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A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly.

Lott BB, Wang Y, Nakazato T - BMC Biophys (2013)

Bottom Line: However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different.Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction.Additionally, because thermophiles and mesophiles exhibit significantly different amino acid compositions in their sequences but not in the identities of contact sites, we conclude that this electrostatic component of interaction is insensitive to temperature and is not the determining factor differentiating the temperature sensitivity of ribosome assembly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry, The University of Memphis, 38152 Memphis TN, USA. ywang@memphis.edu.

ABSTRACT

Background: Assembly of the ribosome from its protein and RNA constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. Since the early 1960's, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear.We utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembly process. We compared small subunit (30S) r-protein sequences to those of other housekeeping proteins from 560 bacterial species and searched for correlations between r-protein amino acid content and factors such as assembly binding order, environmental growth temperature, protein size, and contact with ribosomal RNA (rRNA) in the 30S complex.

Results: We find r-proteins have a significantly high percent of positive residues, which are highly represented at rRNA contact sites. An inverse correlation between the percent of positive residues and r-protein size was identified and is mainly due to the content of Lysine residues, rather than Arginine. Nearly all r-proteins carry a net positive charge, but no statistical correlation between the net charge and the binding order was detected. Thermophilic (high-temperature) r-proteins contain increased Arginine, Isoleucine, and Tyrosine, and decreased Serine and Threonine compared to mesophilic (lower-temperature), reflecting a known distinction between thermophiles and mesophiles, possibly to account for protein thermostability. However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different.

Conclusions: Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction. However, the binding order of r-proteins in assembly does not appear to depend on these electrostatics interactions. Additionally, because thermophiles and mesophiles exhibit significantly different amino acid compositions in their sequences but not in the identities of contact sites, we conclude that this electrostatic component of interaction is insensitive to temperature and is not the determining factor differentiating the temperature sensitivity of ribosome assembly.

No MeSH data available.


Proportion of Lysine residues correlates with average protein length but Arginine does not. Lysine (A) shows a highly significant negative correlation with protein length (Spearman’s rank correlation: ρ = −0.802, p=2.60x10-5), whereas Arginine (B) shows a weaker correlation with no statistical significance (ρ = −0.484, p=0.032).
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Figure 4: Proportion of Lysine residues correlates with average protein length but Arginine does not. Lysine (A) shows a highly significant negative correlation with protein length (Spearman’s rank correlation: ρ = −0.802, p=2.60x10-5), whereas Arginine (B) shows a weaker correlation with no statistical significance (ρ = −0.484, p=0.032).

Mentions: Upon analyzing the data shown in Figure 3A, we noticed a second general trend: increasing percentage of positively charged residue from S2 to S21. Because r-proteins are named in order of decreasing size, this relationship appears to be between positive charges and protein length. We have already shown the high incidence of positively charged residues is an important feature of all ribosomal proteins, and here we find that smaller proteins tend to have higher proportions of them. Interestingly, this relationship appears to be due to Lysine content rather than Arginine content (Figure 4; Spearman’s rank correlation ρ = −0.802, p = 2.60×10-5 for Lys, ρ = −0.484, p = 0.032 for Arg; see Additional file 8 and Additional file 9). This result is intriguing, as it provides evidence that amino acids usually considered chemically equivalent are not necessarily used interchangeably in bacterial proteins. It hints at differential functions of chemically similar residues, even in their roles in the electrostatics component of ribosome assembly. From the current study, it is unclear why Arg does not participate in this trend. We also identified a positive correlation between percent of Glycine and increasing protein size (G; Spearman’s rank correlation, ρ = 0.657, p = 0.002), but none were detected for other residues. Neither was a correlation found between average net protein charge and average length (see Figure 3B; Spearman’s Rank correlation ρ = 0.239), indicating that this is truly an association involving only the content of the Lys residue.


A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly.

Lott BB, Wang Y, Nakazato T - BMC Biophys (2013)

Proportion of Lysine residues correlates with average protein length but Arginine does not. Lysine (A) shows a highly significant negative correlation with protein length (Spearman’s rank correlation: ρ = −0.802, p=2.60x10-5), whereas Arginine (B) shows a weaker correlation with no statistical significance (ρ = −0.484, p=0.032).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016315&req=5

Figure 4: Proportion of Lysine residues correlates with average protein length but Arginine does not. Lysine (A) shows a highly significant negative correlation with protein length (Spearman’s rank correlation: ρ = −0.802, p=2.60x10-5), whereas Arginine (B) shows a weaker correlation with no statistical significance (ρ = −0.484, p=0.032).
Mentions: Upon analyzing the data shown in Figure 3A, we noticed a second general trend: increasing percentage of positively charged residue from S2 to S21. Because r-proteins are named in order of decreasing size, this relationship appears to be between positive charges and protein length. We have already shown the high incidence of positively charged residues is an important feature of all ribosomal proteins, and here we find that smaller proteins tend to have higher proportions of them. Interestingly, this relationship appears to be due to Lysine content rather than Arginine content (Figure 4; Spearman’s rank correlation ρ = −0.802, p = 2.60×10-5 for Lys, ρ = −0.484, p = 0.032 for Arg; see Additional file 8 and Additional file 9). This result is intriguing, as it provides evidence that amino acids usually considered chemically equivalent are not necessarily used interchangeably in bacterial proteins. It hints at differential functions of chemically similar residues, even in their roles in the electrostatics component of ribosome assembly. From the current study, it is unclear why Arg does not participate in this trend. We also identified a positive correlation between percent of Glycine and increasing protein size (G; Spearman’s rank correlation, ρ = 0.657, p = 0.002), but none were detected for other residues. Neither was a correlation found between average net protein charge and average length (see Figure 3B; Spearman’s Rank correlation ρ = 0.239), indicating that this is truly an association involving only the content of the Lys residue.

Bottom Line: However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different.Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction.Additionally, because thermophiles and mesophiles exhibit significantly different amino acid compositions in their sequences but not in the identities of contact sites, we conclude that this electrostatic component of interaction is insensitive to temperature and is not the determining factor differentiating the temperature sensitivity of ribosome assembly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry, The University of Memphis, 38152 Memphis TN, USA. ywang@memphis.edu.

ABSTRACT

Background: Assembly of the ribosome from its protein and RNA constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. Since the early 1960's, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear.We utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembly process. We compared small subunit (30S) r-protein sequences to those of other housekeeping proteins from 560 bacterial species and searched for correlations between r-protein amino acid content and factors such as assembly binding order, environmental growth temperature, protein size, and contact with ribosomal RNA (rRNA) in the 30S complex.

Results: We find r-proteins have a significantly high percent of positive residues, which are highly represented at rRNA contact sites. An inverse correlation between the percent of positive residues and r-protein size was identified and is mainly due to the content of Lysine residues, rather than Arginine. Nearly all r-proteins carry a net positive charge, but no statistical correlation between the net charge and the binding order was detected. Thermophilic (high-temperature) r-proteins contain increased Arginine, Isoleucine, and Tyrosine, and decreased Serine and Threonine compared to mesophilic (lower-temperature), reflecting a known distinction between thermophiles and mesophiles, possibly to account for protein thermostability. However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different.

Conclusions: Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction. However, the binding order of r-proteins in assembly does not appear to depend on these electrostatics interactions. Additionally, because thermophiles and mesophiles exhibit significantly different amino acid compositions in their sequences but not in the identities of contact sites, we conclude that this electrostatic component of interaction is insensitive to temperature and is not the determining factor differentiating the temperature sensitivity of ribosome assembly.

No MeSH data available.