Hierarchy of sequence-dependent features associated with prokaryotic translation

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.

Figure 1

Overview of the analysis.

Figure 2

Shine-Dalgarno (SD) free energy values versus protein abundance. The quantitative measure of the SD mRNA sequence is the free energy gain upon its base-pairing with the 16S rRNA. Scatter plots of the free energy values versus protein abundance are shown for 163 highly expressed E. coli proteins (A) and for 297 highly expressed H. influenzae proteins (B). Protein abundance is shown on a log scale.

Figure 3

Correlation between SD free energy values of orthologs. A total of 1271 orthologs were included in this analysis.

Figure 4

Relationship between codon bias and protein abundance. The bias in codon usage is expressed by the CAI measure. Scatter plots of CAI versus relative protein abundance are shown for 163 highly expressed E. coli proteins (A) and for 297 highly expressed H. influenzae proteins (B). Protein abundance is shown on a log scale.

Figure 5

Correlation between codon bias of orthologs. Codon bias is expressed either by Nc values (A) or by CAI values (B). Scatter plots of the corresponding values in 1271 E. coli and H. influenzae orthologs are shown.

Figure 6

Determination of hierarchy of two different properties associated with translation. The results of the intra- and intergenome analyses for SD mRNA–16S rRNA base-pairing potential and codon bias are shown in steps that are described in the overview (Fig. 1).