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1.
Two previously undetected domains were identified in a variety of RNA-binding proteins, particularly RNA-modifying enzymes,
using methods for sequence profile analysis. A small domain consisting of 60–65 amino acid residues was detected in the ribosomal
protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing
a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small
proteins that may be involved in translation regulation. Another novel domain, designated PUA domain, after PseudoUridine
synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine
synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial
rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous
to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly,
the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of
these enzymes in the regulation of the expression of other genes. We propose that the S4 domain and the PUA domain bind RNA
molecules with complex folded structures, adding to the growing collection of nucleic acid-binding domains associated with
DNA and RNA modification enzymes. The evolution of the translation machinery components containing the S4, PUA, and SUI1 domains
must have included several events of lateral gene transfer and gene loss as well as lineage-specific domain fusions.
Received: 15 May 1998 / Accepted: 20 July 1998 相似文献
2.
When divergence between viral species is large, the analysis and comparison of nucleotide or protein sequences are dependent
on mutation biases and multiple substitutions per site leading, among other things, to the underestimation of branch lengths
in phylogenetic trees. To avoid the problem of multiply substituted sites, a method not directly based on the nucleic or protein
sequences has been applied to retroviruses. It consisted of asking questions about genome structure or organization, and gene
function, the series of answers creating coded sequences analyzed by phylogenic software. This method recovered the principal
retroviral groups such as the lentiviruses and spumaviruses and highlighted questions and answers characteristic of each group
of retroviruses. In general, there was reasonable concordance between the coded genome methodology and that based on conventional
phylogeny of the integrase protein sequence, indicating that integrase was fixing mutations slowly enough to marginalize the
problem of multiple substitutions at sites. To a first approximation, this suggests that the acquisition of novel genetic
features generally parallels the fixation of amino acid substitutions.
Received: 18 May 2001 / Accepted: 7 September 2001 相似文献
3.
Patrick J. Babin Jan Bogerd Frank P. Kooiman Wil J. A. Van Marrewijk Dick J. Van der Horst 《Journal of molecular evolution》1999,49(1):150-160
Large lipid transfer proteins (LLTP) are nonexchangeable apolipoproteins and intracellular lipid-exchange proteins involved
in the assembly, secretion, and metabolism of lipoproteins. We have identified contiguous conserved sequence motifs in alignments
of insect apolipophorin II/I precursor (apoLp-II/I), human apolipoprotein B (apoB), invertebrate and vertebrate vitellogenins
(VTG), and the large subunit of mammalian microsomal triglyceride transfer protein (MTP). Conserved motifs present in the
N-terminal part of nonexchangeable apolipoproteins encompass almost completely the large subunit of MTP, suggesting a derivation
from a common ancestral functional unit, termed large lipid transfer (LLT) module. Divergence of LLTP from a common ancestor
is supported by (1) the statistical significance of the combined match scores obtained after motif-based database searches,
(2) the presence of several identical amino acid residues in all LLTP sequences currently available, (3) the conservation
of hydrophobic clusters in an α-helical domain, (4) the phylogenetic analysis of the conserved sequences related to the von
Willebrand factor D (VWD) module identified in nonexchangeable apolipoproteins, and (5) the presence of four and one ancestral
exon boundaries in the LLT and VWD modules, respectively. Our data indicate that the genes coding for apoLp-II/I, apoB, VTG,
and the MTP large subunit are members of the same multigene superfamily. LLTP have emerged from an ancestral molecule designed
to ensure a pivotal event in the intracellular and extracellular transfer of lipids and liposoluble substances.
Received: 8 June 1998 / Accepted: 15 February 1999 相似文献
4.
Vladimir V. Aleshin Irina A. Milyutina Olga S. Kedrova Natalia S. Vladychenskaya Nikolai B. Petrov 《Journal of molecular evolution》1998,47(5):597-605
Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates
were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the
closest to the coelomate animals. When phylogenetic trees were generated by different methods, the position of nematomorphs
appeared to be unstable. Inclusion of Enoplus brevis, a representative of a slowly evolving nematode lineage, in the set of analyzed species refutes the tree patterns, previously
derived from molecular data, where the nematodes appear as a basal bilateral lineage. The nematodes seem to be closer to the
coelomate animals than was speculated earlier. According to the results obtained, nematodes, nematomorphs, tardigrades, arthropods,
and cephalorhynchs are a paraphyletic association of closely related taxa.
Received: 1 December 1997 / Accepted: 9 April 1998 相似文献
5.
Structure and Origin of Ordered Lipid Domains in Biological Membranes 总被引:16,自引:0,他引:16
6.
