共查询到20条相似文献,搜索用时 15 毫秒
1.
2.
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
3.
Christine Perret Nourredine Lomri Monique Thomasset 《Journal of molecular evolution》1988,27(4):351-364
Summary The evolutionary history of the intracellular calcium-binding protein superfamily is well documented. The members of this gene family are all believed to be derived from a common ancestor, which, itself, was the product of two successive gene duplications. In this study, we have compared and analyzed the structures of the recently described genes coding for these proteins. We propose a series of evolutionary events, which include exon shuffling and intron insertion, that could account for the evolutionary origin of all the members of this super-family. According to this hypothesis, the ancestral gene, a product of two successive duplications, consisted of at least four exons. Each exon coding for a peptide (a calcium-binding domain) was separated by an intron that had mediated the duplication. Each distinct lineage evolved from this ancestor by genomic rearrangement, with insertion of introns being a prominent feature. 相似文献
4.
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
5.
The Peperomia polybotrya coxI gene intron is the only currently reported group I intron in a vascular plant mitochondrial genome and it likely originated
by horizontal transfer from a fungal donor. We provide a clearer picture of the horizontal transfer and a portrayal of the
evolution of the group I intron since it was gained by the Peperomia mitochondrial genome. The intron was transferred recently in terms of plant evolution, being restricted to the single genus
Peperomia among the order Piperales. Additional support is presented for the suggestion that a recombination/repair mechanism was used
by the intron for integration into the Peperomia mitochondrial genome, as a perfect 1:1 correspondence exists between the intron's presence in a species and the presence
of divergent nucleotide markers flanking the intron insertion site. Sequencing of coxI introns from additional Peperomia species revealed that several mutations have occurred in the intron since the horizontal transfer, but sequence alterations
have not caused frameshifts or created stop codons in the intronic open reading frame. In addition, two coxI pseudogenes in Peperomia cubensis were discovered that lack a large region of coxI exon 2 and contain a truncated version of the group I intron that likely cannot be spliced out.
Received: 29 May 1997 / Accepted: 1 November 1997 相似文献
6.
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
7.
Hiroshi Suga Daisuke Hoshiyama Shigehiro Kuraku Kazutaka Katoh Kaoru Kubokawa Takashi Miyata 《Journal of molecular evolution》1999,49(5):601-608
Animals evolved a variety of gene families involved in cell–cell communication and developmental control by gene duplication
and domain shuffling. Each family is made up of several subtypes or subfamilies with distinct structures and functions, which
diverged by gene duplications and domain shufflings before the divergence of parazoans and eumetazoans. Since the separation
from protostomes, vertebrates expanded the multiplicity of members (isoforms) in the same subfamily by further gene duplications
in their early evolution before the fish–tetrapod split. To know the dates of isoform duplications more closely, we have conducted
isolation and sequencing cDNAs encoding the fibroblast growth factor receptor, Eph, src, and platelet-derived growth factor receptor subtypes belonging to the protein tyrosine kinase family from Branchiostoma belcheri, an amphioxus, Eptatretus burgeri, a hagfish, and Lampetra reissneri, a lamprey. From a phylogenetic tree of each subfamily inferred from a maximum likelihood (ML) method, together with a bootstrap
analysis based on the ML method, we have shown that the isoform duplications frequently occurred in the early evolution of
vertebrates around or just before the divergence of cyclostomes and gnathostomes by gene duplications and possibly chromosomal
duplications.
Received: 28 April 1998 / Accepted: 30 June 1999 相似文献
8.
Alexander E. Vinogradov 《Journal of molecular evolution》1999,49(3):376-384
The intron–genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and
maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron
size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its
increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general
trend. In baker's yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected
for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences
in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of
mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic
ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates
and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to
explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition
(dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome
size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium
model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron
size due to its putative link to chromatin structure (and constraints of the splicing machinery).
Received: 23 October 1997 / Accepted: 14 April 1999 相似文献
9.
In this paper we have analyzed 49 vertebrate gene families that were generated in the early stage of vertebrates and/or shortly
before the origin of vertebrates, each of which consists of three or four member genes. We have dated the first (T1) and second (T2) gene duplications of 26 gene families with 3 member genes. The means of T1 (594 mya) and T2 (488 mya) are largely consistent to a well-cited version of two-round (2R) genome duplication theory. Moreover, in most cases,
the time interval between two successive gene duplications is large enough that the fate of duplicate genes generated by the
first gene duplication was likely to be determined before the second one took place. However, the phylogenetic pattern of
23 gene families with 4 members is complicated; only 5 of them are predicted by 2R model, but 11 families require an additional
gene (or genome) duplication. For the rest (7 families), at least one gene duplication event had occurred before the divergence
between vertebrate and Drosophila, indicating a possible misleading of the 4:1 rule (member gene ratio between vertebrates and invertebrates). Our results show
that Ohno's 2R conjecture is valid as a working hypothesis for providing a most parsimonious explanation. Although for some
gene families, additional gene duplication is needed, the credibility of the third genome duplication (3R) remains to be investigated.
