ArticleGenome research2003
Hierarchy of sequence-dependent features associated with prokaryotic translation.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
72 citing papers in PubMed, 151 citations in OpenAlex.
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- Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae.BMC plant biology · 2024Article
- Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization.Annals of medicine and surgery (2012) · 2024Article
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- Targeted Genome Mining-From Compound Discovery to Biosynthetic Pathway Elucidation.Microorganisms · 2020Article
- Codon optimization with deep learning to enhance protein expression.Scientific reports · 2020Article
- Tuning the Cell-Free Protein Synthesis System for Biomanufacturing of Monomeric Human Filaggrin.Frontiers in bioengineering and biotechnology · 2020Article
- Buffalo early pregnancy biomarker coding sequence cloning and partial length expression inHeliyon · 2019Article
- Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer.Genome biology and evolution · 2019Article
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- Stable Expression of Modified Green Fluorescent Protein in Group B Streptococci To Enable Visualization in Experimental Systems.Applied and environmental microbiology · 2018Article
- Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression.Current genetics · 2018Article
- Codon optimality, bias and usage in translation and mRNA decay.Nature reviews. Molecular cell biology · 2018Review
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein expression in the cell is affected by various sequence-dependent features. Several such sequence-dependent features have been individually studied,yet they have not been compared quantitatively in terms of their relative influence on protein expression,and a hierarchy of these elements has not been determined. Here we present a quantitative analysis examining sequence-dependent features involved in prokaryotic translation,namely,the base-pairing potential between the mRNA Shine-Dalgarno sequence and the ribosomal RNA,codon bias,and the identity of the stop codon. We analyzed these features both at intra- and intergenomic levels using the Escherichia coli and Haemophilus influenzae genomes. Within each genome,we examined the relationship between each feature and protein expression levels determined by 2D-gel analyses. At the intergenomic level,comparative genomic principles were applied to study the relative preservation of the different sequence-dependent properties between orthologs. From these analyses,we determined that biased codon usage is the property that is most highly associated with protein expression and that is most conserved. The identity of the stop codon and the base-pairing potential of the mRNA Shine-Dalgarno sequence and the rRNA seem to have less of an effect on protein expression.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.