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PubMed2006

[Construction of Lactococcus lactis expression vector of recombinant human trefoil factor family 2].

OBJECTIVE: To construct a Lactococcus lactis expression vector of c-myc-tagged human trefoil factor family 2 (hTFF2) fusion gene to prepare for genetic modification of Lactococcus lactis that can secrete bioactive c-myc-hTFF2 protein. METHODS: Based on the amino sequence of hTFF2 and optimal Lactococcus lactis codon usage, the cDNA of hTFF2 was designed and extended at their 5' ends with a sequence encoding c-myc as the molecular tag. According to the restriction sites of pBluescript II sk (+), the SalI and BamHI sites were arranged at the 5' and 3' ends of the fusion gene respectively. The sequence of the fusion gene c-myc-hTFF2 was designed as 14 oligonucleotides that overlapped with each other, and by means of PCR, all the oligonucleotides were spliced to complete the construction of c-myc-hTFF2 fusion gene. The target gene of c-myc-hTFF2 was inserted into pBluescript II sk (+) to construct the cloning vector pBS-hTFF2 of c-myc-hTFF2 followed by verification by enzyme digestion and DNA sequencing. By digestion of pBS-TFF2 with BamHI/SalI and of pNBC1000 with BamHI/XhoI, we connected c-myc-hTFF2 with pNBC1000 to construct the expression vector c-myc-hTFF2 in E. coli named as pNTFF2. After digestion of pNTFF2 and pTRKH2 with XbaI, the target gene was subcloned into pTRKH2 and the construction of the expression vector pTRTFF2 in Lactococcus lactis was completed. The constructed vector was identified by restriction enzyme digestion. RESULTS AND CONCLUSION: The expression vector pTRTFF2 of c-myc-hTFF2 fusion gene has been successfully constructed. Assembly of oligonucleotides in vitro is an effective means to synthesize the target fusion gene and this prepares the ground for constructing engineered bacterium of Lactococcus lactis.

Cloning, Molecular↗
PubMedDate not supplied

Abrin-a A chain expressed as soluble form in Escherichia coli from a PCR-synthesized gene is catalytically and functionally active.

Abrin-a A chain (ABRaA) is a potent plant toxin, which possesses N-glycosylase activity toward eukaryotic 28S rRNA, and may have potential use in cancer therapy. To improve levels of expression in Escherichia coli, the gene encoding ABRaA was optimized by replacing rare codons with high-frequency ones, and synthesized using two-step PCR. The optimized ABRaA was cloned into the pET-His vector, and highly expressed in cytoplasm of E. coli. The yield of the purified recombinant (r) ABRaA proteins was up to 80 mg/l of induced culture. The rABRaA was one-step purified to homogeneity and its RNA-N-glycosylase ability to inhibit protein biosynthesis in a cell-free system and to depurinate 28S rRNA in rat liver ribosomes was demonstrated in vitro. The MTT assay showed that it also had a killing effect on human hepatoma cell line SMMC-7721 and myeloma cell line Sp2/0. For the first time, ABRaA expressed as soluble form in E. coli from a PCR-synthesized gene is catalytically and functionally active.

Abrin↗
PubMed2005

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.

A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at http://www.prodoric.de/JCat.

Algorithms↗
PubMed1983

Noise immunity of the genetic code.

Error detection and correction properties are fundamental for informative codes. Hamming's distance allows us to study this noise resistance. We present codes characterized by the resistance optimization to nonsense mutational effects. The calculation of the cumulated Hamming's distance allowing to determine the number of optimal codes and their structure can be detailed. The principle of these laws of optimization of resistance consists of choosing constituent codons connected by mutational neighbouring in such a way that random application of mutations on such a code minimize the occurrence of nonsense n-uplets or terminators. New coding symmetries are then described and screened using Galois's polynomials properties and Baudot's code. Such a study can be applied to any length of the codons. Here we present the principles of this optimization for the most simple doublet codes. Another constraint is discussed: the distribution of optimal subcodes for synonymity and the frequencies of utilization of the different codons. We compare these results to those of the present genetic code, and we observe that all coded amino acids (except the particular case of SER) are using optimal sub-codes of synonymity. This work suggests that the appearance of the genetic code was provoked by mutations while optimizing on several levels its resistance to their effects. Thus genetic coding would have been the best automata that could be produced in prebiotic conditions.

