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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.

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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.


Percentage of positively charged residues correlates with protein size but net charges do not. All thermophilic r-proteins except S11 contain a higher percentage of positively charged residues than their mesophilic homologs (A), and, for some proteins, including all six primary proteins, this difference is statistically significant. R-proteins generally have a net positive charge (B), and thermophiles typically have a higher average charge than mesophiles. For three proteins, this difference is significant. The box-and-whisker plots are represented as in Figure 2.
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Figure 3: Percentage of positively charged residues correlates with protein size but net charges do not. All thermophilic r-proteins except S11 contain a higher percentage of positively charged residues than their mesophilic homologs (A), and, for some proteins, including all six primary proteins, this difference is statistically significant. R-proteins generally have a net positive charge (B), and thermophiles typically have a higher average charge than mesophiles. For three proteins, this difference is significant. The box-and-whisker plots are represented as in Figure 2.

Mentions: Because primary binding proteins bind to the bare, negatively charged RNA during ribosomal assembly and the binding electrostatics of subsequent proteins might differ due to the presence of already-bound r-proteins, one might expect that primary r-proteins have higher proportions of positive residues than secondary and tertiary proteins (which are unlikely to bind before primary proteins) or that primary proteins may have higher net positive charges. Correlations with respect to protein assembly order between the proportion of positive residues and the net charges on the proteins were tested. However, we did not find evidence for higher proportions of positive charges in primary proteins (Figure 3A; see Panel A in Additional file 4 for a visualization of proportion of positive charges according to protein binding order), as Student’s t-test comparing the mean proportions of positive residues between primary and secondary/tertiary r-proteins was not significant (t15 = −0.207, two-tailed p = 0.839), suggesting that binding order is not influenced by fractions of positively charged amino acid of r-proteins. Statistical tests of association between net charge and binding order also revealed no observable correlation (Spearman’s Rank correlation ρ = 0.190; Figure 3B; see Panel B in Additional file 4 for a visualization of net charges according to protein binding order). Because no relationship between the order in which r-proteins attach to the rRNA during assembly (primary versus secondary versus tertiary) and the content of positive residues or the total protein charge was detected, it is likely that binding order is governed by mechanisms other than simple electrostatics interactions with the RNA, possibly the availability of the binding sites on RNA.


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

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

Percentage of positively charged residues correlates with protein size but net charges do not. All thermophilic r-proteins except S11 contain a higher percentage of positively charged residues than their mesophilic homologs (A), and, for some proteins, including all six primary proteins, this difference is statistically significant. R-proteins generally have a net positive charge (B), and thermophiles typically have a higher average charge than mesophiles. For three proteins, this difference is significant. The box-and-whisker plots are represented as in Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Percentage of positively charged residues correlates with protein size but net charges do not. All thermophilic r-proteins except S11 contain a higher percentage of positively charged residues than their mesophilic homologs (A), and, for some proteins, including all six primary proteins, this difference is statistically significant. R-proteins generally have a net positive charge (B), and thermophiles typically have a higher average charge than mesophiles. For three proteins, this difference is significant. The box-and-whisker plots are represented as in Figure 2.
Mentions: Because primary binding proteins bind to the bare, negatively charged RNA during ribosomal assembly and the binding electrostatics of subsequent proteins might differ due to the presence of already-bound r-proteins, one might expect that primary r-proteins have higher proportions of positive residues than secondary and tertiary proteins (which are unlikely to bind before primary proteins) or that primary proteins may have higher net positive charges. Correlations with respect to protein assembly order between the proportion of positive residues and the net charges on the proteins were tested. However, we did not find evidence for higher proportions of positive charges in primary proteins (Figure 3A; see Panel A in Additional file 4 for a visualization of proportion of positive charges according to protein binding order), as Student’s t-test comparing the mean proportions of positive residues between primary and secondary/tertiary r-proteins was not significant (t15 = −0.207, two-tailed p = 0.839), suggesting that binding order is not influenced by fractions of positively charged amino acid of r-proteins. Statistical tests of association between net charge and binding order also revealed no observable correlation (Spearman’s Rank correlation ρ = 0.190; Figure 3B; see Panel B in Additional file 4 for a visualization of net charges according to protein binding order). Because no relationship between the order in which r-proteins attach to the rRNA during assembly (primary versus secondary versus tertiary) and the content of positive residues or the total protein charge was detected, it is likely that binding order is governed by mechanisms other than simple electrostatics interactions with the RNA, possibly the availability of the binding sites on RNA.

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.