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1.
The immunoglobulin superfamily (IgSF) is a heterogenic group of proteins built on a common fold, called the Ig fold, which
is a sandwich of two β sheets. Although members of the IgSF share a similar Ig fold, they differ in their tissue distribution,
amino acid composition, and biological role.
In this paper we report an up-to-date compilation of the IgSF where all known members of the IgSF are classified on the basis
of their common functional role (immune system, antibiotic proteins, enzymes, cytokine receptors, etc.) and their distribution
in tissue (neural system, extracellular matrix, tumor marker, muscular proteins, etc.), or in species (vertebrates, invertebrates,
bacteria, viruses, fungi, and plants). The members of the family can contain one or many Ig domains, comprising two basic
types: the constant domain (C), with seven strands, and the variable domain (V), with eight, nine, or ten strands. The different
overviews of the IgSF led to the definition of new domain subtypes, mainly concerning the C type, based on the distribution
of strands within the two sheets.
The wide occurrence of the Ig fold and the much less conserved sequences could have developed from a common ancestral gene
and/or from a convergent evolutionary process. Cell adhesion and pattern recognition seem to be the common feature running
through the entire family.
Received: 4 June 1997 / Accepted: 15 September 1997 相似文献
2.
The AAA proteins (ATPases Associated with a variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and participate in a large number of cellular
processes, including protein degradation, vesicle fusion, cell cycle control, and cellular secretory processes. The AAA proteins
are characterized by the presence of a 230 to 250-amino acid ATPase domain referred to as the Conserved ATPase Domain or CAD. Phylogenetic analysis of 133 CAD sequences from 38 species reveal that AAA CADs are organized into discrete
groups that are related not only in structure but in cellular function. Evolutionary analyses also indicate that the CAD was
present in the last common ancestor of eubacteria, archaebacteria, and eukaryotes. The eubacterial CADs are found in metalloproteases,
while CAD-containing proteins in the archaebacterial and eukaryotic lineages appear to have diversified by a series of gene
duplication events that lead to the establishment of different functional AAA proteins, including proteasomal regulatory,
NSF/Sec, and Pas proteins. The phylogeny of the CADs provides the basis for establishing the patterns of evolutionary change
that characterize the AAA proteins.
Received: 28 January 1997 / Accepted: 8 May 1997 相似文献
3.
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
4.
Satoru Kanai Hiroyuki Toh Toshiya Hayano Masakazu Kikuchi 《Journal of molecular evolution》1998,47(2):200-210
Protein disulfide isomerase (PDI) is an enzyme that promotes protein folding by catalyzing disulfide bridge isomerization.
PDI and its relatives form a diverse protein family whose members are characterized by thioredoxin-like (TX) domains in the
primary structures. The family was classified into four classes by the number and the relative positions of the TX domains.
To investigate the evolution of the domain structures, we aligned the amino acid sequences of the TX domains, and the molecular
phylogeny was examined by the NJ and ML methods. We found that all of the current members of the PDI family have evolved from
an ancestral enzyme, which has two TX domains in the primary structure. The diverse domain structures of the members have
been generated through domain duplications and deletions. 相似文献
5.
Christiane Elie Marie- France Baucher Christian Fondrat Patrick Forterre 《Journal of molecular evolution》1997,45(1):107-114
We have isolated a new gene encoding a putative 103-kDa protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Analysis of the deduced amino-acid sequence shows an extended central domain, predicted to form coiled-coil structures, and
two terminal domains that display purine NTPase motifs. These features are reminiscent of mechanochemical motor proteins which
use the energy of ATP hydrolysis to move specific cellular components. Comparative analysis of the amino-acid sequence of
the terminal domains and predicted structural organization of this putative purine NTPase show that it is related both to
eucaryal proteins from the ``SMC family' involved in the condensation of chromosomes and to several bacterial and eucaryal
proteins involved in DNA recombination/repair. Further analyses revealed that these proteins are all members of the so called
``UvrA-related NTP-binding proteins superfamily' and form a large subgroup of motor-like NTPases involved in different DNA
processing mechanisms. The presence of such protein in Archaea, Bacteria, and Eucarya suggests an early origin of DNA-motor
proteins that could have emerged and diversified by domain shuffling.
Received: 29 June 1996 / Accepted: 28 February 1997 相似文献
6.
Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA 总被引:10,自引:0,他引:10
Miguel A. Aranda Aurora Fraile Joaquín Dopazo José M. Malpica Fernando García-Arenal 《Journal of molecular evolution》1997,44(1):81-88
The nucleotide sequence of 17 variants of the satellite RNA of cucumber mosaic virus (CMV-satRNA) isolated from field-infected
tomato plants in the springs of 1989, 1990, and 1991 was determined. The sequence of each of the 17 satRNAs was unique and
was between 334 and 340 nucleotides in length; 57 positions were polymorphic. There was much genetic divergence, ranging from
0.006 to 0.141 nucleotide substitutions per site for pairwise comparisons, and averaging 0.074 for any pair. When the polymorphic
positions were analyzed relative to a secondary structure model proposed for CMV-satRNAs, it was found that there were significantly
different numbers of changes in base-paired and non–base-paired positions, and that mutations that did not disrupt base pairing
were preferred at the putatively paired sites. This supports the concept that the need to maintain a functional structure
may limit genetic divergence of CMV-satRNA. Phylogenetic analyses showed that the 17 CMV-satRNA variants clustered into two
subgroups, I and II, and evolutionary lines proceeding by the sequential accumulation of mutations were apparent. Three satRNA
variants were outliers for these two phylogenetic groups. They were shown to be recombinants of subgroup I and II satRNAs
by calculating phylogenies for different molecular regions and by using Sawyer's test for gene conversion. At least two recombination
events were required to produce these three recombinant satRNAs. Thus, recombinants were found to be frequent (∼17%) in natural
populations of CMV-satRNA, and recombination may make an important contribution to the generation of new variants. To our
knowledge this is the first report of data allowing the frequency of recombinant isolates in natural populations of an RNA
replicon to be estimated.
Received: 14 May 1996 / Accepted: 17 July 1996 相似文献
7.
Steinhauser S Beckert S Capesius I Malek O Knoop V 《Journal of molecular evolution》1999,48(3):303-312
RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine
bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing
has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required
extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene
(1104 nt) was analyzed in a large collection of bryophytes and green algae (Charales). The genomic nad5 sequences predict
editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required
in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae,
on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic
sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes
the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by
cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants.
Received: 2 April 1998 / Accepted: 4 August 1998 相似文献
8.
Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes 总被引:36,自引:0,他引:36
The majority of plant disease resistance genes are members of very large multigene families. They encode structurally related
proteins containing nucleotide binding site domains (NBS) and C-terminal leucine rich repeats (LRR). The N-terminal region
of some resistance genes contain a short sequence called TIR with homology to the animal innate immunity factors, Toll and interleukin receptor-like genes. Only a few plant resistance genes have been functionally analyzed and the origin and
evolution of plant resistance genes remain obscure. We have reconstructed gene phylogeny by exhaustive analysis of available
genome and amplified NBS domain sequences. Our study shows that NBS domains faithfully predict whole gene structure and can
be divided into two major groups. Group I NBS domains contain group-specific motifs that are always linked with the TIR sequence
in the N terminus. Significantly, Group I NBS domains and their associated TIR domains are widely distributed in dicot species
but were not detected in cereal databases. Furthermore, Group I specific NBS sequences were readily amplified from dicot genomic
DNA but could not be amplified from cereal genomic DNA. In contrast, Group II NBS domains are always associated with putative
coiled-coil domains in their N terminus and appear to be present throughout the angiosperms. These results suggest that the
two main groups of resistance genes underwent divergent evolution in cereal and dicot genomes and imply that their cognate
signaling pathways have diverged as well.
Received: 17 May 1999 / Accepted: 25 September 1999 相似文献
9.
Saccharomyces cerevisiae and mammals concerning the mechanisms of the translocation step and discuss the roles of the proteins implicated in this
process.
Received: 5 June 1996/Revised: 20 September 1996 相似文献
10.
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
11.
12.
Positive Darwinian Selection Promotes Heterogeneity Among Members of the Antifreeze Protein Multigene Family 总被引:9,自引:0,他引:9
A variety of organisms have independently evolved proteins exhibiting antifreeze activity that allows survival at subfreezing
temperatures. The antifreeze proteins (AFPs) bind ice nuclei and depress the freezing point by a noncolligative absorption–inhibition
mechanism. Many organisms have a heterogeneous suite of AFPs with variation in primary sequence between paralogous loci. Here,
we demonstrate that the diversification of the AFP paralogues is promoted by positive Darwinian selection in two independently
evolved AFPs from fish and beetle. First, we demonstrate an elevated rate of nonsynonymous substitutions compared to synonymous
substitutions in the mature protein coding region. Second, we perform phylogeny-based tests of selection to demonstrate a
subset of codons is subjected to positive selection. When mapped onto the three-dimensional structure of the fish antifreeze
type III antifreeze structure, these codons correspond to amino acid positions that surround but do not interrupt the putative
ice-binding surface. The selective agent may be related to efficient binding to diverse ice surfaces or some other aspect
of AFP function.
Received: 27 February 2001 / Accepted: 12 September 2001 相似文献
13.
Elongation factor (EF) Tu alternates between two interaction partners, EF-Ts and the ribosome, during its functional cycle.