Base Sequence↗
PubMed2003

The optimal eukaryotic signal for translation initiation from non-AUG codons, present upstream of bacteriophage lambda P cistron, is inactive in Escherichia coli.

Expression of the replication genes of bacteriophage lambda, O and P, is believed to be translationally coupled. However, it was previously noted that, under conditions of amino acid starvation, when O is not synthesized, P continues to be expressed at a relatively high level. The results presented in this report, contrary to the previously presented hypothesis, suggest that an AGACUGGAU sequence (an optimal context for translation initiation from non-AUG codons in eukaryotes, and present upstream the P cistron) is inactive in Escherichia coli. Comparative sequence analysis confirms that such a signal is unlikely to be important for P synthesis. Instead, a weak Shine-Dalgarno sequence may be present upstream the P cistron, and be active in the absence of O gene expression.

Bacteriophage lambda↗
PubMed2003

mRNA 5' region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs.

The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.

5' Untranslated Regions↗
PubMed2004

On the optimality of the genetic code, with the consideration of termination codons.

The existence of nonrandom patterns in codon assignments is supported by many statistical and biochemical studies. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations. For example, it is known that when an error induces the conversion of an amino acid to another, the biochemical properties of the resulting amino acid are usually very similar to that of the original. Prior studies include many attempts at quantitative estimation of the fraction of randomly generated codes which, based upon load minimization, score higher than the canonical genetic code. In this study, we took into consideration both the relative frequencies of amino acids and nonsense mistranslations, factors which had been previously ignored. Incorporation of these parameters, resulted in a fitness function (phi) which rendered the canonical genetic code to be highly optimized with respect to load minimization. Considering termination codons, we applied a biosynthetic version of the coevolution theory, however, with low significance. We employed a revised cost for the precursor-product pairs of amino acids and showed that the significance of this approach depends on the cost measure matrix used by the researcher. Thus, we have compared the two prominent matrices, point accepted mutations 74-100 (PAM(74-100)) and mutation matrix in our study.

Amino Acids↗
PubMed1994

Mutational analysis of the translational signal in the human cytomegalovirus gpUL4 (gp48) transcript leader by retroviral infection.

A short upstream open reading frame (uORF2) in the human cytomegalovirus (CMV) gpUL4 (gp48) transcript leader is conserved among CMV strains and inhibits translation of a downstream cistron. Remarkably, this inhibitory effect depends on the amino acid coding information of uORF2, at least in transient transfection assays in diploid human fibroblasts. Using retroviral vectors, we now report that the gp48 leader inhibits downstream translation in multiple additional cell types, even when expressed from a stably integrated gene, and on a transcript containing an additional kilobase of complex leader sequences. The magnitude of inhibition can be augmented approximately 3- to 10-fold by replacing the context of nucleotides flanking the wild-type initiation codon of uORF2 with an optimal context, suggesting that leaky scanning past the wild-type AUG codon accounts for translation of the downstream cistron. Using an in vivo mutagenesis protocol that relies on reverse transcriptase infidelity, we isolated mutants in which the inhibitory effect of the gp48 leader was inactivated as a result of alterations in the coding information of uORF2. These studies demonstrate that, independent of the cell type or expression system used, CMV gp48 uORF2 is a potent translational inhibitory element.

3T3 Cells↗
PubMed2003

Expression of the genomic form of the bovine viral diarrhea virus E2 ORF in a bovine herpesvirus-1 vector.

Bovine viral diarrhea virus (BVDV) is a ubiquitous pathogen of cattle with a world-wide distribution. Recently, the possibility of using recombinant virus vectors to immunize cattle against selected BVDV genes has gained widespread interest. Among the virus vectors tested, bovine herpesvirus-1 (BHV1) provides many unique advantages. However, results of recent studies have raised the possibility that the codon usage pattern required for optimal expression in a BHV1-infected cell may be incompatible with the codon usage pattern of BVDV. If true, use of BHV1 to express BVDV proteins would require construction of synthetic BVDV genes that have been modified to resemble the codon pattern of BHV1. To explore this possibility, we constructed a BHV1 recombinant containing the genomic form of the BVDV (NADL) E2 ORF and compared expression of the E2 protein with that of the endogenous BHV1 gD protein. We observed that E2 was expressed at a significant rate compared to that of the gD protein. We conclude that codon usage problems are unlikely to constitute a serious problem for expression of BVDV proteins in BHV1 vectors.

