基因表达水平与同义密码子使用关系的初步研究

提出一个预测基因表达水平和同义密码子使用的自洽信息聚类方法。将同义密码子分成最适密码子、非最适密码子和稀有密码子,认为三者的使用频率是调控基因表达水平的主要因素。基于这一观点,对Ｅｃｏｌｉ和Ｙｅａｓｔ两类生物的基因表达水平和密码子的使用,用自洽信息聚类方法进行了预测。发现高低表达基因明显分开,基因表达水平被分为四级;甚高表达基因（ＶＨ）、高表达基因（Ｈ）、较低表达基因（ＬＭ）和低表达基因（ＬＬ）;     

Nucleotide sequence of ompV, the gene for a major Vibrio cholerae outer membrane protein

Summary The nucleotide sequence of the ompV gene of Vibrio cholerae was determined. The product of the gene is a 28,000 dalton protein which, after the removal of a 19 amino acid signal sequence, produces a mature outer membrane protein of 26,000 daltons. The cleavage site was determined by amino-terminal amino acid sequencing of the purified mature protein. The DNA upstream of the gene shows the presence of a typical promoter region as judged from the Escherichia coli consensus information; however, the Shine-Dalgarno sequence is associated with a region capable of forming a secondary structure in the mRNA. The formation of this structure would inhibit binding of the mRNA to the ribosome and reduce translation. It is proposed that this structure is recognized by a positive activator in V. cholerae and because of its absence in E. coli ompV is poorly expressed. The distribution of rare codons within ompV suggests that they may serve to slow down the translation of particular domains such that the nascent polypeptide has an opportunity to take up its conformation without interference from the later formed regions. Such a mechanism could aid localization of the protein if export were by a cotranslational secretion system.     

Polyubiquitin gene expression contributes to oxidative stress resistance in respiratory yeast (Saccharomyces cerevisiae)

A gene (ORFB) from Streptomyces antibioticus (an oleandomycin producer) encoding a large, multifunctional polyketide synthase (PKS) was cloned and sequenced. Its product shows an internal duplication and a close similarity to the third subunit of the PKS involved in erythromycin biosynthesis by Saccharopolyspora erythraea, showing the equivalent nine active site domains in the same order along the polypeptide. An unusual feature of this ORF is the GC content of most of the sequence, which is surprisingly low, for a Streptomyces gene; the large number of codons with T in the third position is particularly striking. The last 800 by of the gene stand out as being normal in their GC content, this region corresponding almost exactly to the thioesterase domain of the gene and suggesting that this domain was a late addition to the PKS. Based on the high degree of similarity between the ORFB product and the third subunit of the erythromycin PKS and the occurrence nearby of a gene conferring oleandomycin resistance, it is possible that this gene might be involved in the biosynthesis of the oleandomycin lactone ring.     

Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene"

Recently Anders Fuglsang provided a modified way for calculating N(c) when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each synonymous family type (as proposed by Wright) [Gene 87 (1990) 23] Fuglsang considered codon homozygosity of each amino acid individually. Marsashi and Najafabadi [Biochem. Biophys. Res. Commun. 324 (2004) 1] in their recent article demonstrated that the readjustment for overestimation at the level of individual amino acids results in loss of considerable amount of information. Immediately after the publication of Marsashi and Najafabadi, Fuglsang proposed that codon homozygosities can be calculated based on the classical population genetics [Biochem. Biophys. Res. Commun. 327 (2005) 1]. Though Fuglsang's approach is a novel one, it fails when any of the amino acids are absent in a gene. However, the inherent cause of overestimation at the level of individual amino acids is still obscured in the literature. Here in this communication we have presented a general condition where effective number of codons is overestimated using Wright's formula and also we propose a new way to calculate N(c), which is independent of amino acid composition.     

