人β神经生长因子基因稀有密码子及mRNA二级结构对其在大肠杆菌中表达的影响

目的:研究人β神经生长因子(β-NGF)基因中稀有密码子及其mRNA二级结构对其在大肠杆菌中表达量的影响。方法:根据对人β-ngf中稀有密码子及其mRNA二级结构的研究,同义突变人β-ngf基因,通过PCR得到人β-ngf的5’端同义突变基因rh-β-ngfp32和全同义突变基因rh-β-ngfmu,将这2个序列克隆入载体pET3a中,得到重组质粒pET3a-ngfp32和pET3a-ngfmu,分别转化大肠杆菌BL21(DE3)感受态,IPTG诱导表达,收集菌体,SDS-PAGE检测其表达量的改变。结果:构建的pET3a-ngfp32和pET3a-ngfmu表达载体酶切和测序结果正确,SDS-PAGE结果显示,与在重组菌pET3a-NGF总蛋白中的表达量相比,目的蛋白rh-β-NGF在重组菌pET3a-NGFP32和pET3a-NGFmu中的表达量均明显增高,并且在重组菌pET3a-NGFmu中的表达量高于重组菌pET3a-NGFP32。结论:目的蛋白rh-β-NGF在重组菌pET3a-NGFP32和pET3a-NGFmu中表达量的增高,说明人β-ngf基因中稀有密码子和mRNA的二级结构对其在大肠杆菌中的表达有较为明显的影响,结果为构建rh-β-NGF的大肠杆菌工程菌株奠定了基础。     

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'

Synonymous codon usage is a commonly used means for estimating gene expression levels of Escherichia coli genes and has also been used for predicting highly expressed genes for a number of prokaryotic genomes. By comparison of expression level-dependent features in codon usage with protein abundance data from two proteome studies of exponentially growing E. coli and Bacillus subtilis cells, we try to evaluate whether the implicit assumption of this approach can be confirmed with experimental data. Log-odds ratio scores are used to model differences in codon usage between highly expressed genes and genomic average. Using these, the strength and significance of expression level-dependent features in codon usage were determined for the genes of the Escherichia coli, Bacillus subtilis and Haemophilus influenzae genomes. The comparison of codon usage features with protein abundance data confirmed a relationship between these to be present, although exceptions to this, possibly related to functional context, were found. For species with expression level-dependent features in their codon usage, the applied methodology could be used to improve in silico simulations of the outcome of two-dimensional gel electrophoretic experiments.     

Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models

With the advent of larger genome databases detection of horizontal gene transfer events has been transformed into an increasingly important issue. Here we present a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detect HTG (Horizontally transferred genes), which are based on (a) the codon adaptation index, codon usage, and GC percentage (CAI/GC); (b) a distributional profile (DP) approach made by a gene search in the closely related phylogenetic genomes; (c) a Bayesian model (BM); and (d) a first-order Markov model (MM). All methods exhibit limitations although, as shown here, the BM and the MM are better approximations. Moreover, the MM has demonstrated a more accurate rate of detections when genes from closely related organisms are evaluated. The application of the MM to detect recently transferred genes in the genomes of E. coli strains K12 MG1655, O157 EDL933, and Salmonella typhimurium, shows that these organisms have undergone a rather significant amount of HTG, most of which appear to be pseudogenes. Few of these sequences that have undergone HGT appear to have well defined functions and may be involved in the organism's adaptation.     

Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli

The codon that follows the AUG initiation triplet (+2 codon) affects gene expression in Escherichia coli. We have extended this analysis using two model genes lacking any apparent Shine-Dalgarno sequence. Depending on the identity of the +2 codon a difference in gene expression up to 20-fold could be obtained. The effects did not correlate with the levels of intracellular pools of cognate tRNA for the +2 codon, with putative secondary mRNA structures, or with mRNA stability. However, most +2 iso-codons that were decoded by the same species of tRNA gave pairwise similar effects, suggesting that the effect on gene expression was associated with the decoding tRNA. High adenine content of the +2 codon was associated with high gene expression. Of the fourteen +2 codons that mediated the highest efficiency, all except two had an adenine as the first base of the codon. Analysis of the 3540 E. coli genes from the TransTerm database revealed that codons associated with high gene expression in the two expression systems are over-represented at the +2 position in natural genes. Codons that are associated with low gene expression are under-represented. The data suggest that evolution has favored codons at the +2 position that give high translation initiation.     

