Effect of tandem repeated AUG codons on translation efficiency of eukaryotic mRNA carrying a short leader sequence

The effect on translation of multiple copies of the initiation codon AUG at the initiation site in a eukaryotic mRNA carrying a short leader sequence was tested in translation experiments in vitro. DNA, corresponding to a chimeric mRNA sequence consisting of the 5 leader region of brome mosaic virus (BMV) RNA4 and the goat pre--lactalbumin mRNA sequence, was prepared and transcribed in vitro using SP6 RNA polymerase. Site-directed mutagenesis was carried out to change the sequence around the initiation codon AUG. In a wheat germ translation system, the yield of protein obtained using the mRNA with a duplication of the AUG codons at the initiation site was 1.6 times that achieved when only one AUG was present. The rate of formation of the 80S initiation complex was measured by the ribosome binding assay using cycloheximide. A good correlation was observed between the ability to form the complex and translation efficiency.     

Causal signals between codon bias,mRNA structure,and the efficiency of translation and elongation

Ribosome profiling data report on the distribution of translating ribosomes, at steady‐state, with codon‐level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate‐reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation.     

Incorporation of glycosylated amino acid into protein by an in vitro translation system

O-GalNAcα-modified proteins are the precursor of mucin-type O-glycosylated proteins. Homogeneously O-glycosylated proteins are required to investigate the biological functions of glycoproteins and to develop biopharmaceuticals. Here we show that the incorporation of GalNAcα-Thr into proteins successfully proceeded by the use of a chemically aminoacylated tRNA. GalNAcα-Thr was chemoenzymatically attached to amber suppressor tRNA and the product was subjected to in vitro translation together with streptavidin mRNA containing the UAG codon. Gel electrophoresis and mass analysis showed that GalNAcα-Thr was successfully incorporated into the N-terminus, although it was not incorporated at the interior. This method will facilitate the preparation of homogeneous GalNAcα-proteins.     

Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG

Leaderless mRNAs are translated in the absence of upstream signals that normally contribute to ribosome binding and translation efficiency. In order to identify ribosomal components that interact with leaderless mRNA, a fragment of leaderless cI mRNA from bacteriophage λ, with a 4-thiouridine (4^S-U) substituted at the +2 position of the AUG start codon, was used to form cross-links to Escherichia coli ribosomes during binary (mRNA+ribosome) and ternary (mRNA+ribosome+initiator tRNA) complex formation. Ribosome binding assays (i.e., toeprints) demonstrated tRNA-dependent binding of leaderless mRNA to ribosomes; however, cross-links between the start codon and 30S subunit rRNA and r-proteins formed independent of initiator tRNA. Toeprints revealed that a leaderless mRNA's 5′-AUG is required for stable binding. Furthermore, the addition of a 5′-terminal AUG triplet to a random RNA fragment can make it both competent and competitive for ribosome binding, suggesting that a leaderless mRNA's start codon is a major feature for ribosome interaction. Cross-linking assays indicate that a subset of 30S subunit r-proteins, located at either end of the mRNA tunnel, contribute to tRNA-independent contacts and/or interactions with a leaderless mRNA's start codon. The interaction of leaderless mRNA with ribosomes may reveal features of mRNA binding and AUG recognition that are distinct from known signals but are important for translation initiation of all mRNAs.     

Factors affecting DNA synthesis in an in vitro system

Summary Mononucleated striated muscle cells and one type of endoderm can be isolated from anthomedusae and cultivated in artificial sea-water. In the cultivated muscle the differentiated state is maintained. In the cultivated endoderm flagella are formed, but no new cell types differentiate and DNA synthesis or mitosis is not observed. When isolated muscle is grafted upon endoderm, regeneration or formation of new cell types is not observed. Following treatingment with bacterial collagenase DNA synthesis and flagellum formation are initiated in the isolated muscle; in the isolated endoderm, collagenase treatment has no effect. When striated muscle treated with collagenase is grafted upon endoderm, DNA synthesis is observed in the endoderm, and a regenerate is formed involving transdifferentiation. Although desmosomal contact between collagenase treated muslce and the endoderm is established, it is not sufficient to induce DNA synthesis; complete covering of the endoderm by the muscle is required.     

