5′-cyclic monophosphate (cAMP), the changes in the reversal potential of macroscopic currents were studied
at NaCl concentrations from 25 to 300 mm. In symmetrical NaCl solutions without the addition of divalent cations, the current-voltage relations were almost linear,
reversing close to 0 mV. When the external NaCl concentration was maintained at 150 mm and the internal concentrations were varied, the reversal potentials of the cAMP-activated currents closely followed the
Na+ equilibrium potential indicating that P
Cl/P
Na≈ 0. However, at low external NaCl concentrations (≤100 mm) there was some significant chloride permeability. Our results further indicated that Na+ currents through these channels: (i) did not obey the independence principle; (ii) showed saturation kinetics with K
ms in the range of 100–150 mm and (iii) displayed a lack of voltage dependence of conductance in asymmetric solutions that suggested that ion-binding sites
were situated midway along the channel. Together, these characteristics indicate that the permeation properties of the olfactory
CNG channels are significantly different from those of photoreceptor CNG channels.
Received: 7 November 1996/Revised: 24 March 1997 相似文献
19.
Albert Jeltsch 《Journal of molecular evolution》1999,49(1):161-164
Circular permutations of genes during molecular evolution often are regarded as elusive, although a simple model can explain
these rearrangements. The model assumes that first a gene duplication of the precursor gene occurs in such a way that both
genes become fused in frame, leading to a tandem protein. After generation of a new start codon within the 5′ part of the
tandem gene and a stop at an equivalent position in the 3′ part of the gene, a protein is encoded that represents a perfect
circular permutation of the precursor gene product. The model is illustrated here by the molecular evolution of adenine-N6 DNA methyltransferases. β- and γ-type enzymes of this family can be interconverted by a single circular permutation event.
Interestingly, tandem proteins, proposed as evolutionary intermediates during circular permutation, can be directly observed
in the case of adenine methyltransferases, because some enzymes belonging to type IIS, like the FokI methyltransferase, are built up by two fused enzymes, both of which are active independently of each other. The mechanism
for circular permutation illustrated here is very easy and applicable to every protein. Thus, circular permutation can be
regarded as a normal process in molecular evolution and a changed order of conserved amino acid motifs should not be interpreted
to argue against divergent evolution.
Received: 17 November 1998 / Accepted: 19 February 1999 相似文献
20.
Steven T. Case Carol Cox Walter C. Bell Rosemary T. Hoffman Jon Martin Robert Hamilton 《Journal of molecular evolution》1997,44(4):452-462
Aquatic larvae of the midge, Chironomus tentans, synthesize a 185-kDa silk protein (sp185) with the cysteine-containing motif Cys-X-Cys-X-Cys (where X is any residue) every
20–28 residues. We report here the cloning and full-length sequence of cDNAs encoding homologous silk proteins from Chironomus pallidivittatus (sp185) and Chironomus thummi (sp220). Deduced amino acid sequences reveal proteins of nearly identical mass composed of 72 blocks of 20–28 residues, 61%
of which can be described by the motif X5–8-Cys-X5-(Trp/Phe/Tyr)-X4-Cys-X-Cys-X-Cys. Spatial arrangement of these residues is preserved more than surrounding sequences. cDNA clones enabled
us to map the genes on polytene chromosomes and identify for the first time the homolog of the Camptochironomus Balbiani ring 3 locus in Chironomus thummi. The apparent molecular weight difference between these proteins (185 vs 220 kDa) is not attributable to primary structure
and may be due to differential N-linked glycosylation. DNA distances and codon substitutions indicate that the C. tentans and C. pallidivittatus genes are more related to each other than either is to C. thummi; however, substitution rates for the 5′- and 3′-halves of these genes are different. Blockwise sequence comparisons suggest
intragenic variation in that some regions evolved slower or faster than the mean and may have been subjected to different
selective pressures.
Received: 30 August 1996 / Accepted: 6 November 1996 相似文献