The primary structure of protein S14 from the small ribosomal subunit of Escherichia coli

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The Contribution of the Zinc-Finger Motif to the Function of Thermus thermophilus Ribosomal Protein S14

In the crystal structure of the 30S ribosomal subunit from Thermus thermophilus, cysteine 24 of ribosomal protein S14 (TthS14) occupies the first position in a CXXC-X12-CXXC motif that coordinates a zinc ion. The structural and functional importance of cysteine 24, which is widely conserved from bacteria to humans, was studied by its replacement with serine and by incorporating the resulting mutant into Escherichia coli ribosomes. The capability of such modified ribosomes in binding tRNA at the P and A-sites was equal to that obtained with ribosomes incorporating wild-type TthS14. In fact, both chimeric ribosomal species exhibited 20% lower tRNA affinity compared with native E. coli ribosomes. In addition, replacement of the native E. coli S14 by wild-type, and particularly by mutant TthS14, resulted in reduced capability of the 30S subunit for association with 50S subunits. Nevertheless, ribosomes from transformed cells sedimented normally and had a full complement of proteins. Unexpectedly, the peptidyl transferase activity in the chimeric ribosomes bearing mutant TthS14 was much lower than that measured in ribosomes incorporating wild-type TthS14. The catalytic center of the ribosome is located within the 50S subunit and, therefore, it is unlikely to be directly affected by changes in the structure of S14. More probably, the perturbing effects of S14 mutation on the catalytic center seem to be propagated by adjacent intersubunit bridges or the P-site tRNA molecule, resulting in weak donor-substrate reactivity. This hypothesis was verified by molecular dynamics simulation analysis.

Structural and functional implications in the eubacterial ribosome as revealed by protein-rRNA and antibiotic contact sites

Contact sites between protein and rRNA in 30S and 50S ribosomal subunits of Escherichia coli and Bacillus stearothermophilus were investigated at the molecular level using UV and 2-iminothiolane as cross-linkers. Thirteen ribosomal proteins (S3, S4, S7, S14, S17, L2, L4, L6, L14, L27, L28, L29, and L36) from these organisms were cross-linked in direct contact with the RNAs, and the peptide stretches as well as amino acids involved were identified. Further, the binding sites of puromycin and spiramycin were established at the peptide level in several proteins that were found to constitute the antibiotic-binding sites. Peptide stretches of puromycin binding were identified from proteins S7, S14, S18, L18, AND L29; those of spiramycin attachment were derived from proteins S12, S14, L17, L18, L27, and L35. Comparison of the RNA-peptide contact sites with the peptides identified for antibiotic binding and with those altered in antibiotic-resistant mutants clearly showed identical peptide areas to be involved and, hence, demonstrated the functional importance of these peptides. Further evidence for a functional implication of ribosomal proteins in the translational process came from complementation experiments in which protein L2 from Halobacterium marismortui was incorporated into the E. coli ribosomes that were active. The incorporated protein was present in 50S subunits and 70S particles, in disomes, and in higher polysomes. These results clearly demonstrate the functional implication of protein L2 in protein biosynthesis. Incorporation studies with a mutant of HmaL2 with a replacement of histidine-229 by glycine completely abolished the functional activity of the ribosome. Accordingly, protein L2 with histidine-229 is a crucial element of the translational machinery.

Studies on S14 protein from Thermus thermophilus possessing zinc finger-like motifs

The amino acid sequence of the ribosomal protein S14 of Thermus thermophilus has been determined both by automated sequence analysis of the intact protein as well as by DNA sequence analysis of the gene. The carboxy-terminal region was verified by both amino acid sequence analysis of the carboxy-terminal peptide produced after Glu-C digestion and by DNA sequence analysis. The protein contains 60 amino acid residues with a calculated molecular weight of 7008. The most extensive homology is observed in the carboxy-terminal regions of all S14 proteins compared. Interestingly, the carboxy-terminal region of most S14 proteins of all species studied so far, form zinc-finger domains in the variety of C2-C2 form.

Complete amino acid sequence of ribosomal protein S14 from Bacillus stearothermophilus and homology studies to other ribosomal proteins

The complete amino acid sequence of protein S14 from the small subunit of Bacillus stearothermophilus was determined by N-terminal sequence analysis and by sequencing of overlapping peptides obtained from enzymatic digestions. Protein S14 consists of 60 amino acid residues with a molecular mass of 7148 Da. It has a high content of basic amino acids and a predicted isoelectric point of 11.46. Protein S14 contains two pairs of cysteines in the carboxyl-terminal region, presumably linked by two sulphur bridges. A comparison between protein S14 of B. stearothermophilus and homologous proteins from other organisms revealed highly conserved carboxyl-termini for this protein in eubacteria, archaebacteria and eukaryotes.