Chemosensory transduction and adaptation are important aspects of signal transduction mechanisms in many cell types, ranging
from prokaryotes to differentiated tissues such as neurons. The eukaryotic ciliated protozoan, Tetrahymena thermophila, is capable of responding to both chemoattractants (O'Neill et al., 1985; Leick, 1992; Kohidai, Karsa & Csaba, 1994, 1995)
and chemorepellents (Francis & Hennessey, 1995; Kuruvilla, Kim & Hennessey, 1997). An example of a nontoxic, depolarizing
chemorepellent in Tetrahymena is extracellular lysozyme (Francis & Hennessey, 1995; Hennessey, Kim & Satir, 1995). Lysozyme is an effective chemorepellent
at micromolar concentrations, binds to a single class of externally facing membrane receptors and prolonged exposure (10 min)
produces specific chemosensory adaptation (Kuruvilla et al., 1997). We now show that this lysozyme response is initiated by
a depolarizing chemoreceptor potential in Tetrahymena and we have purified the membrane lysozyme receptor by affinity chromatography of solubilized Tetrahymena membrane proteins. The solubilized, purified protein is 42 kD and it exhibits saturable, high affinity lysozyme binding.
Polyclonal antibodies raised against this 42 kD receptor block the in vivo lysozyme chemoresponse. This is not only the first
time that a chemoreceptor potential has been recorded from Tetrahymena but also the first time that a chemorepellent receptor has been purified from any unicellular eukaryote.
Received: 28 July 1997/Revised: 14 November 1997 相似文献
7.
Grishin NV 《Journal of molecular evolution》1999,48(3):264-273
The reliable reconstruction of tree topology from a set of homologous sequences is one of the main goals in the study of
molecular evolution. If consistent estimators of distances from a multiple sequence alignment are known, the distance method
is attractive because the tree reconstruction is consistent. To obtain a distance estimate d, the observed proportion of differences p (p-distance) is usually ``corrected' for multiple and back substitutions by means of a functional relationship d=f(p). In this paper the conditions under which this correction of p-distances will not alter the selection of the tree topology are specified. When these conditions are not fulfilled the selection
of the tree topology may depend on the correction function applied. A novel method which includes estimates of distances not
only between sequence pairs, but between triplets, quadruplets, etc., is proposed to strengthen the proper selection of correction
function and tree topology. A ``super' tree that includes all tree topologies as special cases is introduced.
Received: 17 February 1998 / Accepted: 20 July 1998 相似文献
8.
9.
The Evolutionary History of Prosaposin: Two Successive Tandem-Duplication Events Gave Rise to the Four Saposin Domains in Vertebrates 总被引:1,自引:0,他引:1
Einat Hazkani-Covo Neta Altman Mia Horowitz Dan Graur 《Journal of molecular evolution》2002,54(1):30-34
Prosaposin is a multifunctional protein encoded by a single-copy gene. It contains four saposin domains (A, B, C, and D)
occurring as tandem repeats connected by linker sequences. Because the saposin domains are similar to one another, it is deduced
that they were created by sequential duplications of an ancestral domain. There are two types of evolutionary scenarios that
may explain the creation of the four-domain gene: (1) two rounds of tandem internal gene duplication and (2) three rounds
of duplications. An evolutionary and phylogenetic analysis of saposin DNA and amino acid sequences from human, mouse, rat,
chicken, and zebrafish indicates that the first evolutionary scenario is the most likely. Accordingly, an ancestral saposin-unit
duplication produced a two-domain gene, which, subsequently, underwent a second complete tandem duplication to give rise to
the present four-domain structure of the prosaposin gene.
Received: 8 February 2001 / Accepted: 29 June 2001 相似文献
10.
I. King Jordan Darren A. Natale Eugene V. Koonin Michael Y. Galperin 《Journal of molecular evolution》2001,53(6):622-633
Copper chaperones are small cytoplasmic proteins that bind intracellular copper (Cu) and deliver it to Cu-dependent enzymes
such as cytochrome oxidase, superoxide dismutase, and amine oxidase. Copper chaperones are similar in sequence and structure
to the Cu-binding heavy metal-associated (HMA) domains of Cu-transporting ATPases (Cu-ATPases), and the genes for copper chaperones
and Cu-ATPases are often located in the same operon. Phylogenetic analysis shows that Cu chaperones and HMA domains of Cu-ATPases
represent ancient and distinct lineages that have evolved largely independently since their initial separation. Copper chaperone–Cu-ATPase
operons appear to have evolved independently in different prokaryotic lineages, probably due to a strong selective pressure
for coexpression of these genes.
Received: 14 December 2000 / Accepted: 9 May 2001 相似文献
11.
