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1.
Leslie L. Domier James J. Rivard Linda M. Sabatini Martin Blumenfeld 《Journal of molecular evolution》1986,23(2):149-158
Summary Approximately 30–40% ofDrosophila virilis DNA complementary to clonedDrosophila histone genes is reduced to 3.4-kilobase-pair (kbp) segments by Bgl I or Bgl II digestion. The core histone genes of a 3.4-kbp Bgl II segment cloned in the plasmid pDv3/3.4 have the same order as theD. melanogaster core histone genes in the plasmid cDm500:
. Nonetheless, pDv3/3.4 and cDm500 have different histone gene configurations: In pDv3/3.4, the region between the H2B and H3 genes contains 0.35 kbp and cannot encode histone H1; in cDm500, the region contains 2.0 kbp and encodes histone H1. The lack of an H1 gene between the H2B and H3 genes in 30–40% ofD. virilis histone gene clusters suggests that changes in histone gene arrays have occurred during the evolution ofDrosophila. The ancestors of modernDrosophila may have possessed multiple varieties of histone gene clusters, which were subsequently lost differentially in thevirilis andmelanogaster lineages. Alternatively, they may have possessed a single variety, which was rearranged during evolution. The H1 genes ofD. virilis andD. melanogaster did not cross-hybridize in vitro under conditions that maintain stable duplexes between DNAs that are 75% homologous. Consequently,D. virilis H1 genes could not be visualized by hybridization to an H1-specific probe and thus remain unidentified. Our observations suggest that the coding segments in the H1 genes ofD. virilis andD. melanogaster are >25% divergent. Our estimate of sequence divergence in the H1 genes ofD. virilis andD. melanogaster seems high until one considers that the coding sequences of cloned H1 genes from the closely related speciesD. melanogaster andD. simulans are 5% divergent. 相似文献
2.
3.
Cecropin is a type of antibacterial peptide that is synthesized in response to infection and has been characterized in many
insect species and one mammal. The Cecropin locus of Drosophila melanogaster also contains the gene Andropin, which has been identified only in this species and encodes a male-specific antibacterial peptide. As a first step in studying
the molecular evolution of the cecropin and andropin genes among Drosophila species, we have isolated genomic clones that cover the Cecropin locus in Drosophila virilis. The cloned region totals approximately 25 kb, within which a 9-kb fragment contains four cecropin genes and one pseudogene.
All four genes have a high level of sequence homology to D. melanogaster Cecropin, about 80% identity in the coding regions, and the intron positions are conserved. As in D. melanogaster and other insects, κB-related cis-regulatory elements are found upstream of these cecropin genes. An Andropin-related sequence was not identified in D. virilis; however, genome Southern hybridizations suggest that Andropin-related sequences are present in at least the melanogaster species subgroup. Analysis of 19 insect cecropin genes identifies a common ancestral Cecropin before the divergence of Diptera and Lepidoptera. In addition, D. melanogaster and D. virilis can be identified by monophyletic clades for Cecropin. In contrast, the Lepidopteran species show polyphyletic relationships for duplicated cecropin genes.
Received: 12 August 1996 / Accepted: 18 October 1996 相似文献
4.
Birgit Drabent Jae-Sun Kim Werner Albig Eva Prats Luis Cornudella Detlef Doenecke 《Journal of molecular evolution》1999,49(5):645-655
We isolated five different phage clones containing histone gene clusters with up to five H1 genes per phage clone from a
Mytilus edulis genomic library. Among these H1 genes, nine gene types coding for five different H1 proteins have been identified. All H1
histone genes were located on repetitive restriction fragments with only slightly different sizes. The H1 coding regions show
highly related sequences, suggesting that the multitude of H1 genes has evolved by gene duplication events. Core histone genes
could not be found on these five Mytilus edulis genome fragments.
Received: 28 July 1998 / Accepted: 17 May 1999 相似文献
5.
Ronald W. DeBry 《Journal of molecular evolution》1998,46(3):355-360
Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published sequence from M. musculus shows that this gene has likely been a pseudogene throughout the evolution of the genus Mus, while the gene from Rattus norvegicus is likely functional. Three large (>20 bp) deletions were found among the Mus pseudogenes, a feature that is very unusual compared to surveys of processed pseudogenes. In addition, there are two single-base
deletions and one 4-bp insertion among the Mus pseudogenes. The species distributions of one of the large deletions and the 4-bp insertion require either independent insertions
of an identical sequence, independent deletions with identical boundaries, or a deletion followed by precise reintegration
of the original sequence. The evidence favors the hypothesis of multiple deletions with identical boundaries. The ``coding'
regions of the Mus pseudogenes show a much reduced level of among-species variability in the 3′ half of the pseudogene, compared both to the
5′ half and to flanking sequences. This supports a hypothesis that the 3′ end of the pseudogene is the target of frequent
gene conversion by functional H2a genes.
Received: 1 April 1997 / Accepted: 12 June 1997 相似文献
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7.
The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared
both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly
related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we
undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out
of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4
genes including the intergenic region.
The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the
ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences.
The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all
sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones.
The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly
with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the
ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates.
