Analysis of protein--protein relationships in 30S ribosome assembly intermediates using protection from proteolytic digestion

Assembly of the 30S ribosomal subunit

Ribosomes are large macromolecular complexes responsible for cellular protein synthesis. The smallest known cytoplasmic ribosome is found in prokaryotic cells; these ribosomes are about 2.5 MDa and contain more than 4000 nucleotides of RNA and greater than 50 proteins. These components are distributed into two asymmetric subunits. Recent advances in structural studies of ribosomes and ribosomal subunits have revealed intimate details of the interactions within fully assembled particles. In contrast, many details of how these massive ribonucleoprotein complexes assemble remain elusive. The goal of this review is to discuss some crucial aspects of 30S ribosomal subunit assembly.

The role of protein L16 and its fragments in the peptidyltransferase activity of 50-S ribosomal subunits

Two large polypeptide fragments of ribosomal protein L16 were obtained by limited hydrolysis with trypsin and chymotrypsin. The chymotryptic fragment, lacking nine N-terminal amino acids residues, is fully active in the restoration of the peptidyltransferase activity of the LiCl-stripped 50-S ribosomal subunits, whereas the tryptic fragment, lacking an additional six residues, is inactive. We also show that under the optimized ionic conditions protein L16 is not needed for the peptidyltransferase activity.

Polynucleotide . ribosomal-protein complexes and their decoding properties

Polyadenylic acid, polycytidylic acid, polyuridylic acid or phage MS2 RNA, immobilized on Sepharose, form a complex with Escherichia coli ribosomal proteins. Regardless of their particular nucleotide composition, all four polynucleotides bind an invariable set of proteins consisting of S1, S3, S4, S5, S9, S13, L2 and L17. We found that these polynucleotide . protein complexes bind tRNA. Furthermore, it was possible to show that the poly(A) . protein and poly(U) . protein complexes select efficiently their cognate tRNAs, tRNALys and tRNAPhe respectively. This important functional property of the polynucleotide . protein complexes suggests that these ribosomal proteins belong in the ribosome to a functional domain responsible for the decoding of mRNA.

The properties of the tRNA . protein complex of the Escherichia coli ribosome. Interaction with tRNA, 5-S RNA and 30-S ribosomal subunit

A complex between immobilized tRNA and Escherichia coli 50-S ribosomal subunit proteins provides binding sites for several other components of the protein biosynthesis system. We found that this complex binds 5-S RNA. tRNA and 30-S ribosomal subunits. The binding of 5-S RNA and tRNA takes place at equilibrium; in 10 mM Tris/HCl buffer pH 7.5, containing 10 mM MgCl2 and 100 mM KCl at 4 degrees C it is characterized by the dissociation constants 1.7 X 10(-7) M and 4 X 10(-7) M respectively. We show that the performed complex between tRNA and 50-S ribosomal subunit protein can bind these two RNAs simultaneously by forming a subribosomal domain consisting of two molecules of tRNA, 5-S RNA and the ribosomal proteins L2, L15, L16, L17, L18, L22, L33 and L34. The preformed tRNA . protein complex interacts also with the 30-S ribosomal subunit, suggesting that is located at the ribosomal interface.

Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25

The structure of Escherichia coli 5S RNA fragments 1-41 and 42-120 has been studied by the read-off gel sequencing technique using S1 nuclease and cobra venom RNase as probes. Comparison of the digestion patterns with those of reassociated and intact 5S RNA suggests that the structure of both fragments is very similar to that of the corresponding regions in the intact molecule. Six different fragments obtained by partial digestion with T1 RNase and S1 nuclease have been used for reconstitution of 5S RNA, its certain structural regions and complexes with ribosomal proteins L18 and L25 recognizes the double-helix consisting of nucleotides 79-97 (i.e. prokaryotic stem), whereas a loop-region around position 40 (possible positions 39-47) is involved in the interaction with protein L18.

The composition and properties of the Escherichia coli 5-S RNA-protein complex

At a high concentration of MgCl2 (30 mM) and a low concentration of proteins from the 50-S subunit (0.2 mg/ml), only three proteins, L15, L18 and L25, bind to 5-S RNA in significant amounts. On the other hand, in a buffer containing only 1 mM Mg Cl2, but otherwise at the same ionic strength (0.2 M), or at a protein concentration about 1.5 mg/ml, a large, stable complex can form between immobilized 5-S RNA and 50-S ribosomal proteins. This complex contains proteins L2, L3, L5, L15, L16, L17, L18, L21, L22, L25, L33 and L34, and it possess properties relevant to the function of the 50-S subunit; it has a binding site for deacylated tRNA, with a dissociation constant of 4.5 x 10(-7) M. The complex formed with 5-S RNA immobilized on an affinity column interacts also with 30-S subunits. The 5-S RNA-protein complex is interpreted as a sub-ribosomal domain which includes a considerable fraction of the peptidyl transferase center of the Escherichia coli ribosome.