共查询到20条相似文献,搜索用时 31 毫秒
1.
Sana Bachali Xavier Bailly Jacqueline Jollès Pierre Jollès Jean S Deutsch 《European journal of biochemistry》2004,271(2):237-242
On the basis of a partial N-terminal sequence, Jollès and Jollès previously proposed that the lysozyme from the starfish Asterias rubens represents a new form of lysozyme, called type i (invertebrate) lysozyme. Indeed, it differed from both the types c (chicken) and g (goose) known in other animals, as well as from plant and phage lysozymes. Recently, several proteins belonging to the same family have been isolated from protostomes. Here we report the complete mature protein sequence and cDNA sequence of the lysozyme from Asterias. These sequences vindicate the previously proposed homology between the starfish, a deuterostome, and protostome lysozymes. In addition, we present a structural analysis that allows us to postulate upon the function of several conserved residues. 相似文献
2.
Langenkämper G Fung RW Newcomb RD Atkinson RG Gardner RC MacRae EA 《Journal of molecular evolution》2002,54(3):322-332
We present phylogenetic analyses to demonstrate that there are three families of sucrose phosphate synthase (SPS) genes present
in higher plants. Two data sets were examined, one consisting of full-length proteins and a second larger set that covered
a highly conserved region including the 14-3-3 binding region and the UDPGlu active site. Analysis of both datasets showed
a well supported separation of known genes into three families, designated A, B, and C. The genomic sequences of Arabidopsis thaliana include a member in each family: two genes on chromosome 5 belong to Family A, one gene on chromosome 1 to Family B, and
one gene on chromosome 4 to Family C. Each of three Citrus genes belong to one of the three families. Intron/exon organization of the four Arabidopsis genes differed according to phylogenetic analysis, with members of the same family from different species having similar
genomic organization of their SPS genes. The two Family A genes on Arabidopsis chromosome 5 appear to be due to a recent duplication. Analysis of published literature and ESTs indicated that functional
differentiation of the families was not obvious, although B family members appear not to be expressed in roots. B family genes
were cloned from two Actinidia species and southern analysis indicated the presence of a single gene family, which contrasts to the multiple members of
Family A in Actinidia. Only two family C genes have been reported to date.
Received: 17 April 2001 / Accepted: 27 August 2001 相似文献
3.
Potenza N del Gaudio R Rivieccio L Russo GM Geraci G 《Journal of molecular evolution》2002,54(3):312-321
A novel member of the innexin family (cv-inx) has been isolated from the annelid polychaete worm Chaetopterus variopedatus using a PCR approach on genomic DNA and sequence analysis on genomic DNA clones. The gene is present in a HindIII-HindIII segment of 2250 bp containing an uninterrupted open reading frame of 1196 bp encoding a protein of 399 amino acids. The
predicted protein shows the typical structural features of innexins and consensus sites for phosphorylation. Analyses on genomic
DNA demonstrate that cv-inx is a single copy gene with no introns in the coding region, exactly corresponding to the cDNA
sequence. The gene expression is regulated during development as shown by Northern blots analyses of the RNA and by immunoreaction
with antibodies against the protein at several embryonic stages. The finding of an innexin in the phylum Annelida, outside
of the Ecdysozoa clade, and its peculiar gene structure suggest the necessity to reconsider the current hypothesis on the
origin and evolution of gap junctional proteins.
Received: 15 December 2000 / Accepted: 27 August 2001 相似文献
4.
Alessandra Gambacurta Maria Cristina Piro Franca Ascoli 《Journal of molecular evolution》1998,47(2):167-171
Vertebrate and many invertebrate globin genes have a three-exon/two-intron organization, with introns in highly conserved
positions. According to the ``intron early' hypothesis, introns are the vestigial segments which flank previously independent
coding sequences, thus providing evidence for the assembly of the ancient proteins by ``exon shuffling.' In this paper, we
report the analysis of the genes of the bivalve mollusk Scapharca inaequivalvis tetrameric hemoglobin (HbII), which support this hypothesis, at least for the hemoglobin genes. We show the existence of
``minigenes' in the IIA and IIB globin genes, spanning part of the first and second introns, ``in frame' with the heme-binding
domain coded by the second exon. Further support for the exon shuffling hypothesis can be found in the degree of identity
of the ``new' translated sequences with those flanking the central protein domain of some invertebrate hemoglobins.
Received: 31 July 1997 / Accepted: 12 December 1997 相似文献
5.