Role of Actin Cytoskeleton in Regulation of Ion Transport: Examples from Epithelial Cells 总被引:5,自引:0,他引:5
Verkman AS 《The Journal of membrane biology》2000,178(2):73-87
The identification of molecular water transporters and the generation of transgenic mice lacking water transporting proteins
has created a need for accurate methods to measure water permeability. This review is focused on methodology to characterize
water permeability in living cells and complex multicellular tissues. The utility of various parameters defining water transport
is critically evaluated, including osmotic water permeability (P
f
), diffusional water permeability (P
d
), Arrhenius activation energies (E
a
), and solute reflection coefficients (σ
p
). Measurements in cellular and complex tissues can be particularly challenging because of uncertainties in barrier geometry
and surface area, heterogeneity in membrane transporting properties, and unstirred layer effects. Strategies to measure plasma
membrane P
f
in cell layers are described involving light scattering, total internal reflection fluorescence microscopy, confocal microscopy,
interferometry, spatial filtering microscopy, and volume-sensitive fluorescent indicators. Dye dilution and fluorescent indicator
methods are reviewed for measurement of P
f
across cell and tissue barriers. Novel fluorescence and gravimetric methods are described to quantify microvascular and epithelial
water permeabilities in intact organs, using as an example lungs from aquaporin knockout mice. Finally, new measurement strategies
and applications are proposed, including high-throughput screening for identification of aquaporin inhibitors.
Received: 3 August 1999/Revised: 22 September 1999 相似文献
12.
The mammalian immune system has cytotoxic mechanisms, both cellular and humoral, that destroy the membrane integrity of target
cells. The main effector molecules of these cytolytic mechanisms—perforin, used by killer lymphocytes, and the membrane attack
complex (MAC) components of the complement system—share a unique module called the MAC/perforin module. Until now, both immunological
cytotoxicity and the MAC/perforin module have been reported only in jawed vertebrates. Here, we report the identification
of a protein containing the MAC/perforin module from the invertebrate cephalochordate, amphioxus (Branchiostoma belcheri), using expressed sequence tag (EST) analysis of the notochord. The deduced amino acid sequence of this molecule is most
similar to the primary structure of human complement component C6 and is designated AmphiC6. AmphiC6 shares a unique modular
structure, including the MAC/perforin module, with human C6 and other MAC components. Another EST clone predicts the presence
of a thioester-containing protein with the closest structural similarity to vertebrate C3 (therefore designated AmphiC3).
AmphiC3 retains most of the functionally important residues of vertebrate C3 and is shown by phylogenetic analysis to be derived
directly from the common ancestor of vertebrate C3, C4, and C5. Only opsonic activity has been assigned to the invertebrate
complement system until now. Therefore, this is the first molecular evidence for complement-mediated immunological cytotoxicity
in invertebrates.
Received: 24 August 2001 / Accepted: 12 November 2001 相似文献
13.
14.
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all.
Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate
variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of
Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate
chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot
be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae
by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA
trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast
phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora)
have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
Received: 27 December 1999 / Accepted: 24 March 2000 相似文献
15.
16.
The hammerhead and the hairpin ribozymes of plant viroids/virusoids and the hepatitis delta ribozyme were generally considered
to be unrelated to one another. Here we report notable sequence interrelationships and some structural ones connecting all
three.
Received: 8 September 1999 / Accepted: 31 March 2000 相似文献
17.
Annexin homologues in the kingdoms of Planta and Protista were characterized by molecular sequence analysis to determine
their phylogenetic and structural relationship with annexins of Animalia. Sequence fragments from 19 plant annexins were identified
in sequence databases and composite sequences were also assembled from expressed sequence tags for Arabidopsis thaliana. Length differences in protein amino-termini and evidence for unique exon splice sites indicated that plant annexins were
distinct from those of animals. A third annexin gene of Giardia lamblia (Anx21-Gla) was identified as a distant relative to other protist annexins and to those of higher eukaryotes, thus providing a suitable
outgroup for evolutionary reconstruction of the family tree. Rooted evolutionary trees portrayed protist, plant, and Dictyostelium annexins as early, monophyletic ramifications prior to the appearance of closely related animal annexin XIII. Molecular phylogenetic
analyses of DNA and protein sequence alignments revealed at least seven separate plant subfamilies, represented by Anx18 (alfalfa, previously classified), Anx22 (thale cress), Anx23 (thale cress, cotton, rape and cabbage), Anx24 (bell pepper and tomato p34), Anx25 (strawberry, horseradish, pea, soybean, and castor bean), Anx26-Zma, and Anx27-Zma (maize). Other unique subfamilies may exist for rice, tomato p35, apple, and celery annexins. Consensus sequences compiled
for each eukaryotic kingdom showed some breakdown of the ``annexin-fold' motif in repeats 2 and 3 of protist and plant annexins
and a conserved codon deletion in repeat 3 of plants. The characterization of distinct annexin genes in plants and protists
reflects their comparable diversity among animal species and offers alternative models for the comparative study of structure–function
relationships within this important gene family.