Received: 4 April 1997 / Accepted: 1 August 1997 相似文献
8.
9.
de Q Robin GC Claudianos C Russell RJ Oakeshott JG 《Journal of molecular evolution》2000,51(2):149-160
A cluster composed of 10 active α-esterase genes and a pseudogene is distributed over 60 kb in the Drosophila melanogaster genome. This paper describes the corresponding cluster in Drosophila buzzatii, whose lineage diverged from that of D. melanogaster when the subgenera Drosophila and Sophophora diverged about 50 Mya. With three exceptions we find that the composition of
the cluster is conserved in the two lineages. The location of αE1 in D. melanogaster differs from that of its nearest relative in D. buzzatii, and αE4 has duplicated independently in the two lineages. The nature of these differences indicates that a mechanism exists whereby
copies of genes can be placed in opposite orientation and nonadjacent positions within a gene cluster, although this does
not seem to be a feature of earlier events in the cluster's evolution. The rates of amino acid change are not significantly
different between orthologs, but the rates differ sevenfold among paralogs, indicating that very different selective forces
are acting on the genes of the cluster. Mapping of sequence differences onto a model of the tertiary structure of the enzymes
indicates that motifs contributing to substrate binding and catalysis have changed radically in the αE4s and suggest that
this subgroup of α-esterases may be evolving into a substantially different functional niche.
Received: 4 January 2000 / Accepted: 18 April 2000 相似文献
10.
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
11.
12.
Phylogenetic analysis of histone H3 protein sequences demonstrates the independent origin of the replacement histone H3 genes
in animals and in plants. Multiple introns in the replacement histone H3 genes of animals in a pattern distinct from that
in plant replacement H3 genes supports this conclusion. It is suggested that replacement H3 genes arose at the same time that,
independently, multicellular forms of animals and of plants evolved. Judged by the degree of invariant and functionally constrained
amino acid positions, histones H3 and H4, which form together the tetramer kernel of the nucleosome, have co-evolved with
equal rates of sequence divergence. Residues 31 and 87 in histone H3 are the only residues that consistently changed across
each gene duplication event that created functional replacement histone H3 variant forms. Once changed, these residues have
remained invariant across divergent speciation. This suggests that they are required to allow replacement histone H3 to participate
in the assembly of nucleosomes in non–S-phase cells. The abundant occurrence of polypyrimidine sequences in the introns of
all replacement H3 genes, and the replacement of an intron by a polypyrimidine motif upstream of the alfalfa replacement H3
gene, suggests a function. It is speculated that they may contribute to the characteristic cell-cycle-independent pattern
of replacement histone H3 genes by binding nucleosome-excluding proteins. 相似文献
13.
14.
The sequence of a cloned Anopheles stephensi gene showed 72% inferred amino acid identity with Drosophila melanogaster Dox-A2 and 93% with its putative ortholog in Anopheles gambiae. Dox-A2 is the reported but herein disputed structural locus for diphenol oxidase A2. Database searches identified Dox-A2 related gene sequences from 15 non-insect species from diverse groups. Phylogenetic trees based on alignments of inferred
protein sequences, DNA, and protein motif searches and protein secondary structure predictions produced results consistent
with expectations for genes that are orthologous. The only inconsistency was that the C-terminus appears to be more primitive
in the yeasts than in plants. In mammals, plants, and yeast these genes have been shown to code for a non-ATPase subunit of
the PA700 (19S) regulatory complex of 26S proteasome. The analyses indicated that the insect genes contain no divergent structural
features, which taken within an appraisal of all available data, makes the reported alternative function highly improbable.
A plausible additional role, in which the 26S proteasome is implicated in regulation of phenol oxidase, would also apply to
at least the mammalian genes. No function has yet been reported for the other included sequences. These were from genome projects
and included Caenorhabiditus elegans, Arabidopsis thaliana, Fugu rubripes, and Toxoplasma gondii. A consensus of the results predicts a protein containing exceptionally long stretches of helix with a hydrophilic C-terminus.
Phosphorylation site motifs were identified at two conserved positions. Possible SRY and GATA-1 binding motifs were found
at conserved positions upstream of the mosquito genes. The location of A. stephensi Dox-A2 was determined by in situ hybridization at 34D on chromosome arm 3R. It is in a conserved gene cluster with respect to the
other insects. However, the A. stephensi cluster contains a gene showing significant sequence identity to human and pigeon carnitine acetyltransferase genes, therefore
showing divergence with the distal end of the D. melanogaster cluster.
Received: 3 July 1998 / Accepted: 22 December 1999 相似文献
15.
Sequence analysis of 27 alleles of each of the three Ras-related genes in Drosophila melanogaster indicates that they all have low levels of polymorphism but may experience slightly different evolutionary pressures. No
amino acid replacement substitutions were indicated in any of the sequences, or in the sibling species D. simulans and D. mauritiana. The Dras1 gene, which is the major ras homologue in Drosophila, has less within-species variation in D. melanogaster relative to the amount of divergence from the sibling species than does Dras2, although the contrast was not significant by the HKA test. Dras2 appears to be maintaining two classes of haplotype in D. melanogaster, one of which is closer to the alleles observed in the sibling species, suggesting that this is not likely to be a pseudogene
despite the absence of a mutant phenotype. Although differences in level of expression may affect the function of the genes,
it is concluded that genetic variation in the Ras signal transduction pathways cannot be attributed to catalytic variation
in the Ras proteins.
