Localization of in vivo ribosome pause sites

Preparation of ribosomal protein S14 polyclonal antibody in broiler pulmonary artery: Its application in broiler ascites syndrome

RPS14 (ribosomal protein S14) gene maintains the normal physiological activities of the body by regulating the biosynthesis of ribosomes and the translation of important proteins. This study aims to explore the potential role of RPS14 in broiler ascites syndrome (BAS). We successfully prepared polyclonal antibody against RPS14 and studied the localization and expression of RPS14 protein in a variety of animal key tissues. In this experiment, the recombinant expression plasmid PET28a-RPS14 was constructed using the prokaryotic expression technology of foreign genes. Under the conditions of IPTG induction, a His-RPS14 protein with a molecular weight of about 22 kDa was expressed, and the purified recombinant protein was used as an antigen to prepare rabbit anti-chicken serum. Western blot results showed that the serum could specifically identify RPS14 protein in important tissues of broilers. Immunofluorescence combined with homology analysis showed that the antiserum had significant species specificity. Compared with other species, the expression of this protein in key tissues of broilers and ducks was more significant. More importantly, western blotting and immunofluorescence showed that BAS significantly reduced the expression level of RPS14. This further indicated that RPS14 protein can be used as one of the important entry points for BAS research.

Associations of CALM1 and DRD1 polymorphisms, and their expression levels, with Taihang chicken egg-production traits

Egg production by hens is an important reproductive performance index in the poultry industry. To investigate the effects of the CALM1 and DRD1 genes on egg production in chicken, their mRNA expression and single nucleotide polymorphisms (SNP) levels were investigated, and bioinformatics and egg-production association analyses were performed. Three SNPs (g.44069941G > A and g.44069889A > G in CALM1 and g.10742639C > T in DRD1) were detected in the exons and introns of CALM1 and DRD1 in 400 Taihang chickens. Among them, g.44069941G > A was significantly associated with Taihang chicken egg production on the 500th day (p < 0.05), whereas g.10742639C > T was significantly associated with the 300th day (p < 0.05). The expression levels of CALM1 and DRD1 in ovarian tissues of a high-yielding Taihang group were greater than in a low-yielding group (p < 0.05). The bioinformatics analysis revealed that the mutations influenced the mRNA secondary structures of CALM1 and DRD1. This study provides new insights into the potential effects of CALM1 and DRD1 polymorphisms on chicken egg production. The two SNPs g.44069941G > A and g.10742639C > T are potential molecular markers for improving the reproductive traits of Taihang chicken.

Mutant Huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease

The polyglutamine expansion of huntingtin (mHTT) causes Huntington disease (HD) and neurodegeneration, but the mechanisms remain unclear. Here, we found that mHtt promotes ribosome stalling and suppresses protein synthesis in mouse HD striatal neuronal cells. Depletion of mHtt enhances protein synthesis and increases the speed of ribosomal translocation, while mHtt directly inhibits protein synthesis in vitro. Fmrp, a known regulator of ribosome stalling, is upregulated in HD, but its depletion has no discernible effect on protein synthesis or ribosome stalling in HD cells. We found interactions of ribosomal proteins and translating ribosomes with mHtt. High-resolution global ribosome footprint profiling (Ribo-Seq) and mRNA-Seq indicates a widespread shift in ribosome occupancy toward the 5' and 3' end and unique single-codon pauses on selected mRNA targets in HD cells, compared to controls. Thus, mHtt impedes ribosomal translocation during translation elongation, a mechanistic defect that can be exploited for HD therapeutics.

Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

BACKGROUND

Porcine reproductive and respitatory syndrome virus (PRRSV) is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression.

RESULTS

In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection.

CONCLUSIONS

The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process.

Electrostatics in the ribosomal tunnel modulate chain elongation rates

Electrostatic potentials along the ribosomal exit tunnel are nonuniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel and measured chain elongation rates. Positively charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively charged residues than for those containing positively charged residues. We provide experimental evidence that extraribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide.

Cool temperatures interfere with D1 synthesis in tomato by causing ribosomal pausing

Photodamage occurs when leaves are exposed to light in excess of what can be used for photosynthesis and in excess of the capacity of ancillary photoprotective as well as repair mechanisms. An important site of photodamage is the chloroplast encoded D1 protein, a component of the photosystem II (PSII) reaction center. Even under optimal growth irradiance, D1 is photodamaged necessitating rapid turnover to prevent the accumulation of photodamaged PSII reaction centers and consequent inhibition of photosynthesis. However, this on-going process of D1 turnover and replacement was impeded in the chilling-sensitive tomato (Solanum lycopersicum) plants when exposed to high-growth light at cool temperature. The decrease in D1 turnover and replacement was found not to be due to changes in the steady-state level of the psbA message. While the recruitment of ribosomes to psbA transcript, initiation of D1 translation, and the association of polysomes with the thylakoid membrane occurred normally, chilling temperatures caused ribosomal pausing during D1 peptide elongation in tomato. The pause locations were non-randomly located on the D1 transcript. The interference with translation caused by ribosomal pausing allowed photodamaged PSII centers to accumulate leading to the consequent inhibition of photosynthesis.