Efficient suppression of the amber codon in E. coli in vitro translation system

An mRNA encoding the esterase from Alicyclobacillus acidocaldarius with catalytically essential serine codon (ACG) replaced by an amber (UAG) codon was used to study the suppression in in vitro translation system. Suppression of UAG by tRNA(Ser(CUA)) was monitored by determination of the full-length and active esterase. It was shown that commonly used increase of suppressor tRNA concentration inhibits protein production and therefore limits suppression. In situ deactivation of release factor by specific antibodies leads to efficient suppression already at low suppressor tRNA concentration and allows an in vitro synthesis of fully active enzyme in high yield undistinguishable from wild-type protein.     

qa-3稀有密码子和mRNA结构改造及其在大肠杆菌中的高效表达

奎尼酸脱氢酶的高表达是奎尼酸生物合成的代谢工程研究的关键和基础。粗糙脉孢菌基因组中编码奎尼酸脱氢酶的基因qa-3在大肠杆菌中不表达,根据大肠杆菌密码子使用频率分析qa-3基因,发现有27个稀有密码子,其中编码Arg(R)的有8个,编码Gly(G)的有9个。编码精氨酸的AGG(AGA)两个稀有密码子紧密相连(R区),另外还有个相对比较集中的GGG密集区G区。进一步通过计算机分析其qa-3基因mRNA二级结构,发现改变5′和3′末端个别碱基对其二级结构的影响很大,可以使mRNA的自由能由野生型的-374.3kJ/mol降低到最小-80.5kJ/mol,从而大大减少mRNA两端二级结构的产生,而仅仅改变R区和G区的稀有密码子自由能变化很小。通过对该基因密码子改造和优化5′和3′末端对其mRNA二级结构的影响,在大肠杆菌中表达真菌的基因qa-3,并测到了奎尼酸脱氢酶活性,为构建产奎尼酸工程菌株奠定基础。     

Use of an in vitro tuberization system to study tuber protein gene expression

Summary Nodal cuttings from micropropagated potato plantlets give rise to microtubers when placed on Murashige and Skoog medium containing 6% sucrose and 2.5 mg/liter kinetin and incubated in the dark at 19°C. Microtubers produced from the cultivar Superior were shown to contain the same characteristic group of proteins as field-grown tubers. As with field-grown tubers, the 40 000-dalton major tuber glycoprotein, patatin, accumulated to high levels in microtubers, reaching 3.7±0.2 mg/g fresh weight after 90 d. Also in agreement with field-grown plants, stems and leaves of micropropagated plantlets did not contain detectable levels of patatin, but small amounts of an electrophoretically distinct form accumulated transiently in roots. Patatin mRNA is readily detectable in developing microtubers 15 d after transfer of the cuttings to inductive medium. Patatin mRNA was also present in roots, but as with field-grown plants, was 50- to 100-fold less abundant and could be distinguished from that in tubers by primer extension. Microtuber development and patatin accumulation were inhibited by gibberellic acid. This work was supported by grants 83-CRCR-1-1348 and 85-CRCR-I-1792 from the U.S. Department of Agriculture Competitive Grants program and with funds from the Texas Agricultural Experiment Station.     

Translational Activity of mRNA Coding for Cytoskeletal Brain Proteins in Newborn and Adult Mice: A Comparative Study

Translational activity of mRNA coding for cytoskeletal brain proteins was used to determine the relative abundance of the mRNA in the brains of newborn and adult mice. mRNA was translated in a cell-free system containing rabbit reticulocyte factors. The products of translation were analyzed by two-dimensional gel electrophoresis and characterized by peptide map analysis. Comparison of the products of translation from newborn and from adult brain mRNA shows a 50% decrease in actin and tubulin from newborn to the adult stage. In contrast, the 70 kd neurofilament protein and glial fibrillary acidic protein show a twofold increase in the adult stage. The heat-shock protein HSP70 increases slightly (30%) whereas the brain isozyme of creatine kinase and the heat-shock protein HSP90 are three times as high in adult subjects as in newborns.     

Bacterial cell-free system for high-throughput protein expression and a comparative analysis of Escherichia coli cell-free and whole cell expression systems

Sixty-three proteins of Pseudomonas aeruginosa in the size range of 18-159 kDa were tested for expression in a bacterial cell-free system. Fifty-one of the 63 proteins could be expressed and partially purified under denaturing conditions. Most of the expressed proteins showed yields greater than 500 ng after a single affinity purification step from 50 microl in vitro protein synthesis reactions. The in vitro protein expression plus purification in a 96-well format and analysis of the proteins by SDS-PAGE were performed by one person in 4 h. A comparison of in vitro and in vivo expression suggests that despite lower yields and less pure protein preparations, bacterial in vitro protein expression coupled with single-step affinity purification offers a rapid, efficient alternative for the high-throughput screening of clones for protein expression and solubility.     

A possible contribution of mRNA secondary structure to translation initiation efficiency in Lactococcus lactis

Gene expression signals derived from Lactococcus lactis were linked to lacZ-fused genes with different 5'-nucleotide sequences. Computer predictions of mRNA secondary structure were combined with lacZ expression studies to direct base-substitutions that could possibly influence gene expression. Mutations were made such that the DNA sequence upstream of the ATG start codon was not changed. Moreover, care was taken that the substitutions, which were all within the first six codons, neither affected the amino acid sequence of the gene product nor introduced codons rarely used in L. lactis. The results suggest that mRNA secondary structure contributes to the efficiency of translation initiation in L. lactis.     

An in vitro transposon system for highly regulated gene expression: construction of Escherichia coli strains with arabinose-dependent growth at low temperatures.