On the ribosome, the interaction involves, among others, ribosomal protein L7/12. Here we compare EF-Ts and L7/12 with respect
to the conservation of sequence and structure. There is significant conservation of functionally important residues in the
N-terminal domain of EF-Ts and in the C-terminal domain of L7/12. The structure alignment based on the crystal structures
of the two domains suggests a high degree of similarity between the αA–βD–αB motif in L7/12 and the h1–turn–h2 motif in EF-Ts
which defines a common structural motif. The motif is remarkably similar with respect to fold, bulkiness, and charge distribution
of the solution surface, suggesting that it has a common function in binding EF-Tu.
Received: 12 June 2000 / Accepted: 10 October 2000 相似文献
14.
15.
Charles M. Matthews Cassandra J. Vandenberg Clive N.A. Trotman 《Journal of molecular evolution》1998,46(6):729-733
The Artemia hemoglobin is a dimer comprising two nine-domain covalent polymers in quaternary association. Each polymer is encoded by
a gene representing nine successive globin domains which have different sequences and are presumed to have been copied originally
from a single-domain gene. Two different polymers exist as the result of a complete duplication of the nine-domain gene, allowing
the formation of either homodimers or the heterodimer. The total population size of 18 domains comprising nine corresponding
pairs, coupled with the probability that they reflect several hundred million years of evolution in the same lineage, provides
a unique model in which the process of gene multiplication can be analyzed. The outcome has important implications for the
reliability of local molecular clocks.
The two polymers differ from each other at 11.7% of amino acid sites; however when corresponding individual domains are compared
between polymers, amino acid substitution fluctuates by a factor of 2.7-fold from lowest to highest. This variation is not
obvious at the DNA level: Domain pair identity values fluctuate by 1.3-fold. Identity values are, however, uncorrected for
multiple substitutions, and both silent and nonsilent changes are pooled. Therefore, to determine the variability in relative
substitution rates at the DNA level, we have used the method of Li (1993, J Mol Evol 36:96–99) to determine estimates of nonsynonymous (K
A
) and synonymous (K
S
) substitutions per site for the nine pairs of domains. As expected, the overall level of silent substitutions (K
S
of 56.9%) far exceeded nonsilent substitutions (K
A
of 6.7%); however, for corresponding domain pairs, K
A
fluctuates by 2.3-fold and K
S
by 1.7-fold. The large discrepancies reflected in the expressed protein have accrued within a single lineage and the implication
is that divergence dates of different genera based on amino acid sequences, even with well-studied proteins of reasonable
size, can be wrong by a factor well in excess of 2.
Received: 4 June 1997 / Accepted: 17 December 1997 相似文献
16.
Evolutionary Comparisons of RecA-Like Proteins Across All Major Kingdoms of Living Organisms 总被引:17,自引:0,他引:17
Volker Brendel Luciano Brocchieri Steven J. Sandler Alvin J. Clark Samuel Karlin 《Journal of molecular evolution》1997,44(5):528-541
Protein sequences with similarities to Escherichia coli RecA were compared across the major kingdoms of eubacteria, archaebacteria, and eukaryotes. The archaeal sequences branch
monophyletically and are most closely related to the eukaryotic paralogous Rad51 and Dmc1 groups. A multiple alignment of
the sequences suggests a modular structure of RecA-like proteins consisting of distinct segments, some of which are conserved
only within subgroups of sequences. The eukaryotic and archaeal sequences share an N-terminal domain which may play a role
in interactions with other factors and nucleic acids. Several positions in the alignment blocks are highly conserved within
the eubacteria as one group and within the eukaryotes and archaebacteria as a second group, but compared between the groups
these positions display nonconservative amino acid substitutions. Conservation within the RecA-like core domain identifies
possible key residues involved in ATP-induced conformational changes. We propose that RecA-like proteins derive evolutionarily
from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like
proteins acting in series or cooperatively.
Received: 25 October 1996 / Accepted: 31 December 1996 相似文献
17.
Gene structure of a chlorophyll a/c-binding protein from a brown alga: Presence of an intron and phylogenetic implications 总被引:5,自引:0,他引:5
Lise Caron Dominique Douady Michelle Quinet-Szely Susan de Goër Claire Berkaloff 《Journal of molecular evolution》1996,43(3):270-280
A Laminaria saccharina genomic library in the phage EMBL 4 was used to isolate and sequence a full-length gene encoding a fucoxanthin-chlorophyll
a/c-binding protein. Contrary to diatom homologues, the coding sequence is interrupted by an intron of about 900 bp which
is located in the middle of the transit peptide. The deduced amino acid sequence of the mature protein is very similar to
those of related proteins from Macrocystis pyrifera (Laminariales) and, to a lesser extent, to those from diatoms and Chrysophyceae. Seven of the eight putative chlorophyll-binding
amino acids determined in green plants are also present. Alignments of different sequences related to the light-harvesting
proteins (LHC) demonstrate a structural similarity among the three transmembrane helices and suggest a unique ancestral helix
preceded by two β-turns. The β-turns are conserved in front of the second helices of the chlorophyll a/c proteins more so
than in chlorophyll a/b proteins. Phylogenetic trees generated from sequence data indicate that fucoxanthin-chlorophyll-binding
proteins diverged prior to the separation of photosystem I and photosystem II LHC genes of green plants. Among the fucoxanthin-containing
algae, LHC I or II families could not be distinguished at this time.
