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1.
de Miranda AB Alvarez-Valin F Jabbari K Degrave WM Bernardi G 《Journal of molecular evolution》2000,50(1):45-55
Mycobacterium tuberculosis and Mycobacterium leprae are the ethiological agents of tuberculosis and leprosy, respectively. After performing extensive comparisons between genes
from these two GC-rich bacterial species, we were able to construct a set of 275 homologous genes. Since these two bacterial
species also have a very low growth rate, translational selection could not be so determinant in their codon preferences as
it is in other fast-growing bacteria. Indeed, principal-components analysis of codon usage from this set of homologous genes
revealed that the codon choices in M. tuberculosis and M. leprae are correlated not only with compositional constraints and translational selection, but also with the degree of amino acid
conservation and the hydrophobicity of the encoded proteins. Finally, significant correlations were found between GC3 and synonymous distances as well as between synonymous and nonsynonymous distances.
Received: 30 October 1998 / Accepted: 16 August 1999 相似文献
2.
Ferritin, a protein widespread in nature, concentrates iron ∼1011–1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor
(based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin
gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants
but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals
and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization
in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning
of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals
but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the
absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In
plant ferritin genes, the number of introns (n= 7) is higher than in animals (n= 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin
gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary
protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin
genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding
sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional
constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin
gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid,
the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
Received: 25 July 1995 / Accepted: 3 October 1995 相似文献
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Janet L. Siefert Kirt A. Martin Fadi Abdi William R. Widger George E. Fox 《Journal of molecular evolution》1997,45(5):467-472
Five complete bacterial genome sequences have been released to the scientific community. These include four (eu)Bacteria,
Haemophilus influenzae, Mycoplasma genitalium, M. pneumoniae, and Synechocystis PCC 6803, as well as one Archaeon, Methanococcus jannaschii. Features of organization shared by these genomes are likely to have arisen very early in the history of the bacteria and
thus can be expected to provide further insight into the nature of early ancestors. Results of a genome comparison of these
five organisms confirm earlier observations that gene order is remarkably unpreserved. There are, nevertheless, at least 16
clusters of two or more genes whose order remains the same among the four (eu)Bacteria and these are presumed to reflect conserved
elements of coordinated gene expression that require gene proximity. Eight of these gene orders are essentially conserved
in the Archaea as well. Many of these clusters are known to be regulated by RNA-level mechanisms in Escherichia coli, which supports the earlier suggestion that this type of regulation of gene expression may have arisen very early. We conclude
that although the last common ancestor may have had a DNA genome, it likely was preceded by progenotes with an RNA genome.
Received: 10 March 1996 / Accepted: 20 May 1997 相似文献
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Igarashi N Harada J Nagashima S Matsuura K Shimada K Nagashima KV 《Journal of molecular evolution》2001,52(4):333-341
A 37-kb photosynthesis gene cluster was sequenced in a photosynthetic bacterium belonging to the beta subclass of purple bacteria (Proteobacteria), Rubrivivax gelatinosus. The cluster contained 12 bacteriochlorophyll biosynthesis genes (bch), 7 carotenoid biosynthesis genes (crt), structural genes for photosynthetic apparatuses (puf and puh), and some other related genes. The gene arrangement was markedly different from those of other purple photosynthetic bacteria, while two superoperonal structures, crtEF-bchCXYZ-puf and bchFNBHLM-lhaA-puhA, were conserved. Molecular phylogenetic analyses of these photosynthesis genes showed that the photosynthesis gene cluster of Rvi. gelatinosus was originated from those of the species belonging to the alpha subclass of purple bacteria. It was concluded that a horizontal transfer of the photosynthesis gene cluster from an ancestral species belonging to the alpha subclass to that of the beta subclass of purple bacteria had occurred and was followed by rearrangements of the operons in this cluster. 相似文献
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Liao D 《Journal of molecular evolution》2000,51(4):305-317
Multiple copies of a given ribosomal RNA gene family undergo concerted evolution such that sequences of all gene copies are
virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal
crossing over are the proposed mechanisms for concerted evolution of tandemly repeated sequences, whereas dispersed genes
are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic
rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12
prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were
found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events
convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly,
the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization
do not affect rRNA gene homogenization. Thus, gene conversion underlies concerted evolution of bacterial rRNA genes, which
normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic
sequence.
Received: 31 March 2000 / Accepted: 15 June 2000 相似文献
10.
