2017
DOI: 10.1371/journal.pcbi.1005549
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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 t… Show more

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Cited by 59 publications
(64 citation statements)
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References 37 publications
(75 reference statements)
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“…To verify if ribosome accumulation is implicated in the ramp formation, we compared the average ribosome footprint count per nucleotide of two groups of genes, genes with scores higher than 4.2 versus scores lower than 4.2, using ribosome profiling data. Some protocols, especially those that include antibiotics, can introduce artifacts in the ribosome profiling data [6][7][8][9] and the best practices for generating ribosome profiling libraries in bacteria are still in debate 30 . So, we decided to use ribosome profiling data obtained by two distinct protocols, with flash frozen or filtered cells; both protocols were avoiding the use of antibiotics 30 .…”
Section: Biological Distribution Of the Short Translational Rampmentioning
confidence: 99%
See 1 more Smart Citation
“…To verify if ribosome accumulation is implicated in the ramp formation, we compared the average ribosome footprint count per nucleotide of two groups of genes, genes with scores higher than 4.2 versus scores lower than 4.2, using ribosome profiling data. Some protocols, especially those that include antibiotics, can introduce artifacts in the ribosome profiling data [6][7][8][9] and the best practices for generating ribosome profiling libraries in bacteria are still in debate 30 . So, we decided to use ribosome profiling data obtained by two distinct protocols, with flash frozen or filtered cells; both protocols were avoiding the use of antibiotics 30 .…”
Section: Biological Distribution Of the Short Translational Rampmentioning
confidence: 99%
“…This hypothesis, however, has been challenged by several subsequent papers. One strong criticism of the work is the use of translation inhibitors, which is now known to distort ribosome profiling data, especially at the N-terminal 6,7,8,9,10 . By ribosome profiling analyses of S. cerevisiae performed in the absence of such inhibitors, we have already demonstrated that only a small number of genes with sequences containing an extremely high concentration of non-optimal codons possess lower elongation rates 11 .…”
Section: Introductionmentioning
confidence: 99%
“…In order to characterize the distribution of positively charged protein stretches in several organisms, we used a program that can screen a protein sequence and calculate the net charge every consecutive frame of 30-amino-acid residues (Q30res) (24). We analyzed total Swiss-Prot reviewed proteome (559,052 sequences) and compared with viral, Drosophila melanogaster, Arabidopsis thaliana, and H. sapiens data sets.…”
Section: Resultsmentioning
confidence: 99%
“…1). The adverse effect of exceptionally positively charged protein segments on ribosomal synthesis efficiency may be among the selective pressures acting against repetitions of R or K in all organisms (24). Additionally, the size and composition of viral positively charged domains might be controlled by other factors.…”
Section: Discussionmentioning
confidence: 99%
“…The orthogonality between high‐pH and low‐pH conditions may be related to different polarities of five amino acids (Glu, Asp, Arg, His, and Lys) under different pH conditions . Proteoform retention behaviors are less molecular weight dependent under high‐pH conditions, which may be due to different distributions of charges in the proteoform primary structure . A potential drawback is that some proteins are less charged under high‐pH conditions and cannot be efficiently eluted from the column.…”
Section: Separation Of Proteoformsmentioning
confidence: 99%