Essential factors determining codon usage in ubiquitin genes

Summary Ubiquitin is ubiquitous in all eukaryotes and its amino acid sequence shows extreme conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences coding for 13 ubiquitin genes from 11 species reported so far have been compiled and analyzed. The G+C content of codon third base reveals a positive linear correlation with the genome G+C content of the corresponding species. The slope strongly suggests that the overall G+C content of codons of polyubiquitin genes clearly reflects the genome G+C content by AT/GC substitutions at the codon third position. The G+C content of ubiquitin codon third base also shows a positive linear correlation with the overall G+C content of coding regions of compiled genes, indicating the codon choices among synonymous codons reflect the average codon usage pattern of corresponding species. On the other hand, the monoubiquitin gene, which is different from the polyubiquitin gene in gene organization, gene expression, and function of the encoding protein, shows a different codon usage pattern compared with that of the polyubiquitin gene. From comparisons of the levels of synonymous substitutions among ubiquitin repeats and the homology of the amino acid sequence of the tail of monomeric ubiquitin genes, we propose that the molecular evolution of ubiquitin genes occurred as follows: Plural primitive ubiquitin sequences were dispersed on genome in ancestral eukaryotes. Some of them situated in a particular environment fused with the tail sequence to produce monomeric ubiquitin genes that were maintained across species. After divergence of species, polyubiquitin genes were formed by duplication of the other primitive ubiquitin sequences on different chromosomes. Differences in the environments in which ubiquitin genes are embedded reflect the differences in codon choice and in gene expression pattern between poly- and monomeric ubiquitin genes.     

Patterns of context-dependent codon biases

The association of codon context and codon usage was studied in seven bacteria as well as Schizosaccharomyces pombe and Encephalitozoon cuniculi. The association is strongest in magnitude closest to the codons of interest but there is apparently no rule about which of the two contexts is generally strongest associated to codon usage. In all bacterial species and in the intron-rich Sch. pombe it was furthermore observed from plots of chi2 versus N that the wobble positions of codons in the proximity cause regular peaks both upstream and downstream. This observation is discussed in relation to a possible effect of mutational pressure on the association of codon usage and codon context. Absence of peaks corresponding to the wobble positions in the intron-poor En. cuniculi, and presence in Sch. pombe, may indicate that the role of introns in the context-dependent codon bias is negligible.     

基于相对密码子频率的芜菁花叶病毒基因组序列的进化分析

现有92株芜菁花叶病毒(TuMV)的全基因组序列已在GenBank报道,据分析报道其中58株不含重组序列。利用系统聚类法对92株TuMV的全基因组序列和58株TuMV全基因组序列的相对密码子频率RSCU值进行聚类分析。同时利用系统发育分析方法分析了这92株和58株TuMV全基因组序列。结果发现,92株芜菁花叶病毒株的密码子偏性聚类树与其系统进化树的一致度很低;而不含重组序列的58株芜菁花叶病毒株的密码子偏性聚类树与其系统进化树的一致度却非常高,且与寄生宿主类型基本对应。这表明在不存在重组的情况下,TuMV密码子频率的偏性可能是宿主内的一种选择压力,影响TuMV基因组的点突变进化方向,促使TuMV适应宿主内环境。     

DNA sequence of the ribosomal protein genes rp12 and rps19 from a plant-pathogenic mycoplasma-like organism

A segment of a ribosomal protein operon from a plant-pathogenic mycoplasma-like organism (MLO) was cloned and sequenced, to provide supplemental molecular data pertinent to the question of MLO phylogeny. Comparisons of the deduced amino acid sequences indicate an ancient divergence of the MLOs from the animal-pathogenic mycoplasmas. Furthermore, although both the plant and animal pathogens have A-T rich genomes, a fundamental difference was apparent in their usage of the UGA codon.     

Evidence that natural selection acts on silent mutation

Analysis of nucleic acid sequence data of mammalian hemoglobin, yeast cytochrome c, and human interferon reveals strong biases in favor of specific codons. These biases do not appear to dissipate over time, suggesting that an indirect form of selection acts on silent mutations. The data are compatible with the “bootstrapping” hypothesis that silent mutations which alter the rate of evolution can hitchhike with traits whose appearance they facilitate. Selection involving modulating effects of codon usage on gene expression may also be involved, but the data appear to exclude simple maximization of gene expression.     

Modulation of Base-Specific Mutation and Recombination Rates EnablesFunctional Adaptation Within the Context of the Genetic Code

The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of successful adaptation. We introduce a 64 × 64 matrix to quantify base-specific mutation potential, analyzing four different replicative systems, error-prone PCR, mouse antibodies, a nematode, and Drosophila. Mutational tendencies are correlated with the structural evolution of proteins. In systems under strong selective pressure, mutational biases are shown to favor the adaptive search of space, either by base mutation or by recombination. Such adaptability is discussed within the context of the genetic code at the levels of replication and codon usage.Supplementary material to this paper is available in electronic form.Reviewing Editor: Dr. Edward Trifonov