共查询到20条相似文献,搜索用时 656 毫秒
1.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), localized in the cytosol of Trichomonas vaginalis, was partially purified. The enzyme is specific for NAD+ and is similar in most of its catalytic properties to glycolytic GAPDHs from other organisms. Its sensitivity to koningic acid is similar to levels observed in GAPDHs from eubacteria and two orders of magnitude lower than those observed for eukaryotic GAPDHs. The complete amino acid sequence of T. vaginalis GAPDH was derived from the N-terminal sequence of the purified protein and the deduced sequence of a cDNA clone. It showed great similarity to other eubacterial and eukaryotic GAPDH sequences. The sequence of the S-loop displayed a eubacterial signature. The overall sequence was more similar to eubacterial sequences than to cytosolic and glycosomal eukaryotic sequences. In phylogenetic trees obtained with distance matrix and parsimony methods T. vaginalis GAPDH clustered with its eubacterial homologs. GAPDHs of other amitochondriate protists, belonging to early branches of the eukaryotic lineage (Giardia lamblia and Entamoeba histolytica—Smith M.W. and Doolittle R.F., unpublished data in GenBank), showed typical eukaryotic signatures and clustered with other eukaryotic sequences, indicating that T. vaginalis GAPDH occupies an anomalous position, possibly due to horizontal gene transfer from a eubacterium.
Correspondence to: M. Müller 相似文献
2.
Detailed nucleotide diversity studies revealed that the fil1 gene of Antirrhinum, which has been reported to be single copy, is a member of a gene family composed of at least five genes. In four Antirrhinum majus populations with different mating systems and one A. graniticum population, diversity within populations is very low. Divergence among Antirrhinum species and between Antirrhinum and Digitalis is also low. For three of these genes we also obtained sequences from a more divergent member of the Scrophulariaceae, Verbascum nigrum. Compared with Antirrhinum, little divergence is again observed. These results, together with similar data obtained previously for five cycloidea genes,
suggest either that these gene families (or the Antirrhinum genome) are unusually constrained or that there is a low rate of substitution in these lineages. Using a sample of 52 genes,
based on two measures of codon usage (ENC and GC3 content), we show that cyc and fil1 are among the least biased Antirrhinum genes, so that their low diversity is not due to extreme codon bias.
Received: 20 June 2000 / Accepted: 25 October 2000 相似文献
3.
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
4.
Bouzat JL McNeil LK Robertson HM Solter LF Nixon JE Beever JE Gaskins HR Olsen G Subramaniam S Sogin ML Lewin HA 《Journal of molecular evolution》2000,51(6):532-543
We employed a phylogenomic approach to study the evolution of α subunits of the proteasome gene family from early diverging
eukaryotes. BLAST similarity searches of the Giardia lamblia genome identified all seven α proteasome genes characteristic of eukaryotes from the crown group. In addition, a PCR strategy
for the amplification of multiple α subunit sequences generated single α proteasome products for representatives of the Kinetoplastida
(Leishmania major), the Parabasalia (Trichomonas vaginalis), and the Microsporidia (Vairimorpha sp., Nosema sp., Endoreticulata sp., and Spraguea lophii). The kinetoplastid Trypanosoma cruzi and the eukaryote crown group Acanthamoeba castellanii yielded two distinct α proteasome genes each. The presence of seven distinct α proteasome genes in G. lamblia, one of the earliest-diverging eukaryotes, indicates that the α proteasome gene family evolved rapidly from a minimum of one
gene in Archaea to seven or more in Eukarya. Results from the phylogenomic analysis are consistent with the idea that the
Diplomonida (as represented by G. lamblia), the Kinetoplastida, the Parabasalia, and the Microsporidia diverged after the duplication events that originated the α
proteasome gene family. A model for the early origin and evolution of the proteasome gene family is presented.
Received: 14 February 2000 / Accepted: 14 August 2000 相似文献
5.
