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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

A Comparative Study of Ribosomal Proteins: Linkage between Amino Acid Distribution and Ribosomal Assembly

Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and here we utilize a comparative analysis approach to relate the composition of ribosomal proteins (r-proteins) to their role in the assembly process. We computed the amino acid distributions for the 30S subunit r-protein sequences from 560 bacterial species and compared this composition to those of other house-keeping proteins from the same species. We found that r-proteins have a significantly higher content of positively charged residues (Lysine, K, and Arginine, R) than do non-ribosomal proteins (10% for R and 11% for K in r-proteins, versus 4.7% R and 5.9% K in non-ribosomal proteins), which is consistent with prior knowledge of net positive charges carried by r-proteins (Baker, Sept et al. 2001; Klein, Moore et al. 2004; Burton, Zimmermann et al. 2012). Furthermore, these two residues are also highly represented at contact sites along the protein/RNA interface (contact enrichment factor (CEF) > 1). These results provide further evidence of the importance of electrostatic interactions between the positively charged proteins and negatively charged ribosomal RNA (rRNA) during ribosome assembly. Other highly represented contact residues include polar and aromatic residues, which are likely to interact with rRNA via hydrogen bonds and base stacking interactions, respectively. Interestingly, the proportion of K residues generally decreases with r-protein size, reflecting a negative correlation between protein lengths and the proportion of K (Spearman’s rank correlation, ρ = -0.802, p = 2.60e-5). We suggest that this trend helps the smaller r-proteins, which experience higher translational entropy than large proteins, overcome the increased free energy barrier during assembly. When the r-protein sequences were categorized according to the species’ optimal growth temperature (OGT), we found that thermophiles show increased R, Isoleucine (I), and Tyrosine (Y) content, whereas mesophiles have increased proportions of Serine (S) and Threonine (T). These results reflect one typical distinction between thermophiles and mesophiles (Kumar and Nussinov 2001), yet these differences in amino acid distributions do not extend to their respective contact sites. That is, the makeup of thermophilic and mesophilic r-protein contact residues are not significantly different (p > 0.01). This indicates that, while the percent compositions of amino acids relating to qualities such as thermostability and protein folding are expected to vary with environmental temperature, the distributions of residues in contact with rRNA are comparable for all bacterial species. From this, we conclude that the electrostatic interactions that guide ribosome assembly are independent of temperature.

References

Baker, N. A., D. Sept, et al. (2001). Electrostatics of nanosystems: application to microtubules and the ribosome.: Proc Natl Acad Scie U S A 98(18): 10037-10041.

Burton, B., M. T. Zimmermann, et al. (2012). A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. Plos Computational Biology 8(5): e1002530.

Klein, D. J., P. B. Moore, et al. (2004). The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol 340(1): 141-177.

Kumar, S. and R. Nussinov (2001). How do thermophilic proteins deal with heat? Cellular and Molecular Life Sciences 58(9): 1216-1233.

Brittany Burton Lott 1
Takuya Nakazato*2,3
Yongmei Wang**2,3

1 Department of Chemistry
2Department of Bioinformatics; 3Department of Biological Sciences;
The University of Memphis
Memphis, TN 38152

*Tel.: (901) 678-5539
Fax: (901)678-4457
tnkazato@memphis.edu
**Tel.: (901) 678-2629
Fax: (901)678-3447
ywang@memphis.edu