Received: 13 December 1999 / Accepted: 7 April 2000 相似文献
10.
Base composition is not uniform across the genome of Drosophila melanogaster. Earlier analyses have suggested that there is variation in composition in D. melanogaster on both a large scale and a much smaller, within-gene, scale. Here we present analyses on 117 genes which have reliable intron/exon
boundaries and no known alternative splicing. We detect significant heterogeneity in G+C content among intron segments from
the same gene, as well as a significant positive correlation between the intron and the third codon position G+C content within
genes. Both of these observations appear to be due, in part, to an overall decline in intron and third codon position G+C
content along Drosophila genes with introns. However, there is also evidence of an increase in third codon position G+C content at the start of genes;
this is particularly evident in genes without introns. This is consistent with selection acting against preferred codons at
the start of genes.
Received: 24 February 1997 / Accepted: 10 November 1997 相似文献
11.
Summary In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern
of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based
on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates
both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin,
C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin
dendrograms computed from DNA and from protein sequences.
In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms
based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that
introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond
to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family.
Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3′-tail sequence, intron
sequences, and intron positions all show significant differences. 相似文献
12.
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
13.
Calpains, the Ca2+-dependent intracellular proteinases, are involved in the regulation of distinct cellular pathways including signal transduction
and processing, cytoskeleton dynamics, and muscle homeostasis. To investigate the evolutionary origin of diverse calpain subfamilies,
a phylogenetic study was carried out. The topology of the calpain phylogenetic tree has shown that some of the gene duplications
occurred before the divergence of the protostome and deuterostome lineages. Other gene doublings, leading to vertebrate-specific
calpain forms, took place during early chordate evolution and coincided with genome duplications as disclosed by the localization
of calpain genes to paralogous chromosome regions in the human genome. On the basis of the phylogenetic tree, the time of
gene duplications, and the localization of calpain genes, we propose a model of tandem and chromosome duplications for the
evolution of vertebrate-specific calpain forms. The data presented here are consistent with scenarios proposed for the evolution
of other multigene families.
Received: 17 November 1998 / Accepted: 30 April 1999 相似文献
14.
15.
In this work detailed statistics on ancestral gene duplication and gene conservation in completely sequenced cellular genomes
are presented. Analysis of open reading frame (ORF) products having simultaneous matches in several distinct organisms showed
a significant correlation between duplication and conservation. Systematic comparisons of predicted proteomes of 23 organisms
(including 20 that have been completely sequenced), have allowed us to quantify the degree of ancestral duplication within
each genome and the level of conservation between genomes, using threshold values calculated for individual organisms. Statistical
analysis of various gene proportions revealed interesting trends in gene structure and evolution, such as that (a) more than
one-quarter (25%–66%) of the predicted ORF products of the surveyed organisms are not unique, indicating a high level of ancestral
duplications; (b) levels of exclusive conservation within Bacteria are higher than those within the eukaryal or archaeal domains;
and (c) at least one-half (47–99%) of the total predicted ORF products in the surveyed genomes have one or several highly
significant matches in another genome. Significant matches are based on simulations taking into account the mean size of ORF
products and the composition of each target organism's proteome. The methodology we have developed ensures stability and comparability
of our results as the number of completely sequenced genomes increases.
Received: 4 May 1998 / Accepted: 28 September 1998 相似文献
16.
We characterized a full-length gene encoding wild silkmoth Antheraea pernyi fibroin (Ap-fibroin) to clarify the conformation of repetitive sequences. The gene consisted of a first exon encoding 14
amino acid residues, a short intron (120 bp), and a long second exon encoding 2,625 amino acid residues. Three amino acids,
alanine, glycine, and serine, amounted to 81% of the Ap-fibroin sequence. The Ap-fibroin, except for 155 residues of the amino
terminus, was composed of 80 tandemly arranged polyalanine-containing units (motifs). A motif was a doublet of a polyalanine
block (PAB) and a nonpolyalanine block (NPAB). Seventy-eight of the 80 motifs were classified into four types based on differences
in the NPAB sequences. Although respective motifs were significantly conserved, many rearrangements were observed within the
second exon, i.e., the triplication of a 558-bp-long sequence and other duplication events of shorter sequences. Chi-like
sequences, GCTGGAG, might contribute to the rearrangement within the gene as described in human minisatellite loci, because
they were found at specific sites of NPAB-encoding sequences in three of four types of motifs. The present results support
the idea that the Ap-fibroin gene is unstable like minisatellite sequences and that the evolution of this gene is strongly
associated with its instability.