In many unicellular organisms, invertebrates, and plants, synonymous codon usage biases result from a coadaptation between
codon usage and tRNAs abundance to optimize the efficiency of protein synthesis. However, it remains unclear whether natural
selection acts at the level of the speed or the accuracy of mRNAs translation. Here we show that codon usage can improve the
fidelity of protein synthesis in multicellular species. As predicted by the model of selection for translational accuracy,
we find that the frequency of codons optimal for translation is significantly higher at codons encoding for conserved amino
acids than at codons encoding for nonconserved amino acids in 548 genes compared between Caenorhabditis elegans and Homo sapiens. Although this model predicts that codon bias correlates positively with gene length, a negative correlation between codon
bias and gene length has been observed in eukaryotes. This suggests that selection for fidelity of protein synthesis is not
the main factor responsible for codon biases. The relationship between codon bias and gene length remains unexplained. Exploring
the differences in gene expression process in eukaryotes and prokaryotes should provide new insights to understand this key
question of codon usage.
Received: 18 June 2000 / Accepted: 10 November 2000 相似文献
6.
Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages 总被引:8,自引:0,他引:8
Brian R. Morton 《Journal of molecular evolution》1998,46(4):449-459
In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study
the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each
gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons
based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared
to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias
is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among
the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation
efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities
in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity
among the various genomes are discussed.
Received: 6 June 1997 / Accepted: 24 July 1997 相似文献
7.
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
8.
Héctor Musto Héctor Romero Helena Rodríguez-Maseda 《Journal of molecular evolution》1998,46(2):159-167
Synonymous codon choices vary considerably among Schistosoma mansoni genes. Principal components analysis detects a single major trend among genes, which highly correlates with GC content in
third codon positions and exons, but does not discriminate among putatively highly and lowly expressed genes. The effective
number of codons used in each gene, and its distribution when plotted against GC3, suggests that codon usage is shaped mainly by mutational biases. The GC content of exons, GC3, 5′, 3′, and flanking (5′+ 3′+ introns) regions are all correlated among them, suggesting that variations in GC content may
exist among different regions of the S. mansoni genome. We propose that this genome structure might be among the most important factors shaping codon usage in this species,
although the action of selection on certain sequences cannot be excluded.
Received: 10 March 1997 / Accepted: 27 June 1997 相似文献
9.
The Nonrandom Location of Synonymous Codons Suggests That Reading Frame-Independent Forces Have Patterned Codon Preferences 总被引:6,自引:0,他引:6
Biased codon usage is common in eukaryotic and prokaryotic genes. Evidence from Escherichia, Saccharomyces, and Drosophila indicates that it favors translational efficiency and accuracy. However, to date no functional advantages have been identified
in the codon–anticodon interactions involving the most frequently used (preferred) codons. Here we present evidence that forces
not related to the individual codon–anticodon interaction may be involved in determining which synonymous codons are preferred
or avoided. We show that the ``off-frame' trinucleotide motif preferences inferrable from Drosophila coding regions are often in the same direction as Drosophila's ``in-frame' codon preferences, i.e., its codon usage. The off-frame preferences were inferred from the nonrandomness of
the location of confamilial synonymous codons along coding regions—a pattern often described as a context dependence of nucleotide
choice at synonymous positions or as codon-pair bias. We relied on randomizations of the location of confamilial codons that
do not alter, and cannot be influenced by, the encoded amino acid sequences, codon usage, or base composition of the genes
examined. The statistically significant congruency of in-frame and off-frame trinucleotide preferences suggests that the same
kind of reading-frame-independent force(s) may also influence synonymous codon choice. These forces may have produced biases
in codon usage that then led to the evolution of the translational advantages of these motifs as preferred codons. Under this
scenario, tRNA pool size differences between preferred and nonpreferred codons initially were evolved to track the default
overrepresentation of codons with preferred motifs. The motif preference hypothesis can explain the structuring of codon preferences
and the similarities in the codon usages of distantly related organisms.
Received: 10 November 1998 / Accepted: 23 February 1999 相似文献
10.