Organization and nucleotide sequence of ten ribosomal protein genes from the region equivalent to the spectinomycin operon in the archaebacterium Halobacterium marismortui

The nucleotide sequence has been determined of a 4700 bp region from a ribosomal protein gene cluster of Halobacterium marismortui (Haloarcula marismortui), which is equivalent to part of the spectinomycin operon of Escherichia coli. The genes were localized on the recombinant lambda EMBL3 clone PP*7, which also contains several other ribosomal protein genes from the DNA region in H. marismortui equivalent to the linked S10/spc operon. The genes analysed encode ten ribosomal proteins, namely HmaL5, HmaS14, HmaS8, HmaL6, HL5, HL24, HmaL18, HmaS5, HmaL30 and HmaL15. The gene organization of the archaebacterial cluster is similar to that in eubacteria but has two additional genes, namely those encoding HL5 and HL24, which were identified as extra proteins that are apparently not present in E. coli. These correspond to the gene products of orfd and orfe in Methanococcus vannielii and also have eukaryotic counterparts.

Organization and structure of the Methanococcus transcriptional unit homologous to the Escherichia coli "spectinomycin operon". Implications for the evolutionary relationship of 70 S and 80 S ribosomes

By means of an immunological approach and a subsequent chromosome-walking strategy a chromosomal region encoding ribosomal proteins in the archaebacterium Methanococcus vannielii was cloned. The determination of the nucleotide sequence of the 7.8 x 10(3) base DNA fragment revealed the existence of 14 putative ribosomal protein genes and two unidentified open reading frames. They are organized in a transcriptional unit that is very similar to the Escherichia coli "spectinomycin operon" in respect of both gene composition and gene order. The Methanococcus transcriptional unit contains, in addition to those genes whose products have a homologue in the E. coli operon, three genes whose products share sequence similarity with eukaryotic 80 S but not with eubacterial ribosomal proteins. The Methanococcus ribosomal proteins almost exclusively exhibit a higher sequence similarity to eukaryotic 80 S ribosomal proteins than to those of eubacteria and many of them have a size intermediate between those of their eukaryotic and eubacterial homologues. These results are discussed in terms of a hypothesis that implies that the recent eubacterial ribosome developed by a "minimization" process from a more complex organelle and that the archaebacterial ribosome has maintained features of this ancestor.

The complete amino acid sequence of ribosomal protein S18 from the moderate thermophile Bacillus stearothermophilus

The amino acid sequence of ribosomal protein S18 from Bacillus stearothermophilus has been completely determined by automated sequence analysis of the intact protein as well as of peptides derived from digestion with Staphylococcus aureus protease at pH 4.0 and cleavage with cyanogen bromide. The carboxy-terminal region was verified by both amino acid analyses of chymotryptic peptides and by mass spectrometry from the terminal region. The protein contains 77 amino acid residues and has an Mr of 8838. Comparison of this sequence with the sequences of the S18 proteins from tobacco and liverwort chloroplasts and E. coli shows a relatively high similarity, ranging from 42 to 55% identical residues with the B. stearothermophilus S18 protein. The regions of homology common to all four proteins consist of several positively charged sections spanning the entire length of the protein.

On the statistical significance of homologous structures among the Escherichia coli ribosomal proteins

Completion of the sequence determination of all 52 Escherichia coli ribosomal proteins enabled a final comparison of their sequences. Similarities in amino acid compositions were compared to the relatedness of the sequences, which was analyzed statistically with the aid of the computer programs RELATE and ALIGN. Among the examined 52 X 52 possible protein pairs at least 40 pairs were found that can be regarded as distantly related (showing segment comparison score values slightly above 3.0 S.D. units). These protein pairs were further examined with the programs ALIGN and SEEK to locate homologous sequence stretches. In no case were two complete homologous sequences found (with the exception of the known identical pairs L7/L12 and S20/L26). However, short homologous sequence regions were observed. Beside those protein pairs that show significant although distant relatedness, other pairs were slightly below the threshold value of 3.0 S.D. units. Those pairs observed to be distantly related consisted either of two proteins from the same subunit or of one protein from each of the different subunits. A further analysis of these pairs revealed a correlation between their relatedness and their time of incorporation into the ribosome during assembly.