Codon usage in bacteria: correlation with gene expressivity

The nucleic acid sequence bank now contains over 600 protein coding genes of which 107 are from prokaryotic organisms. Codon frequencies in each new prokaryotic gene are given. Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome (chromosome, transposons and plasmids) is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration. The codon composition of each gene is summarized using two indexes: one is based on the differential usage of iso-tRNA species during gene translation, the other on choice between Cytosine and Uracil for third base. A strong relationship between codon composition and mRNA expressivity is confirmed, even for genes transcribed in the same operon. The influence of codon use of peptide elongation rate and protein yield is discussed. Finally, the evolutionary aspect of codon selection in mRNA sequences is studied.     

Predicting gene expression level from codon usage bias

The "expression measure" of a gene, E(g), is a statistic devised to predict the level of gene expression from codon usage bias. E(g) has been used extensively to analyze prokaryotic genome sequences. We discuss 2 problems with this approach. First, the formulation of E(g) is such that genes with the strongest selected codon usage bias are not likely to have the highest predicted expression levels; indeed the correlation between E(g) and expression level is weak among moderate to highly expressed genes. Second, in some species, highly expressed genes do not have unusual codon usage, and so codon usage cannot be used to predict expression levels. We outline a simple approach, first to check whether a genome shows evidence of selected codon usage bias and then to assess the strength of bias in genes as a guide to their likely expression level; we illustrate this with an analysis of Shewanella oneidensis.     

‘ATG vectors’ for regulated high-level expression of cloned genes in Escherichia coli

A plasmid cloning vector system has been constructed that allows for the production of large quantities of foreign proteins or fragments thereof, in an unfused state. These vectors provide strong regulated trp-lac fusion promoters and the lacZ ribosome-binding site (RBS) followed by an ATG translation initiation codon at an appropriate distance from the RBS. The ATG codon is located within a unique NcoI restriction site (CCATGG). Digestion with NcoI exposes the ATG for fusion. Gene fragments lacking a prokaryotic RBS and/or ATG start codons can be inserted in several ways. Expression experiments using a truncated cI gene of bacteriophage A or a large portion of the coding region of the Herpes simplex virus type l glycoprotein D gene have been performed. The results of these studies show that the vectors are useful for the high-level expression of prokaryotic and eukaryotic genes in Escherichia coli.     

猴B病毒被膜糖蛋白gC的原核表达及诊断价值评价

目的:原核表达猴B病毒糖蛋白gC胞外区片段,评价其在猴B病毒血清学检测中的特异性和敏感性,为猴B病毒检测奠定基础。方法:利用PCR方法扩增gC胞外区基因片段,同时合成该片段的优化密码子序列,将其插入表达载体pET-28b(+)形成重组质粒,转化至大肠杆菌BL21(DE3)并进行诱导表达;纯化蛋白先以Western印迹进行验证,再以ELISA方法和标准阳性、阴性血清评价其诊断价值。结果:直接从病毒DNA模板上获得的基因片段未能表达,而优化后的基因片段表达水平较高,表达蛋白的相对分子质量约为48×103,为包涵体形式,占菌体总蛋白的30%左右;Western印迹显示,重组蛋白能与猴B病毒阳性血清和His单克隆抗体发生免疫反应;34份标准阳性血清和25份阴性血清的ELISA检测结果显示,重组蛋白的敏感性和特异性分别为94.1%(32/34)和100%(25/25)。结论:利用原核表达系统制备的gC胞外区重组蛋白,可作为猴B病毒血清学检测抗原,其特异性和敏感性都较好。     