Received: 18 February 2000 / Accepted: 30 June 2000 相似文献
17.
A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated
gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated
gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only
2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions
of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning
three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative
rates of duplication and deletion may contribute to the compactness of the C. elegans genome.
Received: 30 July 1998 / Accepted: 12 October 1998 相似文献
18.
Thirty complete coding sequences of human major histocompatibility complex (Mhc) class II DRB alleles, spanning 237 codons, were analyzed for phylogenetic information using distance, parsimony, and likelihood approaches.
Allelic genealogies derived from different parts of the coding sequence (exon 2, the 5′ and 3′ ends of exon 2, respectively,
and exons 3–6) were compared. Contrary to prior assertions, a rigorous analysis of allelic genealogies in this gene family
cannot be used to justify the claim that the lineage leading to modern humans contained on average at least 100,000 individuals.
Phylogenetic inferences based upon the exon 2 region of the DRB loci are complicated by selection and recombination, so this part of the gene does not provide a complete and accurate view
of allelic relationships. Attempts to reconstruct human history from genetic data must use realistic models which consider
the complicating factors of nonequilibrium populations, recombination, and different patterns of selection.
Received: 19 February 1997 / Accepted: 12 June 1997 相似文献
19.
Wytze T. Stam Jaap J. Beintema Rossana D’Avino Maurizio Tamburrini Guido di Prisco 《Journal of molecular evolution》1997,45(4):437-445
Amino acid sequences of α- and β-chains of human hemoglobin and of hemoglobins of coelacanth and 24 teleost fish species,
including 11 antarctic and two temperate Notothenioidei, were analyzed using maximum parsimony. Trees were derived for the
α- and β-chains separately and for tandemly arranged sequences, using the human and coelacanth sequences as outgroups in all
analyses. The topologies of the trees of the α-and β-chains are highly congruent and indicate a specific pattern of gene duplications
and gene expression of teleost hemoglobins which has not yet been investigated into more detail. The Notothenioid fish generally
contain a single major hemoglobin and often a second minor component. The α- and β-chains of the major components form a monophyletic
group in all investigated trees, with the nonantarctic Pseudaphritis as their sister taxon. The minor chains also are a monophyletic group and form an unresolved cluster with the major chains
and the hemoglobins of tuna and red gurnard. The Notothenioid families Nototheniidae and Bathydraconidae appear to be paraphyletic.
Received: 26 March 1997 / Accepted: 7 May 1997 相似文献
20.
Suga H Koyanagi M Hoshiyama D Ono K Iwabe N Kuma K Miyata T 《Journal of molecular evolution》1999,48(6):646-653
To know whether genes involved in cell–cell communication typical of multicellular animals dramatically increased in concert
with the Cambrian explosion, the rapid evolutionary burst in the major groups of animals, and whether these genes exist in
the sponge lacking cell cohesiveness and coordination typical of eumetazoans, we have carried out cloning of the G-protein
α subunit (Gα) and the protein tyrosine kinase (PTK) cDNAs from Ephydatia fluviatilis (freshwater sponge) and Hydra magnipapillata strain 105 (hydra). We obtained 13 Gα and 20 PTK cDNAs. Generally animal gene families diverged first by gene duplication
(subtype duplication) that gave rise to diverse subtypes with different primary functions, followed by further gene duplication
in the same subtype (isoform duplication) that gave rise to isoform genes with virtually identical function. Phylogenetic
trees of Gα and PTK families including cDNAs from sponge and hydra revealed that most of the present-day subtypes had been
established in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among the
extant animal phyla, by extensive subtype duplication: for PTK and Gα families, 23 and 9 subtype duplications were observed
in the early stage before the parazoan–eumetazoan split, respectively, and after that split, only 2 and 1 subtype duplications
were found, respectively. After the separation from arthropods, vertebrates underwent frequent isoform duplications before
the fish–tetrapod split. Furthermore, rapid amino acid changes appear to have occurred in concert with the extensive subtype
duplication and isoform duplication. Thus the pattern of gene diversification during animal evolution might be characterized
by bursts of gene duplication interrupted by considerably long periods of silence, instead of proceeding gradually, and there
might be no direct link between the Cambrian explosion and the extensive gene duplication that generated diverse functions
(subtypes) of these families.
Received: 4 November 1998 / Accepted: 17 November 1998 相似文献