Received: 30 May 1996 / Accepted: 20 August 1996 相似文献
18.
Structure and Functions of Channel-Forming Peptides: Magainins,Cecropins, Melittin and Alamethicin 总被引:26,自引:0,他引:26
B. Bechinger 《The Journal of membrane biology》1997,156(3):197-211
19.
Phylogenetic Studies of Complete Mitochondrial DNA Molecules Place Cartilaginous Fishes Within the Tree of Bony Fishes 总被引:1,自引:0,他引:1
It is commonly acknowledged that cartilaginous fishes, Chondrichthyes, have a basal position among the Gnathostomata (jawed
vertebrates). In order to explore this relationship we have sequenced the complete mitochondrial genome of the spiny dogfish,
Squalus acanthias, and included it in a phylogenetic analysis together with a number of bony fishes and amniotes. The phylogenetic reconstructions
placed the dogfish among the bony fishes. Thus, and contrary to the common view, the analyses have shown that the position
of the sharks is not basal among the gnathostomes. The presently recognized phylogenetic position of the dogfish was identified
irrespective of the outgroup used, echinoderms or agnathan fishes. The lungfish was the most basal gnathostome fish, while
the teleosteans had an apical position in the piscine tree. A basal position of the dogfish among the gnathostomes was statistically
rejected, but the phylogenetic relationship among the coelacanth, spiny dogfish, and teleosts was not conclusively resolved.
The findings challenge the current theory that sharks and other chondrichthyans, if monophyletic, are the sister group to
all other extant gnathostomes. The results open to question the status of several morphological characters commonly used in
piscine phylogenetic reconstruction, most notably the presence versus absence of endochondral bone in the endoskeleton, the
macromeric versus micromeric structure of the exoskeleton, and the presence/absence of swimbladder and/or lung. The study
also confirmed recent findings demonstrating that the origin of the amniotes is deeper than the diversification of extant
bony fishes.
Received: 12 March 1998 / Accepted: 12 June 1998 相似文献
20.
Intracellular Domains of Mouse Connexin26 and -30 Affect Diffusional and Electrical Properties of Gap Junction Channels 总被引:5,自引:0,他引:5
D. Manthey K. Banach T. Desplantez C.G. Lee C.A. Kozak O. Traub R. Weingart K. Willecke 《The Journal of membrane biology》2001,181(2):137-148
To evaluate the influence of intracellular domains of connexin (Cx) on channel transfer properties, we analyzed mouse connexin
(Cx) Cx26 and Cx30, which show the most similar amino acid sequence identities within the family of gap junction proteins.
These connexin genes are tightly linked on mouse chromosome 14. Functional studies were performed on transfected HeLa cells
stably expressing both mouse connexins. When we examined homotypic intercellular transfer of microinjected neurobiotin and
Lucifer yellow, we found that gap junctions in Cx30-transfected cells, in contrast to Cx26 cells, were impermeable to Lucifer
yellow. Furthermore, we observed heterotypic transfer of neurobiotin between Cx30-transfectants and HeLa cells expressing
mouse Cx30.3, Cx40, Cx43 or Cx45, but not between Cx26 transfectants and HeLa cells of the latter group. The main differences
in amino acid sequence between Cx26 and Cx30 are located in the presumptive cytoplasmic loop and C-terminal region of these
integral membrane proteins. By exchanging one or both of these domains, using PCR-based mutagenesis, we constructed Cx26/30
chimeric cDNAs, which were also expressed in HeLa cells after transfection. Homotypic intercellular transfer of injected Lucifer
yellow was observed exclusively with those chimeric constructs that coded for both cytoplasmic domains of Cx26 in the Cx30
backbone polypeptide chain. In contrast, cells transfected with a construct that coded for the Cx26 backbone with the Cx30
cytoplasmic loop and C-terminal region did not show transfer of Lucifer yellow. Thus, Lucifer yellow transfer can be conferred
onto chimeric Cx30 channels by exchanging the cytoplasmic loop and the C-terminal region of these connexins. In turn, the
cytoplasmic loop and C-terminal domain of Cx30 prevent Lucifer yellow transfer when swapped with the corresponding domains
of Cx26. In chimeric Cx30/Cx26 channels where the cytoplasmic loop and C-terminal domains had been exchanged, the unitary
channel conductance was intermediate between those of the parental channels. Moreover, the voltage sensitivity was slightly
reduced. This suggests that these cytoplasmic domains interfere directly or indirectly with the diffusivity, the conductance
and voltage gating of the channels.
Received: 26 July 2000/Revised: 15 February 2001 相似文献