Erik A. C. Wiemer Véronique Hannaert Paul R. L. A. van den Ijssel Joris Van Roy Fred R. Opperdoes Paul A. M. Michels 《Journal of molecular evolution》1995,40(4):443-454
In Trypanoplasma borelli, a representative of the Bodonina within the Kinetoplastida, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity was detected in both the cytosol and glycosomes. This situation is similar to that previously found in Trypanosomatidae, belonging to a different Kinetoplastida suborder. In Trypanosomatidae different isoenzymes, only distantly related, are responsible for the activity in the two cell compartments. In contrast, immunoblot analysis indicated that the GAPDH activity in cytosol and glycosomes of T. borelli should be attributed to identical or at least very similar proteins related to the glycosomal GAPDH of Trypanosomatidae. Moreover, only genes related to the glycosomal GAPDH genes of Trypanosomatidae could be detected. All attempts to identify a gene related to the one coding for the trypanosomatid cytosolic GAPDH remained unsuccessful. Two tandemly arranged genes were found which are 95% identical. The two encoded polypeptides differ in 17 residues. Their sequences are 72–77% identical to the glycosomal GAPDH of the other Kinetoplastida and share with them some characteristic features: an excess of positively charged residues, specific insertions, and a small carboxy-terminal extension containing the sequence -AKL. This tripeptide conforms to the consensus signal for targeting of proteins to glycosomes. One of the two gene copies has undergone some mutations at positions coding for highly conserved residues of the active site and the NAD+-binding domain of GAPDH. Modeling of the protein's three-dimensional structure suggested that several of the substitutions compensate each other, retaining the functional coenzyme-binding capacity, although this binding may be less tight. The presented analysis of GAPDH in T. borelli gives further support to the assertion that one isoenzyme, the cytosolic one, was acquired by horizontal gene transfer during the evolution of the Kinetoplastida, in the lineage leading to the suborder Trypanosomatina (Trypanosome, Leishmania), after the divergence from the Bodonina (Trypanoplasma). Furthermore, the data clearly suggest that the original GAPDH of the Kinetoplastida has been compartmentalized during evolution.Abbreviations GAPDH
glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12)
- HK
hexokinase (EC 2.7.1.1)
- PGI
glucosephosphate isomerase (EC 5.3.1.9)
- PGK
phosphoglycerate kinase (EC 2.7.2.3)
- PYK
pyruvate kinase (EC 2.7.1.40)
- TIM
triosephosphate isomerase (EC 5.3.1.1)
- SDS
sodium dodecyl sulfate
- SSC
saline sodium citrate (0.15 M NaCl, 15 mM sodium citrate, pH 7.0)
- MYR
millions of years
Nucleotide sequence data reported in this paper have been submitted to the EMBL/Genbank/DDBJ nucleotide sequence databases under accession number X74535
Correspondence to: P.A.M. Michels 相似文献
11.
Phylogenetic Relationships of the Glycolytic Enzyme, Glyceraldehyde-3-Phosphate Dehydrogenase, from Parabasalid Flagellates 总被引:4,自引:0,他引:4
Over 90% of the open reading frame of gap genes for glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) was obtained with PCR from five species
of Parabasala. With gap1 from Trichomonas vaginalis obtained earlier, the data include two sequences each for three species. All sequences were colinear with T. vaginalis gap1 and shared with it as a synapomorphy a 10- to 11-residue insertion not found in any other gap and an S-loop with characteristic features of eubacterial GAPDH. All residues known to be highly conserved in this enzyme
were present. The parabasalid sequences formed a robust monophyletic group in phylogenetic reconstructions with distance-based,
maximum-parsimony, and maximum-likelihood methods. The two genes of the amphibian commensal, Trichomitus batrachorum, shared a common ancestor with the rest, which separate into two well-supported lineages. T. vaginalis and Tetratrichomonas gallinarum (both representatives of Trichomonadinae) formed one, while Monocercomonas sp. and Tritrichomonas foetus formed the other. These data agreed with and/or were close to published reconstructions based on other macromolecules. They
did not support the ancestral position of Monocercomonas sp. proposed on the basis of morphological characteristics but confirmed an early emergence of Trichomitus batrachorum. The sequence pairs obtained from three species indicated either gene duplications subsequent to the divergence of the corresponding
lineages or a strong gene conversion later in these lineages. The parabasalid clade was a robust part of the eubacterial radiation
of GAPDH and showed no relationships to the clade that contained all other eukaryotic gap genes. The data clearly reveal that the members of this lineage use in their glycolytic pathway a GAPDH species with properties
and an evolutionary history that are unique among all eukaryotes studied so far.
Received: 28 April 1997 / Accepted: 14 October 1997 相似文献
12.
