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1.
Noboru Sueoka 《Journal of molecular evolution》1999,49(1):49-62
The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely
different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average
G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used
to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides
to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon
position from Parity Rule 2 (PR2), where A=T and G=C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority
of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class
of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that
when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation
coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available,
it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition,
PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint.
Received: 5 November 1998 / Accepted: 1 March 1999 相似文献
2.
Codon Usage in Plastid Genes Is Correlated with Context, Position Within the Gene, and Amino Acid Content 总被引:5,自引:0,他引:5
Highly expressed plastid genes display codon adaptation, which is defined as a bias toward a set of codons which are complementary
to abundant tRNAs. This type of adaptation is similar to what is observed in highly expressed Escherichia coli genes and is probably the result of selection to increase translation efficiency. In the current work, the codon adaptation
of plastid genes is studied with regard to three specific features that have been observed in E. coli and which may influence translation efficiency. These features are (1) a relatively low codon adaptation at the 5′ end of
highly expressed genes, (2) an influence of neighboring codons on codon usage at a particular site (codon context), and (3)
a correlation between the level of codon adaptation of a gene and its amino acid content. All three features are found in
plastid genes. First, highly expressed plastid genes have a noticeable decrease in codon adaptation over the first 10–20 codons.
Second, for the twofold degenerate NNY codon groups, highly expressed genes have an overall bias toward the NNC codon, but
this is not observed when the 3′ neighboring base is a G. At these sites highly expressed genes are biased toward NNT instead
of NNC. Third, plastid genes that have higher codon adaptations also tend to have an increased usage of amino acids with a
high G + C content at the first two codon positions and GNN codons in particular. The correlation between codon adaptation
and amino acid content exists separately for both cytosolic and membrane proteins and is not related to any obvious functional
property. It is suggested that at certain sites selection discriminates between nonsynonymous codons based on translational,
not functional, differences, with the result that the amino acid sequence of highly expressed proteins is partially influenced
by selection for increased translation efficiency.
Received: 21 July 1999 / Accepted: 5 November 1999 相似文献
3.
Mitochondrial Genes Collectively Suggest the Paraphyly of Crustacea with Respect to Insecta 总被引:9,自引:0,他引:9
Erik García-Machado Malgorzata Pempera Nicole Dennebouy Mario Oliva-Suarez Jean-Claude Mounolou Monique Monnerot 《Journal of molecular evolution》1999,49(1):142-149
Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern
of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences
of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a
distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to
insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies,
it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that
of the tree based on all seven genes.
Received: 25 August 1998 / Accepted: 8 March 1999 相似文献
4.
Seiichi Taguchi Shuichi Kojima Mahito Terabe Yoshinori Kumazawa Hiroshi Kohriyama Masayuki Suzuki Kin-ichiro Miura Haruo Momose 《Journal of molecular evolution》1997,44(5):542-551
We previously found that proteinaceous protease inhibitors homologous to Streptomyces subtilisin inhibitor (SSI) are widely produced by various Streptomyces species, and we designated them ``SSI-like proteins' (Taguchi S, Kikuchi H, Suzuki M, Kojima S, Terabe M, Miura K, Nakase
T, Momose H [1993] Appl Environ Microbiol 59:4338–4341). In this study, SSI-like proteins from five strains of the genus Streptoverticillium were purified and sequenced, and molecular phylogenetic trees were constructed on the basis of the determined amino acid
sequences together with those determined previously for Streptomyces species. The phylogenetic trees showed that SSI-like proteins from Streptoverticillium species are phylogenetically included in Streptomyces SSI-like proteins but form a monophyletic group as a distinct lineage within the Streptomyces proteins. This provides an alternative phylogenetic framework to the previous one based on partial small ribosomal RNA sequences,
and it may indicate that the phylogenetic affiliation of the genus Streptoverticillium should be revised. The phylogenetic trees also suggested that SSI-like proteins possessing arginine or methionine at the
P1 site, the major reactive center site toward target proteases, arose multiple times on independent lineages from ancestral
proteins possessing lysine at the P1 site. Most of the codon changes at the P1 site inferred to have occurred during the evolution
of SSI-like proteins are consistent with those inferred from the extremely high G + C content of Streptomyces genomes. The inferred minimum number of amino acid replacements at the P1 site was nearly equal to the average number for
all the variable sites. It thus appears that positive Darwinian selection, which has been postulated to account for accelerated
rates of amino acid replacement at the major reaction center site of mammalian protease inhibitors, may not have dictated
the evolution of the bacterial SSI-like proteins.
Received: 23 August 1996 / Accepted: 20 November 1996 相似文献
5.
The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid
protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this
organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal
genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes
for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI
cDNAs from E. gracilis possess short 5′ and 3′ untranslated transcribed sequences and lack a 3′ poly[A] tail.
The COI gene does not require uridine insertion/deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional,
and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [α-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3′ end structures of mRNAs, phylogenetic
analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes
of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using
nuclear ribosomal RNA sequences.
Received: 5 March 1996 / Accepted: 31 July 1996 相似文献
6.
Francesco Frati Chris Simon Jack Sullivan David L. Swofford 《Journal of molecular evolution》1997,44(2):145-158
The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic
levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic
relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all
insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the
basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions
appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in
some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels
observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or
exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity
of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information
was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical
support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well
supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from
an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.
Received: 12 January 1996 / Accepted: 10 August 1996 相似文献
7.
