Abstract
As proteins are synthesized, the nascent polypeptide must pass through a negatively charged exit tunnel. During this stage, positively charged stretches can interact with the ribosome walls and slow the translation. Therefore, charged polypeptides may be important factors that affect protein expression. To determine the frequency and distribution of positively and negatively charged stretches in different proteomes, the net charge was calculated for every 30 consecutive amino acid residues, which corresponds to the length of the ribosome exit tunnel. The following annotated and reviewed proteins in the UniProt database (Swiss-Prot) were analyzed: 551,705 proteins from different organisms and a total of 180 million protein segments. We observed that there were more negative than positive stretches and that super-charged positive sequences (i.e., net charges ≥ 14) were underrepresented in the proteomes. Overall, the proteins were more positively charged at their N-termini and C-termini, and this feature was present in most organisms and subcellular localizations. To investigate whether the N-terminal charges affect the elongation rates, previously published ribosomal profiling data obtained from S. cerevisiae, without translation-interfering drugs, were analyzed. We observed a nonlinear effect of the charge on the ribosome occupancy in which values ≥ +5 and ≤ -6 showed increased and reduced ribosome densities, respectively. These groups also showed different distributions across 80S monosomes and polysomes. Basic polypeptides are more common within short proteins that are translated by monosomes, whereas negative stretches are more abundant in polysome-translated proteins. These findings suggest that the nascent peptide charge impacts translation and can be one of the factors that regulate translation efficiency and protein expression.
Highlights
The translation of messenger RNAs is the final step in translating the genetic code from DNA to proteins and is an essential, energetic expensive reaction[1]
Which factors shape the sequence of amino acids that will form a protein? The biochemical features of amino acids, such as their charge and hydrophobicity, are important drivers of protein tridimensional folding, which creates interaction sites for binding other molecules and directs proteins to specific cellular compartments
Positively charged protein segments are underrepresented in most proteomes To determine the charge frequency of protein segments in various proteomes, we developed a program that is able to screen the sequence of a given protein and calculate the net charge of Protein charge distribution and translation every 30-amino acid segment, which is the estimated polypeptide length that occupies the ribosome exit tunnel[9]
Summary
The translation of messenger RNAs is the final step in translating the genetic code from DNA to proteins and is an essential, energetic expensive reaction[1]. The translation process is regulated by different mechanisms, primarily at the initiation phase. These mechanisms include initiation factor levels and posttranslational modifications, mRNA accessibility, microRNA activity and trans-acting protein activity[1]. The elongation rate can be influenced by the messenger RNA secondary structure[1], rare codon usage[2,3] or nascent polypeptide charge[4] and appears to be tightly coupled to co-translational folding[5]. The elongation and initiation rates can determine whether the transcripts are translated in the monosomes or polysomes[7]
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