Received: 5 November 1998 / Accepted: 26 March 1999 相似文献
16.
Jean-Luc Da Lage Maurice Wegnez Marie-Louise Cariou 《Journal of molecular evolution》1996,43(4):334-347
While the two amylase genes of Drosophila melanogaster are intronless, the three genes of D. pseudoobscura harbor a short intron. This raises the question of the common structure of the Amy gene in Drosophila species. We have investigated the presence or absence of an intron in the amylase genes of 150 species
of Drosophilids. Using polymerase chain reaction (PCR), we have amplified a region that surrounds the intron site reported
in D. pseudoobscura and a few other species. The results revealed that most species contain an intron, with a variable size ranging from 50 to
750 bp, although the very majoritary size was around 60–80 bp. Several species belonging to different lineages were found
to lack an intron. This loss of intervening sequence was likely due to evolutionarily independent and rather frequent events.
Some other species had both types of genes: In the obscura group, and to a lesser extent in the ananassae subgroup, intronless copies had much diverged from intron-containing genes. Base composition of short introns was found to
be variable and correlated with that of the surrounding exons, whereas long introns were all A-T rich. We have extended our
study to non-Drosophilid insects. In species from other orders of Holometaboles, Lepidoptera and Hymenoptera, an intron was
found at an identical position in the Amy gene, suggesting that the intron was ancestral.
Received: 23 October 1995 / Accepted: 5 March 1996 相似文献
17.
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
18.
Drosophila ananassae is known to produce numerous alpha-amylase variants. We have cloned seven different Amy genes in an African strain homozygous for the AMY1,2,3,4 electrophoretic pattern. These genes are organized as two main clusters:
the first one contains three intronless copies on the 2L chromosome arm, two of which are tandemly arranged. The other cluster,
on the 3L arm, contains two intron-bearing copies. The amylase variants AMY1 and AMY2 have been assigned to the intronless
cluster, and AMY3 and AMY4 to the second one. The divergence of coding sequences between clusters is moderate (6.1% in amino
acids), but the flanking regions are very different, which could explain their differential regulation. Within each cluster,
coding and noncoding regions are conserved. Two very divergent genes were also cloned, both on chromosome 3L, but very distant
from each other and from the other genes. One is the Amyrel homologous (41% divergent), the second one, Amyc1 (21.6% divergent) is unknown outside the D. ananassae subgroup. These two genes have unknown functions.
Received: 30 May 2000 / Accepted: 17 July 2000 相似文献
19.
Jocelyne DiRuggiero James R. Brown Allison P. Bogert Frank T. Robb 《Journal of molecular evolution》1999,49(4):474-484
DNA repair in the Archaea is relevant to the consideration of genome maintenance and replication fidelity in the last universal
common ancestor (LUCA) from two perspectives. First, these prokaryotes embody a mix of bacterial and eukaryal molecular features.
Second, DNA repair proteins would have been essential in LUCA to maintain genome integrity, regardless of the environmental
temperature. Yet we know very little of the basic molecular mechanisms of DNA damage and repair in the Archaea in general.
Many studies on DNA repair in archaea have been conducted with hyperthermophiles because of the additional stress imposed
on their macromolecules by high temperatures. In addition, of the six complete archaeal genome sequences published so far,
five are thermophilic archaea. We have recently shown that the hyperthermophile Pyrococcus furiosus has an extraordinarily high capacity for repair of radiation-induced double-strand breaks and we have identified and sequenced
several genes involved in DNA repair in P. furiosus. At the sequence level, only a few genes share homology with known bacterial repair genes. For instance, our phylogenetic
analysis indicates that archaeal recombinases occur in two paralogous gene families, one of which is very deeply branched,
and both recombinases are more closely related to the eukaryotic RAD51 and Dmc1 gene families than to the Escherichia coli recA gene. We have also identified a gene encoding a repair endo/exonuclease in the genomes of several Archaea. The archaeal sequences
are highly homologous to those of the eukaryotic Rad2 family and they cluster with genes of the FEN-1 subfamily, which are
known to be involved in DNA replication and repair in eukaryotes. We argue that there is a commonality of mechanisms and protein
sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal
set of genes thought to represent the genome of the LUCA. 相似文献
20.
Yury Y. Shevelyov 《Molecular & general genetics : MGG》1993,239(1-2):205-208
A novel retrotransposon, aurora, containing 324 by long terminal repeats (LTRs) was detected in Drosophila melanogaster as a 5 kb insertion in the heterochromatic Stellate gene. This insertion causes a 5 bp duplication of the integration site. Southern analysis and in situ hybridization data show that all detectable copies of aurora are immobilized in the D. melanogaster heterochromatin. However, mobile copies of aurora were revealed in the cuchromatin of D. simulans. The element was also found in various species of the melanogaster subgroup and in the D. virilis genome.The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession numbers X70361 and X70362 相似文献