Evolution of Duplicated <Emphasis Type="BoldItalic">reggie</Emphasis> Genes in Zebrafish and Goldfish 总被引:1,自引:0,他引:1
Málaga-Trillo E Laessing U Lang DM Meyer A Stuermer CA 《Journal of molecular evolution》2002,54(2):235-245
Invertebrates, tetrapod vertebrates, and fish might be expected to differ in their number of gene copies, possibly due the
occurrence of genome duplication events during animal evolution. Reggie (flotillin) genes code for membrane-associated proteins involved in growth signaling in developing and regenerating axons. Until now,
there appeared to be only two reggie genes in fruitflies, mammals, and fish. The aim of this research was to search for additional copies of reggie genes in fishes, since a genome duplication might have increased the gene copy number in this group. We report the presence
of up to four distinct reggie genes (two reggie-1 and two reggie-2 genes) in the genomes of zebrafish and goldfish. Phylogenetic analyses show that the zebrafish and goldfish sequence pairs
are orthologous, and that the additional copies could have arisen through a genome duplication in a common ancestor of bony
fish. The presence of novel reggie mRNAs in fish embryos indicates that the newly discovered gene copies are transcribed and possibly expressed in the developing
and regenerating nervous system. The intron/exon boundaries of the new fish genes characterized here correspond with those
of human genes, both in location and phase. An evolutionary scenario for the evolution of reggie intron-exon structure, where loss of introns appears to be a distinctive trait in invertebrate reggie genes, is presented.
Received: 24 January 2001 / Accepted: 27 July 2001 相似文献
6.
The genomic organization of the hsp83 gene of Drosophila auraria, a far-eastern endemic species belonging to the montium subgroup of the melanogaster species group, is presented here. Based on in situ hybridization on polytene chromosomes, cDNA and genomic clone mapping,
nucleotide sequencing, and genomic Southern analysis, hsp83 is shown to be present as a single-copy gene at locus 64B on the 3L chromosome arm in D. auraria. This gene is organized into two exons separated by a 929-bp intron. The first exon represents the mRNA leader sequence and
is not translated, while the coding region, having a length of 2,151 bp, is solely included in the second exon. Nucleotide
sequence comparisons of D. auraria hsp83 with homologous sequences from other organisms show high conservation of the coding region (88–92% identity) in the genus
Drosophila, in addition to the conserved genomic organization of two-exons–one-intron, of comparable size and arrangement. A phylogenetic
tree based on the protein sequences of homologous genes from representative organisms is in accord with the accredited phylogenetic
position of D. auraria. In the hsp83 gene region, a second case of long antiparallel coupled open reading frames (LAC ORFs) for this species was found. The antiparallel
to the hsp83 gene ORF is 1,554 bases long, while the two ORFs overlap has a size of 1,548 bp. The anti-hsp83 ORF does not show significant homology to any known gene sequences. In addition, no similar LAC ORF structures were found
in homologous gene regions of other organisms.
Received: 18 April 1997 / Accepted: 1 August 1997 相似文献
7.
The ruminant digestion model using bacteria already employed early in evolution by symbiotic molluscs 总被引:4,自引:0,他引:4
Jacqueline Jollès Aline Fiala-Médioni Pierre Jollès 《Journal of molecular evolution》1996,43(5):523-527
The purification and some molecular properties of six lysozymes from the gills of different mytilids and vesicomyids are
described: they belong to the previously described Invertebrate lysozyme family. The predominance of the bacterial nutrition
in these organisms seems to necessitate the presence of a lysozyme as in the case of the ruminant digestion model.
Received: 18 December 1995 / Accepted: 2 May 1996 相似文献
8.
Matsumoto T Nakamura AM Takahashi KG 《Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology》2006,145(3-4):325-330
In bivalve molluscs including oysters, lysozymes play an important role in the host defense mechanisms against invading microbes. However, it remains unclear in which sites/cells the lysozyme genes are expressed and which subsequently produced the enzyme. This study cloned lysozyme cDNAs from the digestive organs of Pacific oyster Crassostrea gigas and European flat oyster Ostrea edulis. Both complete sequences of two oysters' lysozymes were composed of 137 amino acids. Two translated proteins present a high content in cysteine residues. Phylogenetic analyses showed that these oysters' lysozymes clustered with the invertebrate-type lysozymes of other bivalve species. In the Pacific oyster, lysozyme mRNA was expressed in all tissues except for those of the adductor muscle. In situ hybridization analyses revealed that lysozyme mRNA was expressed strongly in basophil cells in the digestive gland tubule of C. gigas, but not in digestive cells. Results indicated that the basophil cells of the oyster digestive gland are the sites of lysozyme synthesis. 相似文献
9.
We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome
b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis
of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other
primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has
remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.
Received: 15 December 1997 / Accepted: 24 February 1998 相似文献
10.
Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide
choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures.
In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding
first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform
to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that
genes from different genomes can be separated with a high degree of accuracy, according to these distance values.
In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their
poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides,
we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects.
Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene
present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking
correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.
Received: 16 January 2001 / Accepted: 30 August 2001 相似文献
11.
Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27
complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected
orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families
are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive
grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the
recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been
laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character
dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders,
and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion
of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences
due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to
these lineages. Finally, artificial ``partial genomes' were generated by randomly selecting ORFs from the complete genomes
in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available.
The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole
genome sequences.
Received: 30 May 2001 / Accepted: 10 October 2001 相似文献
12.
Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists 总被引:1,自引:0,他引:1
Many genes for calmodulin-like domain protein kinases (CDPKs) have been identified in plants and Alveolate protists. To study
the molecular evolution of the CDPK gene family, we performed a phylogenetic analysis of CDPK genomic sequences. Analysis
of introns supports the phylogenetic analysis; CDPK genes with similar intron/exon structure are grouped together on the phylogenetic
tree. Conserved introns support a monophyletic origin for plant CDPKs, CDPK-related kinases, and phosphoenolpyruvate carboxylase
kinases. Plant CDPKs divide into two major branches. Plant CDPK genes on one branch share common intron positions with protist
CDPK genes. The introns shared between protist and plant CDPKs presumably originated before the divergence of plants from
Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal
calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the
beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein
kinase and calmodulin genes facilitated by recombination of ancient introns.
Received: 11 July 2000 / Accepted: 18 April 2001 相似文献
13.
Yves Van de Peer John S. Taylor Ingo Braasch Axel Meyer 《Journal of molecular evolution》2001,53(4-5):436-446
The duplication of genes and even complete genomes may be a prerequisite for major evolutionary transitions and the origin
of evolutionary novelties. However, the evolutionary mechanisms of gene evolution and the origin of novel gene functions after
gene duplication have been a subject of many debates. Recently, we compiled 26 groups of orthologous genes, which included
one gene from human, mouse, and chicken, one or two genes from the tetraploid Xenopus and two genes from zebrafish. Comparative analysis and mapping data showed that these pairs of zebrafish genes were probably
produced during a fish-specific genome duplication that occurred between 300 and 450 Mya, before the teleost radiation (Taylor
et al. 2001). As discussed here, many of these retained duplicated genes code for DNA binding proteins. Different models have
been developed to explain the retention of duplicated genes and in particular the subfunctionalization model of Force et al.
(1999) could explain why so many developmental control genes have been retained. Other models are harder to reconcile with
this particular set of duplicated genes. Most genes seem to have been subjected to strong purifying selection, keeping properties
such as charge and polarity the same in both duplicates, although some evidence was found for positive Darwinian selection,
in particular for Hox genes. However, since only the cumulative pattern of nucleotide substitutions can be studied, clear indications of positive
Darwinian selection or neutrality may be hard to find for such anciently duplicated genes. Nevertheless, an increase in evolutionary
rate in about half of the duplicated genes seems to suggest that either positive Darwinian selection has occurred or that
functional constraints have been relaxed at one point in time during functional divergence.
Received: 4 January 2001 / Accepted: 29 March 2001 相似文献
14.
Herdman M Coursin T Rippka R Houmard J Tandeau de Marsac N 《Journal of molecular evolution》2000,51(3):205-213
The evolutionary origin of the phytochromes of eukaryotes is controversial. Three cyanobacterial proteins have been described
as ``phytochrome-like' and have been suggested to be potential ancestors of these essential photoreceptors: Cph1 from Synechocystis PCC 6803, showing homology to phytochromes along its entire length and known to attach a chromophore; and PlpA from Synechocystis PCC 6803 and RcaE from Fremyella diplosiphon, both showing homology to phytochromes most strongly only in the C-terminal region and not known to bind a chromophore. We
have reexamined the evolution of the photoreceptors using for PCR amplification a highly conserved region encoding the chromophore-binding
domain in both Cph1 and phytochromes of plants and have identified genes for phytochrome-like proteins (PLP) in 11 very diverse
cyanobacteria. The predicted gene products contain either a Cys, Arg, Ile, or Leu residue at the putative chromophore binding
site. In 10 of the strains examined only a single gene was found, but in Calothrix PCC 7601 two genes (cphA and cphB) were identified. Phylogenetic analysis revealed that genes encoding PLP are homologues that share a common ancestor with
the phytochromes of eukaryotes and diverged before the latter. In contrast, the putative sensory/regulatory proteins, including
PlpA and RcaE, that lack a part of the chromophore lyase domain essential for chromophore attachment on the apophytochrome,
are only distantly related to phytochromes. The Ppr protein of the anoxygenic photosynthetic bacterium Rhodospirillum centenum and the bacterial phytochrome-like proteins (BphP) of Deinococcus radiodurans and Pseudomonas aeruginosa fall within the cluster of cyanobacterial phytochromes.
Received: 9 December 1999 / Accepted: 10 May 2000 相似文献
15.