Hiroyuki Sawada Fumihiko Suzuki Izumi Matsuda Naruya Saitou 《Journal of molecular evolution》1999,49(5):627-644
Pseudomonas syringae are differentiated into approximately 50 pathovars with different plant pathogenicities and host specificities. To understand
its pathogenicity differentiation and the evolutionary mechanisms of pathogenicity-related genes, phylogenetic analyses were
conducted using 56 strains belonging to 19 pathovars. gyrB and rpoD were adopted as the index genes to determine the course of bacterial genome evolution, and hrpL and hrpS were selected as the representatives of the pathogenicity-related genes located on the genome (chromosome). Based on these
data, NJ, MP, and ML phylogenetic trees were constructed, and thus 3 trees for each gene and 12 gene trees in total were obtained,
all of which showed three distinct monophyletic groups: Groups 1, 2 and 3. The observation that the same set of OTUs constitute
each group in all four genes suggests that these genes had not experienced any intergroup horizontal gene transfer within
P. syringae but have been stable on and evolved along with the P. syringae genome. These four index genes were then compared with another pathogenicity-related gene, argK (the phaseolotoxin-resistant ornithine carbamoyltransferase gene, which exists within the argK–tox gene cluster). All 13 strains of pv. phaseolicola and pv. actinidiae used had been confirmed to produce phaseolotoxin and to have argK, whose sequences were completely identical, without a single synonymous substitution among the strains used (Sawada et al.
1997a). On the other hand, argK were not present on the genomes of the other 43 strains used other than pv. actinidiae and pv. phaseolicola. Thus, the productivity of phaseolotoxin and the possession of the argK gene were shown at only two points on the phylogenetic tree: Group 1 (pv. actinidiae) and Group 3 (pv. phaseolicola). A t test between these two pathovars for the synonymous distances of argK and the tandemly combined sequence of the four index genes showed a high significance, suggesting that the argK gene (or argK–tox gene cluster) experienced horizontal gene transfer and expanded its distribution over two pathovars after the pathovars had
separated, thus showing a base substitution pattern extremely different from that of the noncluster region of the genome.
Received: 18 January 1999 / Accepted: 25 May 1999 相似文献
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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
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Characterization of the Hydra Lamin and Its Gene: A Molecular Phylogeny of Metazoan Lamins 总被引:4,自引:0,他引:4
Andreas Erber Dieter Riemer Helmut Hofemeister Marc Bovenschulte Reimer Stick Georgia Panopoulou Hans Lehrach Klaus Weber 《Journal of molecular evolution》1999,49(2):260-271
We report sequences for nuclear lamins from the teleost fish Danio and six invertebrates. These include two cnidarians (Hydra and Tealia), one priapulid, two echinoderms, and the cephalochordate Branchiostoma. Combining these results with earlier data on Drosophila, Caenorhabditis elegans, and various vertebrates, the following conclusions on lamin evolution can be drawn. First, all invertebrate lamins resemble
in size the vertebrate B-type lamin. Second, all lamins described previously for amphibia, birds and mammals as well as the
first lamin of a fish, characterized here, show a cluster of 7 to 12 acidic residues in the tail domain. Since this acidic
cluster is absent from all invertebrate lamins including that of the cephalochordate Branchiostoma, it was acquired with the vertebrate lineage. The larger A-type lamin of differentiated cells must have arisen subsequently
by gene duplication and insertion of an extra exon. This extra exon of the vertebrate A-lamins is the only major change in
domain organization in metazoan lamin evolution. Third, the three introns of the Hydra and Priapulus genes correspond in position to the last three introns of vertebrate B-type lamin genes. Thus the entirely different gene
organization of the C. elegans and Drosophila Dmo genes seems to reflect evolutionary drift, which probably also accounts for the fact that C. elegans has the most diverse lamin sequence. Finally we discuss the possibility that two lamin types, a constitutively expressed
one and a developmentally regulated one, arose independently on the arthropod and vertebrate lineages.
Received: 4 February 1999 / Accepted: 1 April 1999 相似文献
16.
Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and
the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and
analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, a unicellular red alga (AF022186). The analysis revealed that this genome shows several unusual structural features,
such as a hypothetical hairpin structure in a gene-free region and absence of large repeat units. We provide evidence that
this structural organization of the cp-genome of C. caldarium may be that of the most ancient cp-genome so far described. We also compared the cp-genome of C. caldarium to the other known cp-genomes of the red lineage. The cp-genome of C. caldarium cannot be readily aligned with that of Porphyra purpurea, a multicellular red alga, or Guillardia theta due to a displacement of a region of the cp-genome. The phylogenetic tree reveals that the secondary endosymbiosis, through
which G. theta evolved, took place after the separation of the ancestors of C. caldarium and P. purpurea.
We found several genes unique to the cp-genome of C. caldarium. Five of them seem to be involved in the building of bacterial cell envelopes and may be responsible for the thermotolerance
of the chloroplast of this alga. Two additional genes may play a role in stabilizing the photosynthetic machinery against
salt stress and detoxification of the chloroplast. Thus, these genes may be unique to the cp-genome of C. caldarium and may be required for the endurance of the extreme living conditions of this alga.
Received: 3 June 2000 / Accepted: 18 July 2000 相似文献
17.
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
18.
The extracellular hemoglobins of cladocerans derive from the aggregation of 12 two-domain globin subunits that are apparently
encoded by four genes. This study establishes that at least some of these genes occur as a tandem array in both Daphnia magna and Daphnia exilis. The genes share a uniform structure; a bridge intron separates two globin domains which each include three exons and two
introns. Introns are small, averaging just 77 bp, but a longer sequence (2.2–3.2 kb) separates adjacent globin genes. A survey
of structural diversity in globin genes from other daphniids revealed three independent cases of intron loss, but exon lengths
were identical, excepting a 3-bp insertion in exon 5 of Simocephalus. Heterogeneity in the extent of nucleotide divergence was marked among exons, largely as a result of the pronounced diversification
of the terminal exon. This variation reflected, in part, varying exposure to concerted evolution. Conversion events were frequent
in exons 1–4 but were absent from exons 5 and 6. Because of this difference, the results of phylogenetic analyses were strongly
affected by the sequences employed in this construction. Phylogenies based on total nucleotide divergence in exons 1–4 revealed
affinities among all genes isolated from a single species, reflecting the impact of gene conversion events. In contrast, phylogenies
based on total nucleotide divergence in exons 5 and 6 revealed affinities among orthologous genes from different taxa.
Received: 8 March 1999 / Accepted: 14 July 1999 相似文献
19.
In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent
biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we
consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In
particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered.
Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary
conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that
strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably
between genomes.
Received: 6 May 1999 / Accepted: 29 October 1999 相似文献
20.
In translation, separate aminoacyl-tRNA synthetases attach the 20 different amino acids to their cognate tRNAs, with the
exception of glutamine. Eukaryotes and some bacteria employ a specific glutaminyl-tRNA synthetase (GlnRS) which other Bacteria,
the Archaea (archaebacteria), and organelles apparently lack. Instead, tRNAGln is initially acylated with glutamate by glutamyl-tRNA synthetase (GluRS), then the glutamate moiety is transamidated to glutamine.
Lamour et al. [(1994) Proc Natl Acad Sci USA 91:8670–8674] suggested that an early duplication of the GluRS gene in eukaryotes
gave rise to the gene for GlnRS—a copy of which was subsequently transferred to proteobacteria. However, questions remain
about the occurrence of GlnRS genes among the Eucarya (eukaryotes) outside of the ``crown' taxa (animals, fungi, and plants),
the distribution of GlnRS genes in the Bacteria, and their evolutionary relationships to genes from the Archaea. Here, we
show that GlnRS occurs in the most deeply branching eukaryotes and that putative GluRS genes from the Archaea are more closely
related to GlnRS and GluRS genes of the Eucarya than to those of Bacteria. There is still no evidence for the existence of
GlnRS in the Archaea. We propose that the last common ancestor to contemporary cells, or cenancestor, used transamidation
to synthesize Gln-tRNAGln and that both the Bacteria and the Archaea retained this pathway, while eukaryotes developed a specific GlnRS gene through
the duplication of an existing GluRS gene. In the Bacteria, GlnRS genes have been identified in a total of 10 species from
three highly diverse taxonomic groups: Thermus/Deinococcus, Proteobacteria γ/β subdivision, and Bacteroides/Cytophaga/Flexibacter.
Although all bacterial GlnRS form a monophyletic group, the broad phyletic distribution of this tRNA synthetase suggests that
multiple gene transfers from eukaryotes to bacteria occurred shortly after the Archaea–eukaryote divergence. 相似文献