A Comparison of Structural and Evolutionary Attributes of Escherichia coli and Thermus thermophilus Small Ribosomal Subunits: Signatures of Thermal Adaptation

Kundu S (2013) A Comparison of Structural and Evolutionary Attributes of Escherichia coli and Thermus thermophilus Small Ribosomal Subunits: Signatures of Thermal Adaptation. PLoS ONE 8(8): e69898. doi:10.1371/journal.pone.0069898 A Comparison of Structural and Evolutionary Attributes of Escherichia coli and Thermus thermophilus Small Ribosomal Subunits: Signatures of Thermal Adaptation Saurav Mallik 0 Sudip Kundu 0 George E. Fox, University of Houston, United States of America 0 Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , Kolkata , India Here we compare the structural and evolutionary attributes of Thermus thermophilus and Escherichia coli small ribosomal subunits (SSU). Our results indicate that with few exceptions, thermophilic 16S ribosomal RNA (16S rRNA) is densely packed compared to that of mesophilic at most of the analogous spatial regions. In addition, we have located species-specific cavity clusters (SSCCs) in both species. E. coli SSCCs are numerous and larger compared to T. thermophilus SSCCs, which again indicates densely packed thermophilic 16S rRNA. Thermophilic ribosomal proteins (r-proteins) have longer disordered regions than their mesophilic homologs and they experience larger disorder-to-order transitions during SSU-assembly. This is reflected in the predicted higher conformational changes of thermophilic r-proteins compared to their mesophilic homologs during SSU-assembly. This high conformational change of thermophilic r-proteins may help them to associate with the 16S ribosomal RNA with high complementary interfaces, larger interface areas, and denser molecular contacts, compared to those of mesophilic. Thus, thermophilic protein-rRNA interfaces are tightly associated with 16S rRNA than their mesophilic homologs. Densely packed 16S rRNA interior and tight protein-rRNA binding of T. thermophilus (compared to those of E. coli) are likely the signatures of its thermal adaptation. We have found a linear correlation between the free energy of protein-RNA interface formation, interface size, and square of conformational changes, which is followed in both prokaryotic and eukaryotic SSU. Disorder is associated with high protein-RNA interface polarity. We have found an evolutionary tendency to maintain high polarity (thereby disorder) at protein-rRNA interfaces, than that at rest of the protein structures. However, some proteins exhibit exceptions to this general trend. - The modern ribosome is a sophisticated ribonucleoprotein complex having a large subunit (LSU) and a small subunit (SSU). The bacterial SSU typically contains a 16S ribosomal RNA (rRNA) and 24 ribosomal proteins (r-protein) attached to it, whereas the LSU contains a 23S rRNA, 5S rRNA and 34 proteins [1]. In the Universal Phylogenetic Tree (UPT), 34 ribosomal proteins (15 of SSU and 19 of LSU) are observed to have homologs in all three phylogenetic domains [2]. The prokaryotic ribosome (SSU and LSU) structures have been resolved at molecular level by high-resolution X-ray crystallography [310]. These works provide a deep insight into the structure of ribosomal RNAs and proteins and their molecular interactions. The association pathways of both the subunits have also been analyzed in detail [1114]. It was shown that the rRNA does not fold into its functional state without the presence of r-proteins [15,16]. Thus, general purpose of the r-proteins is to assist rRNA folding and provide structural stability to the folded rRNAs [4]. Now, apart from this general strategy, if some structural/evolutionary attributes are observed to be significantly different for two species at the same domain of life, but habituated at different environmental conditions (one mesophilic and another thermophilic), then that difference might entail an adaptation strategy with the environment. Every organism is adapted according to its habitat environment. The study of molecular strategies to adapt with the environment is a very interesting scientific field to work on. The thermal adaptation has long been at the center of such studies. Researchers have analyzed these signatures in genome [17,18], transcriptome [19], and proteome level [1926]. Proteome level studies confirm that a significant reduction in the frequency of the thermolabile amino acids (histidine, glutamine, and threonine) and an increment in the frequency of charged residues (arginine, lysine etc) is a common signature of thermal adaptation [25,26]. At the structure level, genomic/transcriptome/proteome level natural selections are directed towards the generation of thermostable biomolecules. Densely packed interior is a common attribute of the thermophilic biomolecules, although there are exceptions [2022]. Researchers of this field have mostly worked on monomeric proteins to study the effects of thermal adaptation. Thus, a detailed study on the nature of thermal adaptation at the biomolecular interfaces is still unavailable. However, it is known that thermophilic and hyperthermophilic proteins have reduced disordered regions compared to mesophilic; proteins related to translation and ribosome biogenesis show an exception to this trend [27]. In this current work, we have established that this disorder is preferably maintained at the interfaces of the r-proteins. At thermophilic conditions, the disorder-to-order transitions due to protein-rRNA interactions generate a strong binding between protein and rRNA constituents of SSU. In this current work, we have calculated the different structural and evolutionary attributes of Escherichia coli and Thermus thermophilus SSU and have made pairwise comparisons. Since SSU is a ribonucleoprotein oligomer, we have conducted our investigation at two levels: (1) what are the signatures of thermal adaptation at the 16S rRNA interior, (2) how the protein-rRNA interactions result towards generation of highly stable SSU structures in thermophilic bacteria. Cavity Analysis of E. coli and T. thermophilus SSU The SSU is a large ribonucleoprotein complex containing a large 16S rRNA and about 24 proteins. We begin our work by comparing the distribution of cavities in the E. coli and T. thermophilus SSUs. Cavities are located both within the interior (cavities) and on the surface (pockets/clefts) of biomolecules [28,29]. The cavities in the interior of biomolecules indicate loose internal packing [30] and their presence can even reduce the structural stability [31]. On the other hand, the presences of cavities at the oligomeric interfaces reduce the interface complementarity [29]. In this current work, we have compared the distribution of cavities at rRNA-interiors (RI cavities) and at protein-rRNA interfaces (PR cavities) of thermophilic and mesophilic SSUs. PR cavities are also divided into two groups: cavities contributed by one single protein and 16S rRNA (SPR) and those contributed by multiple proteins and 16S rRNA (MPR) at the interface. Cavities in 16S rRNA. Here (...truncated)