Translational machinery and protein folding: evidence of conformational variants of the estrogen receptor alpha

As an approach to understand how translation may affect protein folding, we analyzed structural and functional properties of the human estrogen receptor alpha synthesized by different eukaryotic translation systems. A minimum of three conformations of the receptor were detected using limited proteolysis and a sterol ligand-binding assay. The receptor in vitro translated in rabbit reticulocyte lysate was rapidly degraded by protease, produced major bands of about 34kDa and showed a high affinity for estradiol. In a wheat germ translation system, the receptor was more slowly digested. Two soluble co-existing conformations were evident by different degradation patterns and estradiol binding. Our data show that differences in the translation machinery may result in alternative conformations of the receptor with distinct sterol binding properties. These studies suggest that components of the cellular translation machinery itself might influence the protein folding pathways and the relative abundance of different receptor conformers.

Translation in plants--rules and exceptions

Translation processes in plants are very similar to those in other eukaryotic organisms and can in general be explained with the scanning model. Particularly among plant viruses, unconventional mRNAs are frequent, which use modulated translation processes for their expression: leaky scanning, translational stop codon readthrough or frameshifting, and transactivation by virus-encoded proteins are used to translate polycistronic mRNAs; leader and trailer sequences confer (cap-independent) efficient ribosome binding, usually in an end-dependent mechanism, but true internal ribosome entry may occur as well; in a ribosome shunt, sequences within an RNA can be bypassed by scanning ribosomes. Translation in plant cells is regulated under conditions of stress and during development, but the underlying molecular mechanisms have not yet been determined. Only a small number of plant mRNAs, whose structure suggests that they might require some unusual translation mechanisms, have been described.

Translational control of cellular and viral mRNAs

We are becoming increasingly aware of the role that translational control plays in regulating gene expression in plants. There are now many examples in which specific mechanisms have evolved at the translational level that directly impact the amount of protein produced from an mRNA. All regions of an mRNA, i.e., the 5' leader, the coding region, and the 3'-untranslated region, have the potential to influence translation. The 5'-terminal cap structure and the poly(A) tail at the 3' terminus serve as additional elements controlling translation. Many viral mRNAs have evolved alternatives to the cap and poly(A) tail that are functionally equivalent. Nevertheless, for both cellular and viral mRNAs, a co-dependent interaction between the terminal controlling elements appears to be the universal basis for efficient translation.

Ribosome-mediated translational pause and protein domain organization

Because regions on the messenger ribonucleic acid differ in the rate at which they are translated by the ribosome and because proteins can fold cotranslationally on the ribosome, a question arises as to whether the kinetics of translation influence the folding events in the growing nascent polypeptide chain. Translationally slow regions were identified on mRNAs for a set of 37 multidomain proteins from Escherichia coli with known three-dimensional structures. The frequencies of individual codons in mRNAs of highly expressed genes from E. coli were taken as a measure of codon translation speed. Analysis of codon usage in slow regions showed a consistency with the experimentally determined translation rates of codons; abundant codons that are translated with faster speeds compared with their synonymous codons were found to be avoided; rare codons that are translated at an unexpectedly higher rate were also found to be avoided in slow regions. The statistical significance of the occurrence of such slow regions on mRNA spans corresponding to the oligopeptide domain termini and linking regions on the encoded proteins was assessed. The amino acid type and the solvent accessibility of the residues coded by such slow regions were also examined. The results indicated that protein domain boundaries that mark higher-order structural organization are largely coded by translationally slow regions on the RNA and are composed of such amino acids that are stickier to the ribosome channel through which the synthesized polypeptide chain emerges into the cytoplasm. The translationally slow nucleotide regions on mRNA possess the potential to form hairpin secondary structures and such structures could further slow the movement of ribosome. The results point to an intriguing correlation between protein synthesis machinery and in vivo protein folding. Examination of available mutagenic data indicated that the effects of some of the reported mutations were consistent with our hypothesis.

The 3' untranslated region of bovine preprolactin contains a transferable non-poly(A) mRNA sequence that prolongs translation

Preprolactin transcripts, synthesized in vitro, were actively translated for a prolonged period when injected into Xenopus oocytes. As a result, prolactin continued to be secreted into the media for up to 6 days after injection of the transcript. To investigate the role of the preprolactin 3' untranslated sequence in stabilizing transcripts, it was fused to coding regions derived from signal recognition particle receptor alpha-subunit or preproinsulin receptor. The translational half-life of the chimeric RNA was increased for both coding regions, suggesting that a sequence within the preprolactin 3' untranslated region that prolongs translation is transferable. Deletion mutagenesis of this untranslated region demonstrated that a sequence of 98 nucleotides immediately following the prolactin stop codon was sufficient to prolong translation of RNAs injected into Xenopus oocytes.