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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.


R-protein amino acid compositions exhibit typical thermostability differences. Thermophilic r-proteins (red) contain higher percentages of Arginine (R), Isoleucine (I), and Tyrosine (Y), and lower percentages of Serine (S) and Threonine (T) than mesophilic r-proteins (blue). These differences are generally consistent with typical differences among thermophilic and mesophilic proteins and are estimated to function in the thermostability of the protein. In the box-and-whisker representation, the lower and upper circles represent the 5th and 95th percentiles, respectively, and the lower and upper whiskers the 10th and 90th. The colored regions mark the middle 50% of the samples (25th to 75th percentile), with a solid line representing the median and a dotted line the mean. Asterisks mark the amino acids that show a statistically significant difference between mesophilic and thermophilic species.
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Figure 2: R-protein amino acid compositions exhibit typical thermostability differences. Thermophilic r-proteins (red) contain higher percentages of Arginine (R), Isoleucine (I), and Tyrosine (Y), and lower percentages of Serine (S) and Threonine (T) than mesophilic r-proteins (blue). These differences are generally consistent with typical differences among thermophilic and mesophilic proteins and are estimated to function in the thermostability of the protein. In the box-and-whisker representation, the lower and upper circles represent the 5th and 95th percentiles, respectively, and the lower and upper whiskers the 10th and 90th. The colored regions mark the middle 50% of the samples (25th to 75th percentile), with a solid line representing the median and a dotted line the mean. Asterisks mark the amino acids that show a statistically significant difference between mesophilic and thermophilic species.

Mentions: PIC analyses revealed that, at the level of the entire 30S subunit, thermophiles are comprised of significantly lower proportions of polar Serine (S) and Threonine (T) residues and higher proportions of positively charged Arginine (R), nonpolar Isoleucine (I), and aromatic Tyrosine (Y) (Figure 2; according to at least one statistical significance test at α = 0.01; see Methods and Additional file 3). Other differences in mean values between the two groups, though they may appear somewhat large, are not significant according to sign test or t-tests. These results are largely consistent with other thermostability studies (reviewed in Ref. [29]), which have identified an increase in R and Y levels and a decrease in C and T levels in thermophiles. It is worth mentioning that a seeming discrepancy in our report merely involves similar but different polar residues: we report a significant difference in Serine (CH2OH side chain) instead of Cysteine (CH2SH side chain), as found in other studies. The general trends we observed via PIC also match previous thermostability reports: thermophiles contain significantly higher proportions of positive residues and lower proportions of polar residues than mesophiles (at α = 0.01). These tendencies likely reflect the need for stronger interactions at higher temperatures [23,25,29]. On the other hand, no significant directional biases were detected for negative, nonpolar, and aromatic residues.


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

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

R-protein amino acid compositions exhibit typical thermostability differences. Thermophilic r-proteins (red) contain higher percentages of Arginine (R), Isoleucine (I), and Tyrosine (Y), and lower percentages of Serine (S) and Threonine (T) than mesophilic r-proteins (blue). These differences are generally consistent with typical differences among thermophilic and mesophilic proteins and are estimated to function in the thermostability of the protein. In the box-and-whisker representation, the lower and upper circles represent the 5th and 95th percentiles, respectively, and the lower and upper whiskers the 10th and 90th. The colored regions mark the middle 50% of the samples (25th to 75th percentile), with a solid line representing the median and a dotted line the mean. Asterisks mark the amino acids that show a statistically significant difference between mesophilic and thermophilic species.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: R-protein amino acid compositions exhibit typical thermostability differences. Thermophilic r-proteins (red) contain higher percentages of Arginine (R), Isoleucine (I), and Tyrosine (Y), and lower percentages of Serine (S) and Threonine (T) than mesophilic r-proteins (blue). These differences are generally consistent with typical differences among thermophilic and mesophilic proteins and are estimated to function in the thermostability of the protein. In the box-and-whisker representation, the lower and upper circles represent the 5th and 95th percentiles, respectively, and the lower and upper whiskers the 10th and 90th. The colored regions mark the middle 50% of the samples (25th to 75th percentile), with a solid line representing the median and a dotted line the mean. Asterisks mark the amino acids that show a statistically significant difference between mesophilic and thermophilic species.
Mentions: PIC analyses revealed that, at the level of the entire 30S subunit, thermophiles are comprised of significantly lower proportions of polar Serine (S) and Threonine (T) residues and higher proportions of positively charged Arginine (R), nonpolar Isoleucine (I), and aromatic Tyrosine (Y) (Figure 2; according to at least one statistical significance test at α = 0.01; see Methods and Additional file 3). Other differences in mean values between the two groups, though they may appear somewhat large, are not significant according to sign test or t-tests. These results are largely consistent with other thermostability studies (reviewed in Ref. [29]), which have identified an increase in R and Y levels and a decrease in C and T levels in thermophiles. It is worth mentioning that a seeming discrepancy in our report merely involves similar but different polar residues: we report a significant difference in Serine (CH2OH side chain) instead of Cysteine (CH2SH side chain), as found in other studies. The general trends we observed via PIC also match previous thermostability reports: thermophiles contain significantly higher proportions of positive residues and lower proportions of polar residues than mesophiles (at α = 0.01). These tendencies likely reflect the need for stronger interactions at higher temperatures [23,25,29]. On the other hand, no significant directional biases were detected for negative, nonpolar, and aromatic residues.

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.