Silent mutations in secondary Shine-Dalgarno sequences in the cDNA of human serum amyloid A4 promotes expression of recombinant protein in Escherichia coli

The serum amyloid A (SAA) superfamily comprises a number ofdifferentially expressed genes with a high degree of homologyin mammalian species. SAA4, an apolipoprotein constitutivelyexpressed only in humans and mice, is associated almost entirelywith lipoproteins of the high-density range. The presence ofSAA4 mRNA and protein in macrophage-derived foam cells of coronaryand carotid arteries suggested a specific role of human SAA4during inflammation including atherosclerosis. Here we underlinethe importance of ribosome binding site (rbs)-like sequences(also known as Shine–Dalgarno sequences) in the SAA4 cDNAfor expression of recombinant SAA4 protein in Escherichia coli.In contrast to rbs sequences coded by the expression vectors,rbs-like sequences in the cDNA of target protein(s) are knownto interfere with protein translation via binding to the small16S ribosome subunit, yielding low or even no expression. Herewe show that PCR mutations of two rbs-like sequences in thehuman SAA4 cDNA promote expression of considerable amounts ofrecombinant SAA4 in E.coli.     

高产油绿球藻GIEC-38转录本和基因表达谱分析

通过对天然条件下生长好且含油高的绿球藻(Chlorococcum sp.) GIEC-38细胞内转录本的测定,发现:在获得的74 605条转录本、65 984个基因中共得到344条代谢途径，其中核糖体、蛋白质、核苷酸、核糖核酸、碳固定、光合作用以及脂代谢等通路都非常活跃。通过缺N培养发现GIEC-38含油脂可达50%以上，通过对比细胞表达谱发现相比于原始藻株，缺N条件下培养的GIEC-38细胞中有868个基因显著上调、1 157个基因显著下调，分布在41个生物学功能、71条代谢途径中。其中，为脂肪酸的合成提供大量原料的中间产物合成酶，以及脂类代谢相关的几个通路中关键酶的基因，表达都有明显上调，促使细胞脂类的合成，提高了细胞的油脂产量。     

重组融合蛋白IL-3-PE38KDEL对急性髓性白血病细胞增殖和凋亡的影响

目的观察重组融合蛋白IL-3-PE38KDEL对急性髓性白血病(Acute myelocytic leukemia,AML)细胞HL-60(IL-3R阳性)和NB4(IL-3R阴性)增殖和凋亡的影响。方法用不同浓度的IL-3-PE38KDEL分别作用HL-60和NB4细胞,MTT法检测细胞的增殖抑制作用,计算抑制率及半数抑制浓度(IC50)。将HL-60和NB4细胞分别分为IL-3-PE38KDEL组和IL-3+IL-3-PE38KDEL组,IL-3+IL-3-PE38KDEL组加入IL-3(100 ng/ml),孵育4 h后,IL-3-PE38KDEL组和IL-3+IL-3-PE38KDEL组均加入IC50浓度的IL-3-PE38KDEL,计算细胞增殖抑制率;流式细胞术检测2种AML细胞细胞周期的变化及凋亡情况。结果 IL-3-PE38KDEL对HL-60和NB4细胞的增殖均有抑制作用,且呈浓度依赖性,对HL-60细胞的抑制作用强于NB4细胞(P<0.05),IC50值分别为2.5μg/ml和259.2μg/ml。当IL-3-PE38KDEL浓度为IC50时,经IL-3处理后,对HL-60和NB4细胞增殖的抑制率均值分别为32.20%和49.00%。经IL-3-PE38KDEL作用后的HL-60细胞大部分被阻滞于G1/S期。HL-60细胞IL-3-PE38KDEL组的细胞凋亡率均值(19.71%)显著高于IL-3+IL-3-PE38KDEL组(9.39%)(P<0.05),NB4细胞两组差异无统计学意义(P﹥0.05)。结论 IL-3-PE38KDEL能抑制IL-3R阳性的AML细胞HL-60增殖,并诱导其凋亡,但对IL-3R阴性的AML细胞NB4的抑制作用较弱。     

