Ribosomes from the three domains of life, have a universally conserved lateral protuberance, called the stalk (1). This protein complex, composed of acidic proteins, is part of the GTPase-associated-center which is directly responsible for stimulation of translation-factor-dependent GTP hydrolysis (2). In prokaryotes, there is one type of small acidic protein (L12) (3), while two protein families are found in eukaryotes, P1 and P2 (4). The small acidic ribosomal proteins from prokaryotes/eukaryotes L12/P1,P2 are thought to preferentially form dimers (L12)2/(P1-P2)2 (5), and they are not in direct contact with rRNA, but they are attached to the ribosome via L10/P0 protein. Together, they form oligomeric complexes: pentameric P0–(P1-P2)2 in eukaryotes (6) or pentameric/heptameric L10-(L12)4 /L10-(L12)6 in prokayotes (7).
An intergrated structural model, based on the prokaryotic stalk, has been presented (7). However clear understanding of the structure for the eukaryotic stalk is still obscure. Recently, the very first view of the eukaryotic stalk constituents has been reported (8). The results of small-angle X-ray scattering experiments showed the overall shape of the yeast S. cerevisiae P1A-P2B protein complex, which can be described as an elongated molecule with dimensions of 10 nm x 2.5 nm. The report revealed significant structural differences between prokaryotic and eukaryotic acidic proteins, rising the question about structural relationships between them.
To shed more light on the evolutionary relationship among acidic ribosomal proteins from three phylogenetic domains: Prokaryotes – E. coli; Archaea - Sulfolobus solfataricus; Eukaryotes – H. sapiens, we have undertook structural analysis using 1D, 2D and 3D approaches. The combination of SAXS and phylogenetic approaches was used. The analyses have showed, that considering all structural aspects, prokaryotic and archaea/eukaryotic proteins are not structurally related, indicating at the same time, that those proteins have different evolutionary origin. Therefore, they can be regarded as analogous rather than homologous proteins.

1. Liljas A. (2004) Structural Aspects of Protein Synthesis, World Scientific Publishing
2. Gonzalo P. and Reboud, J. P. (2003) Biol Cell 95(3-4) 179-193
3. Wahl M. C. and Moller, W. (2002) Curr Protein Pept Sci 3(1) 93-106
4. Tchorzewski M. (2002) Int J Biochem Cell Biol 34(8) 911-915
5. Tchorzewski M., Boldyreff, B., Issinger, O., and Grankowski, N. (2000) Int J Biochem Cell Biol 32(7) 737-746
6. Krokowski D., Boguszewska, A., Abramczyk, D., Liljas, A., Tchorzewski, M., and Grankowski N. (2006) Mol Microbiol 60(2) 386-400
7. Diaconu M., Kothe U., Schlunzen F., Fischer N., Harms J. M., Tonevitsky A. G., Stark H., Rodnina M. V., and Wahl M. C. (2005) Cell 121(7) 991-1004
8. Grela P., Helgstrand M., Krokowski D., Boguszewska A., Svergun D., Liljas A., Bernado P., Grankowski N., Akke M., and Tchorzewski M. (2007) Biochemistry 46(7) 1988-1998

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1. Trans-Acting Factor Involved in The Stalk Assembly Into 60S Ribosomal Subunit
2. Cellular Localization of The Human Acidic Ribosomal P proteins