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
16.
In this paper we analyzed 49 lactate dehydrogenase (LDH) sequences, mostly from vertebrates. The amino acid sequence differences
were found to be larger for a human–killifish pair than a human–lamprey pair. This indicates that some protein sequence convergence
may occur and reduce the sequence differences in distantly related species. We also examined transitions and transversions
separately for several species pairs and found that the transitions tend to be saturated in the distantly related species
pair, while transversions are increasing. We conclude that transversions maintain a conservative rate through the evolutionary
time. Kimura's two-parameter model for multiple-hit correction on transversions only was used to derive a distance measure
and then construct a neighbor-joining (NJ) tree. Three findings were revealed from the NJ tree: (i) the branching order of
the tree is consistent with the common branch pattern of major vertebrates; (ii) Ldh-A and Ldh-B genes were duplicated near the origin of vertebrates; and (iii) Ldh-C and Ldh-A in mammals were produced by an independent gene duplication in early mammalian history. Furthermore, a relative rate test
showed that mammalian Ldh-C evolved more rapidly than mammalian Ldh-A. Under a two-rate model, this duplication event was calibrated to be approximately 247 million years ago (mya), dating back
to the Triassic period. Other gene duplication events were also discovered in Xenopus, the first duplication occurring approximately 60–70 mya in both Ldh-A and Ldh-B, followed by another recent gene duplication event, approximately 20 mya, in Ldh-B.
Received: 5 October 2001 / Accepted: 24 October 2001 相似文献
17.
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
18.
François Agnès Marguerite-Marie Toux Catherine André Francis Galibert 《Journal of molecular evolution》1997,45(1):43-49
Receptor tyrosine kinases with five, seven, and three Ig-like domains in their extracellular region are grouped in subclasses
IIIa, IIIb, and IIIc, respectively. Here, we describe the genomic organization of the extracellular coding region of the human FGFR4 (IIIc) and FLT4 (IIIb) genes and compare it to that of the human FGFR1(IIIc), KIT, and FMS (IIIa). The results show that while genes belonging to the same subclass have an identical exon/intron structure in their extracellular
coding region—as they do in their intracellular coding region—genes of related subclasses only have a similar exon/intron
structure. These results strongly support the hypothesis that the genes of the three subclasses evolved from a common ancestor
by duplications involving entire genes, already in pieces. Hypotheses on the origin of introns and on the difference in the
number of extracellular Ig-like domains in the three gene subclasses are discussed.
Received: 19 August 1996 / Accepted: 2 January 1997 相似文献
19.
The Family of Major Royal Jelly Proteins and Its Evolution 总被引:8,自引:0,他引:8
Stefan Albert Debashish Bhattacharya Jaroslav Klaudiny Jana Schmitzová Jozef Simúth 《Journal of molecular evolution》1999,49(2):290-297
A cDNA encoding a new member of the gene family of major royal jelly proteins (MRJPs) from the honeybee, Apis mellifera, was isolated and sequenced. Royal jelly (RJ) is a secretion of the cephalic glands of nurse bees. The origin and biological
function of the protein component (12.5%, w/w) of RJ is unknown. We show that the MRJP gene family encodes a group of closely
related proteins that share a common evolutionary origin with the yellow protein of Drosophila melanogaster. Yellow protein functions in cuticle pigmentation in D. melanogaster. The MRJPs appear to have evolved a novel nutritional function in the honeybee.
Received: 26 September 1998 / Accepted: 28 February 1999 相似文献
20.
Pavesi A 《Journal of molecular evolution》2001,53(2):104-113
The GB virus C/hepatitis G virus (GBV-C/HGV) is a newly identified human RNA virus, belonging to the Flaviviridae family. Persistent infection by GBV-C/HGV is common in humans, and genetically divergent isolates have been identified in
different parts of the world. Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely
low mutation rate, this virus is a potential marker to trace prehistoric links between human populations. In this study, origin
and evolution of GBV-C/HGV were examined using a set of fully sequenced strains of worldwide origin. A first phylogenetic
analysis, addressed to the short (255 nucleotides) NS5A overlapping coding region by the neighbor-joining method, suggested
an ancient African origin of GBV-C/HGV. This notion was confirmed when the same analysis was applied to the genomic regions
showing the lowest rate of synonymous substitutions, covering one-fourth (2184 nucleotides) of the total coding potential
of the virus genome. By using a multivariate statistical method and extending the analysis to the complete coding region,
fine details of the evolutionary history of GBV-C/HGV were further elucidated. By this approach, isolates from Southeast Asia
appeared to be the most closely related to those of African origin, consistent with a major route of ancient human migrations
from Africa to southeastern parts of the Asian continent.
Received: 26 October 2000 / Accepted: 28 February 2001 相似文献