We compared the codon usage of sequences of transposable elements (TEs) with that of host genes from the species Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, and Homo sapiens. Factorial correspondence analysis showed that, regardless of the base composition of the genome, the TEs differed from the
genes of their host species by their AT-richness. In all species, the percentage of A + T on the third codon position of the
TEs was higher than that on the first codon position and lower than that in the noncoding DNA of the genomes. This indicates
that the codon choice is not simply the outcome of mutational bias but is also subject to selection constraints. A tendency
toward higher A + T on the third position than on the first position was also found in the host genes of A. thaliana, C. elegans, and S. cerevisiae but not in those of D. melanogaster and H. sapiens. This strongly suggests that the AT choice is a host-independent characteristic common to all TEs. The codon usage of TEs
generally appeared to be different from the mean of the host genes. In the AT-rich genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Saccharomyces cerevisiae, the codon usage bias of TEs was similar to that of weakly expressed genes. In the GC-rich genome of D. melanogaster, however, the bias in codon usage of the TEs clearly differed from that of weakly expressed genes. These findings suggest
that selection acts on TEs and that TEs may display specific behavior within the host genomes.
Received: 2 May 2001 / Accepted: 29 October 2001 相似文献
13.
Sequence analysis of two nuclear-encoded glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes isolated from the dinoflagellate
Gonyaulax polyedra distinguishes them as cytosolic and chloroplastic forms of the enzyme. Distance analysis of the cytosolic sequence shows
the Gonyaulax gene branching early within the cytosolic clade, consistent with other analyses. However, the plastid sequence forms a monophyletic
group with the plastid isoforms of cryptomonads, within an otherwise cytosolic clade, distinct from all other plastid GAPDHs.
This is attributed to lateral gene transfer from an ancestral cryptomonad to a dinoflagellate, providing the first example
of genetic exchange accompanying symbiotic associations between the two, which are common in present day cells.
Received: 29 April 1998 / Accepted: 7 July 1998 相似文献
14.
Julius Lukeš Milan Jirků David Doležel Ivica Kral'ová Laura Hollar Dmitri A. Maslov 《Journal of molecular evolution》1997,44(5):521-527
To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU)
and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome,
Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new
taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of
the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there
is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal
paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade
of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission.
This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the
adaptation to vertebrate hosts.
Received: 5 July 1996 / Accepted: 26 September 1996 相似文献
15.
To characterize the coding-sequence divergence of closely related genomes, we compared DNA sequence divergence between sequences
from a Brassica rapa ssp. pekinensis EST library isolated from flower buds and genomic sequences from Arabidopsis thaliana. The specific objectives were (i) to determine the distribution of and relationship between K
a and K
s, (ii) to identify genes with the lowest and highest K
a:K
s values, and (iii) to evaluate how codon usage has diverged between two closely related species. We found that the distribution
of K
a:K
s was unimodal, and that substitution rates were more variable at nonsynonymous than synonymous sites, and detected no evidence
that K
a and K
s were positively correlated. Several genes had K
a:K
s values equal to or near zero, as expected for genes that have evolved under strong selective constraint. In contrast, there
were no genes with K
a:K
s >1 and thus we found no strong evidence that any of the 218 sequences we analyzed have evolved in response to positive selection.
We detected a stronger codon bias but a lower frequency of GC at synonymous sites in A. thaliana than B. rapa. Moreover, there has been a shift in the profile of most commonly used synonymous codons since these two species diverged
from one another. This shift in codon usage may have been caused by stronger selection acting on codon usage or by a shift
in the direction of mutational bias in the B. rapa phylogenetic lineage. 相似文献
16.
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
17.
We examined a region of high variability in the mosaic mercury resistance (mer) operon of natural bacterial isolates from the primate intestinal microbiota. The region between the merP and merA genes of nine mer loci was sequenced and either the merC, the merF, or no gene was present. Two novel merC genes were identified. Overall nucleotide diversity, π (per 100 sites), of the merC gene was greater (49.63) than adjacent merP (35.82) and merA (32.58) genes. However, the consequences of this variability for the predicted structure of the MerC protein are limited
and putative functional elements (metal-binding ligands and transmembrane domains) are strongly conserved. Comparison of codon
usage of the merTP, merC, and merA genes suggests that several merC genes are not coeval with their flanking sequences. Although evidence of homologous recombination within the very variable
merC genes is not apparent, the flanking regions have higher homologies than merC, and recombination appears to be driving their overall sequence identities higher. The synonymous codon usage bias (ENC) values suggest greater variability in expression of the merC gene than in flanking genes in six different bacterial hosts. We propose a model for the evolution of MerC as a host-dependent,
adventitious module of the mer operon.