Animals↗
PubMed2005

Codon and amino acid usage in two major human pathogens of genus Bartonella--optimization between replicational-transcriptional selection, translational control and cost minimization.

Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection--a characteristic of the genus Bartonella, not exhibited by any other alpha-proteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the cost-minimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.

Amino Acids↗
PubMed1982

Polyamine requirement for efficient translation of amber codons in vivo.

Multiplication of several amber mutants of bacteriophage T7 was decreased in two polyamine-deficient mutants of Escherichia coli K-12 carrying amber suppressors, relative to the multiplication of wild type bacteriophage T7 in the same hosts. In contrast the same T7 amber bacteriophages multiplied well in these strains when supplemented with polyamines. The requirement for polyamines for optimal translation of amber codons in vivo was confirmed by showing that infection of polyamine-depleted E. coli with bacteriophage T7 carrying an amber mutation in gene 1 resulted in an increased accumulation of the amber fragment of the gene 1 protein and a decreased accumulation of the full-length gene 1 protein compared with infection of an amine-supplemented culture. These results indicate that one important function of polyamines in vivo is concerned with protein translation and the protein-synthesizing ribosomal complex.

Codon↗
PubMed2006

Suppression of the acuH13 and acuH31 nonsense mutations in the carnitine/acylcarnitine translocase (acuH) gene of Aspergillus nidulans by the G265S substitution in the domain 2 of the release factor eRF1.

A search for suppressors of the carnitine/acylcarnitine translocase (CACT) deficiency in Aspergillus nidulans permitted the identification of the suaE7 mutation, mapping at a new translational suppressor (suaE) gene. The suaE gene is essential in A. nidulans and encodes the eukaryotic release factor 1 (eRF1). The suaE7 mutation suppresses two acuH alleles (acuH13 and acuH31), both carrying nonsense mutations in the CACT encoding gene that involve the replacement of a CAG (Gln) codon with a premature TAG stop codon. In contrast, the suaE7 gene does not suppress the acuH20 amber nonsense mutation involving a TGG-->TAG change. The phenotype associated to the suaE7 mutation strictly resembles that of mutants at the suaA and suaC genes, two translational suppressor genes previously identified, suggesting that their gene products might functionally interact in translation termination. Sequencing of the suaE7 gene allowed the identification of a mutation in the domain 2 of the omnipotent class-1 eukaryotic release factor involving the Gly265Ser substitution in the A. nidulans eRF1. This mutation creates a structural context unfavourable for normal eRF binding that allows the misreading of stop codons by natural suppressor tRNAs, such as the tRNAs(Gln). Structural analysis using molecular modelling of A. nidulans eRF1 domain 2 bearing the G265S substitution and computer simulation results suggest that this mutation might impair the necessary conformational changes in the eRF1 to optimally recognize the stop codon and simultaneously interact with the peptidyl transferase centre of the 60S ribosomal subunit.

Amino Acid Sequence↗
PubMed2006

Assay design and optimization of mutant-enriched PCR based method for detection of K-ras gene mutations in pancreatic carcinoma.

The aim of our work was to develop a fast, reliable and sensitive PCR method to detect K-ras mutations in various clinical samples. There is a need for an unimpeachable method for early diagnosis and/or screening of pancreatic cancer (PC). We optimized and subsequently analyzed four methods based on mutant-enriched PCR for the sensitivity, cost and time expense. Using the selected optimal method we examined codon 12 K- ras mutations in a study population of 59 patients with upper GIT malignancies. Reliability of the genotyping was confirmed by sequencing. By using the best of our modified mutant-enriched PCR methods we achieved sensitivity of 1:1 x 10(5). Further studies are necessary to determine the optimal biological material sampling in PC.