含翻译增强子的表达载体pSC34的构建及初步应用

１９８８年Ｏｌｉｎｓ［１］发现Ｔ７噬菌体基因１０的先导序列（Ｔ７ｇ１０Ｌ）具有明显的促进基因翻译的作用．本文构建了含Ｔ７ｇ１０Ｌ的表达载体ｐＳＣ３４,并尝试表达了几个不同类型的基因．１材料与方法１．１菌株大肠杆菌菌株ＴＡＰ１０６为本室储存．ＴＡＰ１０...     

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae

A similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. These analyses were performed to obtain an indication as to whether individual genes were Haemophilus-like in nature, or if they probably had more recently entered the H.influenzae gene pool via horizontal gene transfer from other species. The average and SD values were calculated for the similarity statistics from a study of the set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most like other Rd genes. Genes displaying codon usage statistics >1 SD above this range were either considered part of the highly expressed group of H.influenzae genes, or were considered of foreign origin. An alternative determinant for identifying genes of foreign origin was when the similarity statistics produced a value that was much closer to a non-H.influenzae reference organism than to any of the Haemophilus species contained in the reference set. Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced similarity statistics closer to one of the other reference genomes thereby suggesting that these sequences may have entered the H.influenzae gene pool more recently via horizontal transfer.     

一种含ELP60基因的载体pRELPN促进大肠杆菌的外源基因的高表达

类弹性蛋白多肽（ELP）为含有人工合成的ELP60基因的表达载体pRELPN,能促使外源基因在大肠杆菌中的高表达。当ELP60在大肠杆菌表达载体pET28a的多克隆位点被克隆后,其自身的表达低,也不与目的基因构成ELP融合蛋白质,而是促进克隆在ELP60基因后的含起始密码ATG的外源目的基因独立高表达。外源目的基因表达量占宿主蛋白的20% ～ 60%,比用pET28a载体表达的外源基因表达量高2～10倍。此类表达载体pRELPN适合于表达包括抗体、抗原、酶、重组蛋白质、多肽及ELP融合蛋白质等的外源基因的独立高表达。这些结果表明,pRELPN代表了一种有效的表达载体,有助于解决在原核表达中,所受限的普通载体对外源基因低表达或不表达所导致的不能产业化的问题。     

Comprehensive analysis of prokaryotic mechanosensation genes: their characteristics in codon usage.

In the present study, we examined GC nucleotide composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI) and gene length for 308 prokaryotic mechanosensitive ion channel (MSC) genes from six evolutionary groups: Euryarchaeota, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, and Gammaproteobacteria. Results showed that: (1) a wide variation of overrepresentation of nucleotides exists in the MSC genes; (2) codon usage bias varies considerably among the MSC genes; (3) both nucleotide constraint and gene length play an important role in shaping codon usage of the bacterial MSC genes; and (4) synonymous codon usage of prokaryotic MSC genes is phylogenetically conserved. Knowledge of codon usage in prokaryotic MSC genes may benefit from the study of the MSC genes in eukaryotes in which few MSC genes have been identified and functionally analysed.     

A 'phase-shift' fusion system for the regulation of foreign gene expression by lambda repressor in gram-negative bacteria

A 'phase-shift' translation fusion vector was constructed in which mutually compatible restriction sites BamHI, BclI and BglII are positioned in such a manner that the cut point is in a different reading frame, immediately following the ATG start codon and ribosome-binding site of the lambda cro gene. The lambda cro gene is expressed from promoter pR and controlled by a thermosensitive (cI857) lambda repressor. The usefulness of the expression vector was demonstrated using a galK gene lacking the ATG start codon and fusing this to the pR promoter and ATG start codon of the lambda cro gene, resulting in cI857-regulated expression of galactokinase. The vector is of general use for foreign gene expression in Escherichia coli when the target gene has a compatible cohesive end (5'-GATC-3') at the N terminus (provided, for example, by a BamHI linker). The lambda cI857-pR-cro-galK cassette was cloned into pJRD215, a wide-host-range plasmid and transferred by conjugation to a variety of Gram-negative bacteria. In all cases, thermosensitive regulation of galactokinase could be demonstrated, though the levels of induction varied considerably. These results show that the powerful lambda pR promoter and the efficient lambda repressor can be used to regulate expression of foreign genes in Gram-negative organisms other than E. coli.     