Received: 2 June 2000 / Accepted: 23 October 2000 相似文献
18.
Tandemly duplicated actin genes have been isolated from a Helicoverpa armigera genomic library. Sequence comparisons with actin genes from other species suggest they encode cytoplasmic actins, being most
closely related to the Bombyx mori A3 actin gene. The duplicated H. armigera actin genes, termed A3a and A3b, share 98.3% nucleotide sequence identity over their entire putative coding region. Analysis
of the distribution of nucleotide differences shows the first 763 bp are identical between the two coding regions, with the
18 nucleotide changes occurring in the remaining 366 bp. This observation suggests a gene conversion event has taken place
between the duplicated H. armigera A3a and A3b actin genes. Translation of the open-reading frames indicates the products of these genes are identical, apart
from a single amino acid difference at codon 273. Polymerase chain reaction and northern blot analysis have shown both H. armigera A3a and A3b genes are expressed during pupal development and in the brain of newly eclosed adults. A region 5′ of the H. armigera A3a actin gene start codon has been identified which contains regulatory sequences commonly found in the promoter region
of actin genes, including TATA, CAAT, and CArG motifs.
Received: 10 January 1996 / Accepted: 12 March 1996 相似文献
19.
In this study we analyze and compare the trends in codon usage in five
representative species of kinetoplastid protozoans (Crithidia fasciculata,
Leishmania donovani, L. major, Trypanosoma cruzi and T. brucei), with the
purpose of investigating the processes underlying these trends. A principal
component analysis shows that the G+C content at the third codon position
represents the main source of codon-usage variation, both within species
(among genes) and among species. The non- Trypanosoma species exhibit
narrow distributions in codon usage, while both Trypanosoma species present
large within-species heterogeneity. The three non-Trypanosoma species have
very similar codon-usage preferences. These codon preferences are also
shared by the highly expressed genes of T. cruzi and to a lesser degree by
those of T. brucei. This leads to the conclusion that the codon preferences
shared by these species are the ancestral ones in the kinetoplastids. On
the other hand, the study of noncoding sequences shows that Trypanosoma
species exhibit mutational biases toward A + T richness, while the non-
Trypanosoma species present mutational pressure in the opposite direction.
These data taken together allow us to infer the origin of the different
codon-usage distributions observed in the five species studied. In C.
fasciculata and Leishmania, both mutational biases and (translational)
selection pull toward G + C richness, resulting in a narrow distribution.
In Trypanosoma species the mutational pressure toward A + T richness
produced a shift in their genomes that differentially affected coding and
noncoding sequences. The effect of these pressures on the third codon
position of genes seems to have been inversely proportional to the level of
gene expression.
相似文献
20.
Sakai H Imamura C Osada Y Saito R Washio T Tomita M 《Journal of molecular evolution》2001,52(2):164-170
In this study, we analyzed the correlation between codon usage bias and Shine–Dalgarno (SD) sequence conservation, using
complete genome sequences of nine prokaryotes. For codon usage bias, we adopted the codon adaptation index (CAI), which is
based on the codon usage preference of genes encoding ribosomal proteins, elongation factors, heat shock proteins, outer membrane
proteins, and RNA polymerase subunit proteins. To compute SD sequence conservation, we used SD motif sequences predicted by
Tompa and systematically aligned them with 5′UTR sequences. We found that there exists a clear correlation between the CAI
values and SD sequence conservation in the genomes of Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii, and no relationship is found in M. genitalium, M. pneumoniae, and Synechocystis. That is, genes with higher CAI values tend to have more conserved SD sequences than do genes with lower CAI values in these
organisms. Some organisms, such as M. thermoautotrophicum, do not clearly show the correlation. The biological significance of these results is discussed in the context of the translation
initiation process and translation efficiency.
Received: 22 June 2000 / Accepted: 18 October 2000 相似文献