Placing a gene of interest under the control of an inducible promoter greatly aids the purification, localization and functional analysis of proteins but usually requires the sub-cloning of the gene of interest into an appropriate expression vector. Here, we describe an alternative approach employing in vitro transposition of TnΩP_BAD to place the highly regulable, arabinose inducible P_BAD promoter upstream of the gene to be expressed. The method is rapid, simple and facilitates the optimization of expression by producing constructs with variable distances between the P_BAD promoter and the gene. To illustrate the use of this approach, we describe the construction of a strain of Escherichia coli in which growth at low temperatures on solid media is dependent on threshold levels of arabinose. Other uses of the transposable promoter are also discussed.     

Construction of homo- and heteropolymers of plant ferritin subunits using an in vitro protein expression system

Ferritin is a class of iron storage protein composed of 24 subunits. Although many studies on gene expression analyses of plant ferritin have been conducted, the functions and oligomeric assembly of plant ferritin subunits are still largely unknown. In order to characterize the ability to form multimeric protein shells and determine the iron incorporating activity, we produced ferritin homo- and heteropolymers by expressing four cDNAs of ferritin subunits from soybean, sfer1, sfer2, sfer3, and sfer4, using an in vitro protein expression system. Using SDS-PAGE analysis followed by Prussian blue stain, homopolymers of SFER1, SFER2, and SFER3, and heteropolymers of SFER1/SFER2 and SFER1/SFER3 were detected as assembled polymers with iron incorporating activity, whereas only a small amount of SFER4 related homo- and heteropolymer was detected, suggesting that the SFER4 was not competent for oligomeric assembly, unlike every other ferritin. We conclude that certain combinations of plant ferritin subunits can form heteropolymers and that their iron incorporating activities depend on the formation of multimeric protein.     

In vitro expression of natriuretic peptides in cardiomyocytes differentiated from monkey embryonic stem cells

Functional characterization of ES cell-derived cardiomyocytes is important for differentiation control and application to the cell therapy. One of the crucial functions of cardiomyocytes is a production of atrial and brain natriuretic peptides (ANP and BNP, respectively), which have important endocrine, autocrine, and paracrine functions. In this study, we focused on the functional aspect of the cardiomyocytes differentiated from monkey ES cells in vitro and investigated the expression of ANP and BNP. Spontaneously contracting cells showed nodal-like action potentials, and expression of ANP and BNP by RT-PCR and immunocytochemistry. Interestingly, ANP and BNP expressions were detected as immunoreactive granules in the perinuclear area and these signals appeared to co-localize with trans-Golgi network. These findings suggest that monkey ES cells were able to differentiate into cardiomyocytes with functional characteristics in vitro and therefore can be used as a useful model to study mechanisms and functions in early cardiogenesis.     

Analysis of the variability of S-fimbriae expression in an Escherichia coli pathogen

The uropathogenic Escherichia coli wild-type strain 536 produces S-fimbriae, P-related fimbriae and type I fimbriae. Using immuno-colony dot and ELISA techniques, variants were detected showing an increased degree of S-fimbrial production. It was demonstrated by immunofluorescence microscopy that in normal (wild-type) and hyper-S-fimbriated E. coli populations non-fimbriated cells also exist, and that the percentage of S-fimbriated and non-fimbriated bacteria was roughly identical in either population. Hyper-S-fimbriated variants could be stably maintained. The transition from wild-type to hyper-S-fimbriation, which occurs spontaneously, is markedly higher than vice versa. Southern blot analysis of the S fimbrial adhesin (sfa) determinants of normal and hyper-fimbriated strains revealed no marked difference in the gene structure.     

RNA secondary structure and in vitro translation efficiency

Cell-free protein synthesis is a promising technology featuring many advantages compared to in vivo expression techniques. However, most proteins are still synthesized in vivo due to relatively low protein yields commonly achieved in vitro, especially in the batch mode of reaction. In Escherichia coli S30 extract-based cell-free systems protein yields are supposed to be partially limited by a secondary structure formation of the mRNA. In this study we checked promising members of various classes of RNA chaperones and several different RNA helicases on their ability to enhance in vitro translation. The data clearly show that the addition of none of these factors provides a general solution to the problem. However, protein yields can be increased in presence of a microRNA hybridizing with the 5′ untranslated region of mRNAs, possibly by inducing structural changes improving accessibility of the Shine Dalgarno sequence for the ribosomes.     

Recognition of messenger RNA during translational initiation in Escherichia coli

The structural aspects of recognition by E. coli ribosomes of translational initiation regions on homologous messenger RNAs have been reviewed. Also discussed is the location of initiation region on mRNA, its confines, typical nucleotide sequences responsible for initiation signal, and the influence of RNA macrostructure on protein synthesis initiation. Most of the published DNA nucleotide sequences surrounding the start of various E. coli genes and those of its phages have been collected.