Adenocarcinoma↗
PubMed1985

Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs.

We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one position of the D-loop. Neither tRNA has a modified adenosine in the position 3'-adjacent to the anticodon. This can be rationalized on the basis of a structural constraint in the anticodon stem and may be related to optimization of the codon-anticodon interaction. Comparison of all E.coli serine tRNAs (and that encoded by bacteriophage T4) reveals characteristic (possibly functional) features. Evolutionary analysis suggests an eubacterial origin of the T4 tRNASer gene and the existence of a recent common ancestor for the tRNASerGGA and tRNASerGUC genes.

Anticodon↗
PubMed1994

Identification and analysis of the site of -1 ribosomal frameshifting in red clover necrotic mosaic virus.

The genomic RNA-1 of red clover necrotic mosaic dianthovirus (RCNMV) contains the heptanucleotide GGAUUUU that precedes the termination codon of the 5' proximal p27 open reading frame (ORF). This heptanucleotide is followed by a sequence with the potential to form a stable, complex secondary structure. Translation of RNA-1 is postulated to utilize a -1 ribosomal frameshifting mechanism to express the 88-kDa viral RNA polymerase. Using site-directed mutagenesis together with cell-free translation to monitor frameshifting and a biological assay of the mutants in plants, we establish the role of the GGAUUUU as the site where -1 ribosomal frameshifting occurs. The frameshifting signal sequence conforms to the simultaneous slippage model. Stop codons flanking the shifty signal are not required for frameshifting but the p27 ORF termination codon is necessary for maintaining optimal infectivity of the virus. Mutations abolishing the RCNMV RNA-1 internal p57 ORF initiation codon did not affect infectivity of the virus, suggesting that this cistron is only expressed in vivo as an 88-kDa ribosomal frameshifting product. Shifty heptanucleotide signals from a number of animal retroviruses and RNA plant viruses facilitate RCNMV frameshifting in vitro. However, only a limited number of the heterologous shifty heptanucleotides were functional in plant cells. We suggest that specific shifty tRNA populations in the cell facilitate viral -1 ribosomal frameshifting. This analysis also suggests that the slippery sequence requirements are not identical in mammalian and in plant systems.

Base Sequence↗
PubMed1994

Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs.

The prokaryotic mRNA ribosome binding site (RBS) usually contains part or all of a polypurine domain UAAGGAGGU known as the Shine-Dalgarno (SD) sequence found just 5' to the translation initiation codon. It is now clear that the SD sequence is important for identification of the translation initiation site on the mRNA by the ribosome, and that as a result, the spacing between the SD and the initiation codon strongly affects translational efficiency (1). It is not as clear, however, whether there is a unique optimal spacing. Complications involving the definition of the spacing as well as secondary structures have obscured matters. We thus undertook a systematic study by inserting two series of synthetic RBSs of varying spacing and SD sequence into a plasmid vector containing the chloramphenicol acetyltransferase gene. Care was taken not to introduce any secondary structure. Measurements of protein expression demonstrated an optimal aligned spacing of 5 nt for both series. Since aligned spacing corresponds naturally to the spacing between the 3'-end of the 16S rRNA and the P-site, we conclude that there is a unique optimal aligned SD-AUG spacing in the absence of other complicating issues.

Base Sequence↗
PubMed2006

Thermophiles like hot T.

A plethora of mechanisms confer protein stability in thermophilic microorganisms and, recently, it was suggested that these mechanisms might be divided along evolutionary lines. Here, a multi-genome comparison shows that there is a statistically significant increase in the proportion of NTN codons correlated with increasing optimal growth temperature for both Bacteria and Archaea. NTN encodes exclusively non-polar, hydrophobic amino acids and indicates a common underlying use of hydrophobicity for stabilizing proteins in Bacteria and Archaea that transcends evolutionary origins. However, some microorganisms do not follow this trend, suggesting that alternate mechanisms (e.g. intracellular electrolytes) might be used for protein stabilization. These studies highlight the usefulness of large-scale comparative genomics to uncover novel relationships that are not immediately obvious from protein structure studies alone.

Amino Acid Sequence↗