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome

Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, correspondence analysis on codon usage is used to classify E.coli genes into three groups, and the relationship between them and expression levels from microarray experiments is studied. These groups are: group 1, highly biased genes; group 2, moderately biased genes; and group 3, AT-rich genes with low CUB. It is shown that, surprisingly, there is a negative correlation between codon bias and expression levels for group 3 genes, i.e. genes with extremely low codon adaptation index (CAI) values are highly expressed, while group 2 show the lowest average expression levels and group 1 show the usual expected positive correlation between CAI and expression. This trend is maintained over all functional gene groups, seeming to contradict the E.coli-yeast paradigm on CUB. It is argued that these findings are still compatible with the mutation-selection balance hypothesis of codon usage and that E.coli genes form a dynamic system shaped by these factors.     

Translation efficiencies of synonymous codons are not always correlated with codon usage in tobacco chloroplasts

Codon usage in chloroplasts is different from that in prokaryotic and eukaryotic nuclear genomes. However, no experimental approach has been made to analyse the translation efficiency of individual codons in chloroplasts. We devised an in vitro assay for translation efficiencies using synthetic mRNAs, and measured the translation efficiencies of five synonymous codon groups in tobacco chloroplasts. Among four alanine codons (GCN, where N is U, C, A or G), GCU was the most efficient for translation, whereas the chloroplast genome lacks tRNA genes corresponding to GCU. Phenylalanine and tyrosine are each encoded by two codons (UUU/C and UAU/C, respectively). Phenylalanine UUC and tyrosine UAC were translated more than twice as efficiently than UUU and UAU, respectively, contrary to their codon usage, whereas translation efficiencies of synonymous codons for alanine, aspartic acid and asparagine were parallel to their codon usage. These observations indicate that translation efficiencies of individual codons are not always correlated with codon usage in vitro in chloroplasts. This raises an important issue for foreign gene expression in chloroplasts.     

Cold-shock induced high-yield protein production in Escherichia coli

Overexpression of proteins in Escherichia coli at low temperature improves their solubility and stability. Here, we apply the unique features of the cspA gene to develop a series of expression vectors, termed pCold vectors, that drive the high expression of cloned genes upon induction by cold-shock. Several proteins were produced with very high yields, including E. coli EnvZ ATP-binding domain (EnvZ-B) and Xenopus laevis calmodulin (CaM). The pCold vector system can also be used to selectively enrich target proteins with isotopes to study their properties in cell lysates using NMR spectroscopy. We have cloned 38 genes from a range of prokaryotic and eukaryotic organisms into both pCold and pET14 (ref. 3) systems, and found that pCold vectors are highly complementary to the widely used pET vectors.     

Reduced synonymous substitution rate at the start of enterobacterial genes.

Synonymous codon usage is less biased at the start of Escherichia coli genes than elsewhere. The rate of synonymous substitution between E.coli and Salmonella typhimurium is substantially reduced near the start of the gene, which suggests the presence of an additional selection pressure which competes with the selection for codons which are most rapidly translated. Possible competing sources of selection are the presence of secondary ribosome binding sites downstream from the start codon, the avoidance of mRNA secondary structure near the start of the gene and the use of sub-optimal codons to regulate gene expression. We provide evidence against the last of these possibilities. We also show that there is a decrease in the frequency of A, and an increase in the frequency of G along the E.coli genes at all three codon positions. We argue that these results are most consistent with selection to avoid mRNA secondary structure.