Yuen-Ling Chan

The primary structure of rat ribosomal proteins P0, P1, and P2 and a proposal for a uniform nomenclature for mammalian and yeast ribosomal proteins

The covalent structures of rat ribosomal proteins P0, P1, and P2 were deduced from the sequences of nucleotides in recombinant cDNAs. P0 contains 316 amino acids and has a molecular weight of 34,178; P1 has 114 residues and a molecular weight of 11,490: and P2 has 115 amino acids and a molecular weight of 11,684. The rat P-proteins have a near identical (16 of 17 residues) sequence of amino acids at their carboxyl termini and are related to analogous proteins in other eukaryotic species. A proposal is made for a uniform nomenclature for rat and yeast ribosomal proteins.

The primary structure of rat ribosomal protein S16.

The amino acid sequence of rat ribosomal protein S16 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2‐terminal amino acid sequence of the protein. S16 contains 145 amino acids (the NH2‐terminal methionine is removed after translation of the mRNA) and has a molecular mass of 16304. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 11–13 copies of the S16 gene. The mRNA for the protein is about 700 nucleotides in length. Rat S16 is homologous to mouse S16 (there are 2 amino acid changes and a residue is deleted) and related to Halobacterium morismortui ribosomal protein S3 and to Escherichia coli S9.

The primary structure of rat ribosomal proteins : the amino acid sequences of L27a and L28 and corrections in the sequences of S4 and S12

The amino acid sequences of rat ribosomal proteins L27a and L28 were deduced from the sequences of nucleotides in recombinant cDNAs and confirmed from the NH2-terminal amino acid sequences of the proteins. L27a contains 147 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 16 476. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 18-22 copies of the L27a gene. The mRNA for the protein is about 600 nucleotides in length. L27a is homologous to mouse L27a (there are 3 amino acid changes) and to yeast L29. Rat ribosomal protein L28 has 136 amino acids (its NH2-terminal methionine is also processed after translation) and has a molecular weight of 15 707. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 9 or 10 copies of the L28 gene. The mRNA for the protein is about 640 nucleotides in length. L28 contains a possible internal duplication of 9 residues. Corrections are recorded in the sequences reported before for rat ribosomal proteins S4 and S12.

The primary structure of rat ribosomal protein S4.

The amino acid sequence of the rat 40 S ribosomal subunit protein S4 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2-terminal amino-acid sequence of the protein. Ribosomal protein S4 has 282 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 31,841. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 7-11 copies of the S4 gene. The mRNA for the protein is about 1 kb in length. Rat S4 is homologous to Saccharomyces cerevisiae YS6. The protein contains a possible internal duplication of 11 residues.

On the conformation of the alpha sarcin stem-loop of 28S rRNA.

A synthetic RNA that is a substrate for the cytotoxin alpha sarcin has been examined by NMR. The molecule in question includes the entire sequence of the so-called alpha sarcin loop from rat 28S rRNA (U4316-C4332), and it is cleaved at the residue that corresponds to G4325, the site of alpha sarcin cleavage in 28S rRNA. The data show that the terminal stem designed into the molecules sequence exists, as expected, and that its loop has a definite structure, which is stable to at least 40 degrees C under ionic conditions compatible with its cleavage by alpha sarcin.

The primary structure of rat ribosomal protein L26

The amino acid sequence of rat ribosomal protein L26 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2‐terminal amino acid sequence of the protein. Rat L26 contains 145 amino acids and has a molecular mass of 17 266 Da. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 8–16 copies of the L26 gene. The mRNA for the protein is about 650 nucleotides in length. Protein L26 has a sequence of 9 residues that may be repeated in three places.

The primary structure of rat ribosomal protein S20.

The amino acid sequence of the rat 40 S ribosomal subunit protein S20 was deduced from the sequence of nucleotides in two recombinant cDNAs. Ribosomal protein S20 has 119 amino acids and has a molecular weight of 13,364. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 16-19 copies of the S20 gene. The mRNA for the protein is about 600 nucleotides in length. Rat S20 is homologous to Xenopus laevis S22 and is related to Mycoplasma capricolum S10 and to Escherichia coli S10. The protein contains a possible internal duplication of seven residues.

The primary structure of rat ribosomal protein S3

The amino acid sequence of rat ribosomal protein S3, which has been reported to form part of the binding site for initiation factors, was deduced from the sequence of nucleotides in a recombinant cDNA. Ribosomal protein S3 contains 243 amino acids and has a molecular weight of 26,643. Rat S3 and Xenopus laevis ribosomal protein S1 are homologous: There are 62 identities in 63 consecutive residues in the carboxyl-terminal amino acid acid sequence of rat S3 and in a partial sequence of Xenopus S1. Hybridization of rat S3 cDNA to digests of nuclear DNA suggests that there are 8-10 copies of the S3 gene. The mRNA for the protein is about 950 nucleotides in length.

The Identification of the Determinants of the Cyclic, Sequential Binding of Elongation Factors Tu and G to the Ribosome

Experiments dedicated to gaining an understanding of the mechanism underlying the orderly, sequential association of elongation factor Tu (EF-Tu) and elongation factor G (EF-G) with the ribosome during protein synthesis were undertaken. The binding of one EF is always followed by the binding of the other, despite the two sharing the same-or a largely overlapping-site and despite the two having isosteric structures. Aminoacyl-tRNA, peptidyl-tRNA, and deacylated-tRNA were bound in various combinations to the A-site, P-site, or E-site of ribosomes, and their effect on conformation in the peptidyl transferase center, the GTPase-associated center, and the sarcin/ricin domain (SRD) was determined. In addition, the effect of the ribosome complexes on sensitivity to the ribotoxins sarcin and pokeweed antiviral protein and on the binding of EF-G*GTP were assessed. The results support the following conclusions: the EF-Tu ternary complex binds to the A-site whenever it is vacant and the P-site has peptidyl-tRNA; and association of the EF-Tu ternary complex is prevented, simply by steric hindrance, when the A-site is occupied by peptidyl-tRNA. On the other hand, the affinity of the ribosome for EF-G*GTP is increased when peptidyl-tRNA is in the A-site, and the increase is the result of a conformational change in the SRD. We propose that peptidyl-tRNA in the A-site is an effector that initiates a series of changes in tertiary interactions between nucleotides in the peptidyl transferase center, the SRD, and the GTPase-associated center of 23S rRNA; and that the signal, transmitted through a transduction pathway, informs the ribosome of the position of peptidyl-tRNA and leads to a conformational change in the SRD that favors binding of EF-G.

The primary structure of rat ribosomal protein S18

The amino acid sequence of the rat 40S ribosomal subunit protein S18 was deduced from the sequence of nucleotides in a recombinant cDNA. S18 has 152 amino acids and has a molecular weight of 17,707. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 10-13 copies of the S18 gene. The mRNA for the protein is about 600 nucleotides in length. Rat S18 is identical to mouse S18 (also referred to as KE3) and is related to Escherichia coli S13 and to other S13-like ribosomal proteins from Bacillus subtilis, from Bacillus stearothermophilus, and from plant mitochondria (Nicotiana tabacum and Zea mays).