Received: 14 February 1996 / Accepted: 4 April 1996 相似文献
18.
Plant genomes encode a variety of protein kinases, and while some are functional homologues of animal and fungal kinases,
others have a novel structure. This review focuses on three groups of unusual membrane-associated plant protein kinases: receptor-like
protein kinases (RLKs), calcium-dependent protein kinases (CDPKs), and histidine protein kinases.
Animal RLKs have a putative extracellular domain, a single transmembrane domain, and a protein kinase domain. In plants, all
of the RLKs identified thus far have serine/threonine signature sequences, rather than the tyrosine-specific signature sequences
common to animals. Recent genetic experiments reveal that some of these plant kinases function in development and pathogen
resistance.
The CDPKs of plants and protozoans are composed of a single polypeptide with a protein kinase domain fused to a C-terminal
calmodulin-like domain containing four calcium-binding EF hands. No functional plant homologues of protein kinase C or Ca2+/calmodulin-dependent protein kinase have been identified, and no animal or fungal CDPK homologues have been identified.
Recently, histidine kinases have been shown to participate in signaling pathways in plants and fungi. ETR1, an Arabidopsis histidine kinase homologue with three transmembrane domains, functions as a receptor for the plant hormone ethylene. G-protein-coupled
receptors, which often serve as hormone receptors in animal systems, have not yet been identified in plants.
Received: 18 August 1997/Revised: 23 December 1997 相似文献
19.
Benoit Cousineau Fabrice Leclerc Robert Cedergren 《Journal of molecular evolution》1997,45(6):661-670
Sequence similarity has given rise to the proposal that IF-2, EF-G, and EF-Tu are related through a common ancestor. We evaluate
this proposition and whether the relationship can be extended to other factors of protein synthesis. Analysis of amino acid
sequence similarity gives statistical support for an evolutionary affiliation among IF-1, IF-2, IF-3, EF-Tu, EF-Ts, and EF-G
and suggests further that this association is a result of gene duplication/fusion events. In support of this mechanism, the
three-dimensional structures of IF-3, EF-Tu, and EF-G display a predictable domain structure and overall conformational similarity.
The model that we propose consists of three consecutives duplication/fusion events which would have taken place before the
divergence of the three superkingdoms: eubacteria, archaea, and eukaryotes. The root of this protein superfamily tree would
be an ancestor of the modern IF-1 gene sequence. The repeated fundamental motif of this protein superfamily is a small RNA
binding domain composed of two α-helices packed along side of an antiparallel β-sheet.
Received: 17 October 1996 / Accepted: 10 June 1997 相似文献
20.
Arbing MA Dahan D Boismenu D Mamer OA Hanrahan JW Coulton JW 《The Journal of membrane biology》2000,178(3):185-193
Porin of Haemophilus influenzae type b (341 amino acids; M
r
37782) determines the permeability of the outer membrane to low molecular mass compounds. Purified Hib porin was subjected
to chemical modification of lysine residues by succinic anhydride. Electrospray ionization mass spectrometry identified up
to 12 modifications per porin molecule. Tryptic digestion of modified Hib porin followed by reverse phase chromatography and
matrix assisted laser desorption ionization time-of-flight mass spectrometry mapped the succinylation sites. Most modified
lysines are positioned in surface-located loops, numbers 1 and 4 to 7. Succinylated porin was reconstituted into planar lipid
bilayers, and biophysical properties were analyzed and compared to Hib porin: there was an increased average single channel
conductance compared to Hib porin (1.24+/−0.41 vs. 0.85+/−0.40 nanosiemens). The voltage-gating activity of succinylated porin differed considerably from that of Hib porin.
The threshold voltage for gating was decreased from 75 to 40 mV. At 80 mV, steady-state conductance for succinylated porin
was 50–55% of the instantaneous conductance. Hib porin at 80 mV showed a decrease to 89–91% of the instantaneous current levels.
We propose that surface-located lysine residues are determinants of voltage gating for porin of Haemophilus influenzae type b.
Received: 11 August 2000/Revised: 8 September 2000 相似文献