Near Homogeneity of PR2-Bias Fingerprints in the Human Genome and Their Implications in Phylogenetic Analyses 总被引:1,自引:0,他引:1
Noboru Sueoka 《Journal of molecular evolution》2001,53(4-5):469-476
Genes of a multicellular organism are heterogeneous in the G+C content, which is particularly true in the third codon position.
The extent of deviation from intra-strand equality rule of A = T and G = C (Parity Rule 2, or PR2) is specific for individual amino acids and has been expressed as the PR2-bias fingerprint. Previous
results suggested that the PR2-bias fingerprints tend to be similar among the genes of an organism, and the fingerprint of
the organism is specific for different taxa, reflecting phylogenetic relationships of organisms. In this study, using coding
sequences of a large number of human genes, we examined the intragenomic heterogeneity of their PR2-bias fingerprints in relation
to the G+C content of the third codon position (P
3
). Result shows that the PR2-bias fingerprint is similar in the wide range of the G+C content at the third codon position
(0.30–0.80). This range covers approximately 89% of the genes, and further analysis of the high G+C range (0.80–1.00), where
genes with normal PR2-bias fingerprints and those with anomalous fingerprints are mixed, shows that the total of 95% of genes
have the similar finger prints. The result indicates that the PR2-bias fingerprint is a unique property of an organism and
represents the overall characteristics of the genome. Combined with the previous results that the evolutionary change of the
PR2-bias fingerprint is a slow process, PR2-bias fingerprints may be used for the phylogenetic analyses to supplement and
augment the conventional methods that use the differences of the sequences of orthologous proteins and nucleic acids. Potential
advantages and disadvantages of the PR2-bias fingerprint analysis are discussed.
Received: 21 December 2000 / Accepted: 16 February 2001 相似文献
8.
The aminoacyl-tRNA synthetases are ubiquitous enzymes which catalyze a crucial step of the cell life, the specific attachment
of amino acids to their cognate tRNA. The amino acid sequences of three archaeal seryl-tRNA synthetases (SerRS) from Haloarcula marismortui and Methanococcus jannaschii, both belonging to the group of Euryarchaeota, and from Sulfolobus solfataricus, of the group of Crenarchaeota, were aligned with other eubacterial and eukaryal available SerRS sequences. In an attempt to identify some features of adaptation
to extreme environments of these organisms, amino acid composition and amino acid substitutions between mesophilic and thermophilic
SerRS were analyzed. In addition, universal phylogenetic trees of SerRS including the three known archaeal sequences, rooted
by the threonyl-tRNA synthetases were inferred. Amino acid analyses of the SerRS revealed two ways of adaptation to thermophilic
environments between the Eubacteria and the Archaea; most of the usually described amino acid substitutions were nonsignificant in the case of archaeal thermophilic SerRS and
most amino acid composition biases seemed to be linked to the genome G+C content pressure. The phylogenetic analysis of the
SerRS showed the Archaea to be paraphyletic, H. marismortui emerging with the Gram-positive Bacteria, M. jannaschii being near the root of the tree, and S. solfataricus branching with Eucarya.
Received: 30 March 1998 / Accepted: 14 July 1998 相似文献
9.
In the unicellular green alga, Chlamydomonas reinhardtii, cytochrome oxidase subunit 2 (cox2) and 3 (cox3) genes are missing from the mitochondrial genome. We isolated and sequenced a BAC clone that carries the whole cox3 gene and its corresponding cDNA. Almost the entire cox2 gene and its cDNA were also determined. Comparison of the genomic and the corresponding cDNA sequences revealed that the
cox3 gene contains as many as nine spliceosomal introns and that cox2 bears six introns. Putative mitochondria targeting signals were predicted at each N terminal of the cox genes. These spliceosomal introns were typical GT–AG-type introns, which are very common not only in Chlamydomonas nuclear genes but also in diverse eukaryotic taxa. We found no particular distinguishing features in the cox introns. Comparative analysis of these genes with the various mitochondrial genes showed that 8 of the 15 introns were interrupting
the conserved mature protein coding segments, while the other 7 introns were located in the N-terminal target peptide regions.
Phylogenetic analysis of the evolutionary position of C. reinhardtii in Chlorophyta was carried out and the existence of the cox2 and cox3 genes in the mitochondrial genome was superimposed in the tree. This analysis clearly shows that these cox genes were relocated during the evolution of Chlorophyceae. It is apparent that long before the estimated period of relocation
of these mitochondrial genes, the cytosol had lost the splicing ability for group II introns. Therefore, at least eight introns
located in the mature protein coding region cannot be the direct descendant of group II introns. Here, we conclude that the
presence of these introns is due to the invasion of spliceosomal introns, which occurred during the evolution of Chlorophyceae.
This finding provides concrete evidence supporting the ``intron-late' model, which rests largely on the mobility of spliceosomal
introns.
Received: 22 August 2000 / Accepted: 28 February 2001 相似文献
10.
Codon Usage Bias and tRNA Abundance in Drosophila 总被引:5,自引:0,他引:5
Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development.
We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the exception
of Asp which had very low contribution to overall bias. Asp was also the only amino acid that did not show a clear preference
for one of its synonymous codons. Synonymous codon usage in Drosophila was consistent with ``optimal' codons deduced from the isoaccepting tRNA availability. Interestingly, amino acids whose
major isoaccepting tRNAs change during development did not show as strong bias as those with developmentally unchanged tRNA
pools. Asp is the only amino acid for which the major isoaccepting tRNAs change between larval and adult stages. We conclude
that synonymous codon usage in Drosophila is well explained by tRNA availability and is probably influenced by developmental changes in relative abundance.
Received: 5 December 1996 / Accepted: 14 June 1997 相似文献