Activation of ERK and p38 Reduces AZD8055-Mediated Inhibition of Protein Synthesis in Hepatocellular Carcinoma HepG2 Cell Line

Protein synthesis is important for maintaining cellular homeostasis under various stress responses. In this study, we screened an anticancer drug library to select compounds with translational repression functions. AZD8055, an ATP-competitive mechanistic target of rapamycin complex 1/2 (mTORC1/2) inhibitor, was selected as a translational suppressor. AZD8055 inhibited protein synthesis in mouse embryonic fibroblasts and hepatocellular carcinoma HepG2 cells. Extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (MAPK) were activated during the early phase of mTORC1/2 inhibition by AZD8055 treatment. Combined treatment of AZD8055 with the MAPK kinase1/2 (MEK1/2) inhibitor refametinib or the p38 inhibitor SB203580 markedly decreased translation in HepG2 cells. Thus, the inhibition of ERK1/2 or p38 may enhance the efficacy of AZD8055-mediated inhibition of protein synthesis. In addition, AZD8055 down-regulated the phosphorylation of eukaryotic initiation factor 4E-binding protein 1 (4E-BP1), and AZD8055-induced phosphorylation of ERK1/2 and p38 had no effect on phosphorylation status of 4E-BP1. Interestingly, AZD8055 modulated the 4E-BP1 mRNA pool by up-regulating ERK1/2 and p38 pathways. Together, these results suggest that AZD8055-induced activation of MAPKs interferes with inhibition of protein synthesis at an early stage of mTORC1/2 inhibition, and that it may contribute to the development of resistance to mTORC1/2 inhibitors.     

Dwell-Time Distribution,Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex

Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by “hungry” codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.     

Analysis of IgG heavy chain to light chain ratio with mutant Encephalomyocarditis virus internal ribosome entry site

Immunoglobulin G (IgG) is a heterotetrameric protein assembled from two identical heavy chain (HC) and two identical light chain (LC) polypeptides. The HC and LC folding and assembly are a crucial step for IgG production. It is affected by the ratio of HC to LC expression (HC:LC). To date, the HC:LC ratio was analysed mainly by cotransfection of different amounts of two monocistronic HC and LC expression plasmids, an approach biased by different transfection efficiencies. To circumvent this problem, a series of Encephalomyocarditis virus internal ribosome entry site (EMCV IRES) variants with different translation efficiencies were created and used to mediate HC translation in bicistronic constructs. HC and LC were translated from the same mRNA, which provides a more accurate method for the evaluation of the optimal ratio of HC:LC. The results show that the IgG optimal expression levels were obtained when the IRES mediated translation efficiency of the HC was about 50% compared to the cap-dependent translation of the LC. A surprisingly sharp transition to low production was shown when the ratios were below 40%. This study provides a new method to investigate the production of heterodimeric proteins in mammalian cells and adds understanding to the mechanisms of IgG folding and assembly.     

Current Views of the Structure of the Mammalian Mitochondrial Ribosome

Mammalian mitochondria synthesize polypeptides crucial for energy generation using ribosomes with a number of unique features. These ribosomes are very protein rich and have very truncated ribosomal RNAs. The bulk of the mammalian mitochondrial ribosome is composed of proteins, only about half of which are homologs of ribosomal proteins found in other translational systems. A number of distinctive features are found in these ribosomes. Among these is a gate-like structure that allows entrance of the primarily leaderless mRNAs that characterize this system. The exit tunnel of the large subunit is also quite unusual and includes a site in which the nascent peptide is visible to solvent prior to the normal exit site. Further, this region of the mitochondrial ribosome is dominated by ribosomal proteins rather than rRNA and is involved in the interaction of the ribosome with the inner membrane where all of the translation products are ultimately located. The proteins of the mitochondrial ribosome appear to play a number of important roles in the cell in addition to their function in protein biosynthesis, including roles in apoptosis and in cell cycle control.     

