Capsid proteins often present a positively charged arginine-rich sequence at their terminal regions, which has a fundamental role in genome packaging and particle stability for some icosahedral viruses. These sequences show little to no conservation and are structurally dynamic such that they cannot be easily detected by common sequence or structure comparisons. As a result, the occurrence and distribution of positively charged domains across the viral universe are unknown. Based on the net charge calculation of discrete protein segments, we identified proteins containing amino acid stretches with a notably high net charge (Q > + 17), which are enriched in icosahedral viruses with a distinctive bias towards arginine over lysine. We used viral particle structural data to calculate the total electrostatic charge derived from the most positively charged protein segment of capsid proteins and correlated these values with genome charges arising from the phosphates of each nucleotide. We obtained a positive correlation (r = 0.91, p-value <0001) for a group of 17 viral families, corresponding to 40% of all families with icosahedral structures described to date. These data indicated that unrelated viruses with diverse genome types adopt a common underlying mechanism for capsid assembly based on R-arms.

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Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5' UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occurs. For some genes, translation elongation also affects the protein synthesis rate. Recently, it was proposed that the identity of codons three to five, called short translational ramp, have a strong influence on translation elongation and protein expression. By the use of a GFP library where nearly all combinations of nucleotides at these positions were created, it was demonstrated that some of nucleotides combinations increased GFP expression up to four orders of magnitude by enhancing their translation efficiency (TE). While it is clear that the short ramp can influence protein expression levels of artificial constructs, its impact on physiological proteins is still unknown. In this work, we aimed to investigate the relevance of the short translational ramp on a physiological context. Through bioinformatics analysis, we identified the nucleotide combinations from the GFP library on Escherichia coli genes and examined their correlation with TE. We observed that E. coli genes were enriched with nucleotide compositions that enhanced protein expression on the GFP library, but, surprisingly, it seems to affect the TE only marginally.Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as E. coli, suggesting an evolutionary pressure towards the conservation of the short translational ramp.

Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5ʹ UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occur. For some genes, translation elongation also affects the rate of protein synthesis. With a GFP library containing nearly all possible combinations of nucleotides from the 3 rd to the 5 th codon positions in the protein coding region of the mRNA, it was previously demonstrated that some nucleotide combinations increased GFP expression up to four orders of magnitude. While it is clear that the codon region from positions 3 to 5 can influence protein expression levels of artificial constructs, its impact on endogenous proteins is still unknown. Through bioinformatics analysis, we identified the nucleotide combinations of the GFP library in Escherichia coli genes and examined the correlation between the expected levels of translation according to the GFP data with the experimental measures of protein expression. We observed that E. coli genes were enriched with the nucleotide compositions that enhanced protein expression in the GFP library, but surprisingly, it seemed to affect the translation efficiency only marginally. Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as E. coli, suggesting an evolutionary pressure towards the conservation of short translational enhancer sequences.

Removal of an endocrine disrupting compound, Bisphenol A (BPA), from water was investigated using two treatment processes, UV/H2O2 advanced oxidation (AOP) and reverse osmosis (membrane separation). Furthermore, changes in estrogenic activity using in vitro yeast estrogen screen assay as well as the adsorption of BPA by the membrane surface were evaluated. The best UV/H2O2 performance was obtained using the highest established values of all parameters, reaching 48% BPA removal. Within the investigated conditions of the AOP, when lower doses of UV were used, a higher removal efficiency was achieved at a higher initial concentration of BPA. However, the same behavior was not observed for the highest UV dose, in which the removal efficiency was not dependent on BPA initial concentration. In both cases, removal efficiency increased as H2O2 concentration increased. The formation of estrogenic by-products was observed in UV/H2O2. The membrane rejection efficiency varied from 60% to 84% and all experiments showed adsorption of BPA by the membrane surface. The RO membrane showed a greater BPA removal efficiency for samples containing 10 μg·L−1 than UV/H2O2 at the evaluated treatment conditions.

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Highly positively charged protein segments are known to result in poor translation efficiency by the action of the ribosome quality control complex (RQC). This effect may be explained by ribosome stalling caused by electrostatic interactions between the nascent peptide and the negatively charged ribosome exit tunnel. This leads to translation termination followed by activation of mRNA decay pathways and protein degradation by RQC. Polybasic peptides are mainly studied with reporter systems, where artificial sequences are introduced into heterologous genes. The unique example of an endogenous protein targeted by RQC is Rqc1, a protein essential for the RQC activity. RQC arguably regulates Rqc1 levels through a conserved polybasic domain present in its N-term. We aimed to check if RQC act as a regulatory mechanism for other endogenous proteins containing polybasic domains. Here we show by bioinformatics, ribosome profiling data, and western blot protein quantification that endogenous proteins containing polybasic domains similar to or even more positively charged than Rqc1 are not targeted by RQC, suggesting that endogenous polybasic domains are not sufficient to induce degradation by this complex. We further demonstrate that Rqc1 levels are not regulated by the RQC complex, but by Ltn1 alone, in a post-translational fashion.

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