Short Proline‐Rich Antimicrobial Peptides Inhibit Either the Bacterial 70S Ribosome or the Assembly of its Large 50S Subunit

Short proline‐rich antimicrobial peptides (PrAMPs) are a promising class of antibiotics that use novel mechanisms, thus offering the potential to overcome the health threat of multiresistant pathogens. The peptides bind to the bacterial 70S ribosome and can inhibit protein translation. We report that PrAMPs can be divided into two classes, with each class binding to a different site, and thus use different lethal mechanisms. Oncocin‐type peptides inhibit protein translation in Escherichia coli by binding to the exit tunnel of the 70S ribosome with half maximal inhibitory concentrations (IC₅₀ values) of around 2 to 6 μmol L^?1, whereas apidaecin‐type peptides block the assembly of the large (50S) subunit of the ribosome, resulting in similar IC₅₀ values. The revealed mechanisms should allow the design of new antibiotics to overcome current bacterial resistance mechanisms.     

Circular RNA,the Key for Translation

It was thought until the 1990s that the eukaryotic translation machinery was unable to translate a circular RNA. However internal ribosome entry sites (IRESs) and m⁶A-induced ribosome engagement sites (MIRESs) were discovered, promoting 5′ end-independent translation initiation. Today a new family of so-called “noncoding” circular RNAs (circRNAs) has emerged, revealing the pivotal role of 5′ end-independent translation. CircRNAs have a strong impact on translational control via their sponge function, and form a new mRNA family as they are translated into proteins with pathophysiological roles. While there is no more doubt about translation of covalently closed circRNA, the linearity of canonical mRNA is only theoretical: it has been shown for more than thirty years that polysomes exhibit a circular form and mRNA functional circularization has been demonstrated in the 1990s by the interaction of initiation factor eIF4G with poly(A) binding protein. More recently, additional mechanisms of 3′–5′ interaction have been reported, including m⁶A modification. Functional circularization enhances translation via ribosome recycling and acceleration of the translation initiation rate. This update of covalently and noncovalently closed circular mRNA translation landscape shows that RNA with circular shape might be the rule for translation with an important impact on disease development and biotechnological applications.     

A Recombinant Collagen–mRNA Platform for Controllable Protein Synthesis

We have developed a collagen–mRNA platform for controllable protein production that is intended to be less prone to the problems associated with commonly used mRNA therapy as well as with collagen skin‐healing procedures. A collagen mimic was constructed according to a recombinant method and was used as scaffold for translating mRNA chains into proteins. Cysteines were genetically inserted into the collagen chain at positions allowing efficient ribosome translation activity while minimizing mRNA misfolding and degradation. Enhanced green fluorescence protein (eGFP) mRNA bound to collagen was successfully translated by cell‐free Escherichia coli ribosomes. This system enabled an accurate control of specific protein synthesis by monitoring expression time and level. Luciferase–mRNA was also translated on collagen scaffold by eukaryotic cell extracts. Thus we have demonstrated the feasibility of controllable protein synthesis on collagen scaffolds by ribosomal machinery.     

Tethered Ribosomes: Toward the Synthesis of Nonproteinogenic Polymers in Bacteria

The ribosome is the core element of the translational apparatus and displays unrivaled fidelity and efficiency in the synthesis of long polymers with defined sequences and diverse compositions. Repurposing ribosomes for the assembly of nonproteinogenic (bio)polymers is an enticing prospect with implications for fundamental science, bioengineering and synthetic biology alike. Here, we review tethered ribosomes, which feature inseparable large and small subunits that can be evolved for novel function without interfering with native translation. Following a tutorial summary of ribosome structure, function, and biogenesis, we introduce design and optimization strategies for the creation of orthogonal and tethered ribosomes. We also highlight studies, in which (rational) engineering efforts of these designer ribosomes enabled the evolution of new functions. Lastly, we discuss future prospects and challenges that remain for the ribosomal synthesis of tailor-made (bio)polymers.