Role of ribosomal protein S1 in portein synthesis: effects of its addition to Bacillus stearothermophilus cell-free system

Structural basis for the interaction of protein S1 with the Escherichia coli ribosome

In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to its functional importance, S1 is still lacking from the high-resolution structures available for Escherichia coli and Thermus thermophilus ribosomes and thus the molecular mechanism governing the S1-ribosome interaction has still remained elusive. Here, we present the structure of the N-terminal S1 domain D1 when bound to the ribosome at atomic resolution by using a combination of NMR, X-ray crystallography and cryo-electron microscopy. Together with biochemical assays, the structure reveals that S1 is anchored to the ribosome primarily via a stabilizing π-stacking interaction within the short but conserved N-terminal segment that is flexibly connected to domain D1. This interaction is further stabilized by salt bridges involving the zinc binding pocket of protein S2. Overall, this work provides one hitherto enigmatic piece in the 'ribosome puzzle', namely the detailed molecular insight into the topology of the S1-ribosome interface. Moreover, our data suggest novel mechanisms that have the potential to modulate protein synthesis in response to environmental cues by changing the affinity of S1 for the ribosome.

Molecular and functional properties of protein SS1 from small ribosomal subunits of Streptomyces aureofaciens

Small ribosomal subunits of gram-positive cells of Streptomyces aureofaciens contain an acidic protein designated SS1. Purified protein SS1 has the same mobility in sodium dodecyl sulfate/polyacrylamide gel as ribosomal protein S1 of Escherichia coli (apparent Mr 68 000). Protein SS1 was dissected under mild conditions with trypsin and generated fragments were compared with well-characterized fragments of protein S1. The protein SS1 contains a structure homologous with the C-terminal fragment of protein S1. The affinity of protein SS1 to poly(U) is virtually identical with that of E. coli protein S1. In contrast to protein S1, the addition of SS1 to partially S1-depleted ribosomes of E. coli had no stimulatory effect on poly(U)-directed synthesis of polyphenylalanine. At molar excess of SS1 over ribosomes, the protein had comparable inhibitory effect on polypeptide synthesis as had S1 of E. coli. Ribosomes of S. aureofaciens required about one order of magnitude higher concentration of poly(U) for maximum synthetic activity than did ribosomes of E. coli. The addition of proteins SS1 or S1 to ribosomes of S. aureofaciens had no stimulatory effect on translation of poly(U). Our data indicate that the high-molecular-mass acidic protein SS1 of small ribosomal subunits of S. aureofaciens exhibits only a part of the functional properties of E. coli protein S1.

The DNA sequence of the gene rpsA of Escherichia coli coding for ribosomal protein S1

The DNA sequence of the gene rpsA as well as of its neighboring regions has been determined using the dideoxyribonucleotide method. It was found that there is an "open-reading-frame" of 350 bp which precedes the gene rpsA. Furthermore, an extensive internal repeats of nucleotide sequence have been found in this gene.

Primary structure of Escherichia coli ribosomal protein S1 and features of its functional domains

The complete covalent structure of ribosomal protein S1 of Escherichia coli has been determined and predictions made of its secondary structure. Protein S1 (E. coli MRE 600) is a single-chain, acidic protein with 557 amino acid residues of the composition Asp43, Asn23, Thr25, Ser25, Glu60, Gln14, Pro10, Gly48, Ala48, Val67, Met6, Ile30, Leu45, Tyr6, Phe17, His8, Lys43, Arg30, Trp7, Cys2 and an Mr of 61159. The two -SH groups of S1 are located in the central region of the chain at positions 292 and 349, the latter being the reactive group whose modification results in the reported loss of the nucleic-acid-unfolding ability of S1. The central region also contains the majority of the tryptophan, histidine and methionine residues of S1 and is predicted to have a secondary structure dominated by beta-sheets and turns. A direct proof for the location of the nucleic-acid-binding domain of S1 in the central region has recently been obtained [Subramanian et al. (1981) Eur. J. Biochem. 119, 245-249]. The N-terminal region of S1, which contains the ribosome-binding domain has a relatively high predicted alpha-helix content and no preponderance of basic amino acids. The facile trypsin-sensitive site in S1 is located at Arg-171, approximately at the border between the N-terminal and central regions. The acidic and basic amino acids of S1 (32.8% of all residues) are distributed throughout the chain, often in small clusters of between two and six residues. The amino acid sequence of S1 contains three 24-residue stretches with strong internal homology. Two of the stretches are located in the central, RNA-binding region, suggesting a possible role in the RNA-binding and helix-destabilizing functions of S1. A fragment of Mr 10(4) from the central region of S1 gives an anomalously high apparent Mr by dodecylsulfate gel electrophoresis, indicating a stable structural element therein and accounting for the apparent high Mr of S1 as determined by gel electrophoresis.

Initiation factor-independent translation of mRNAs from Gram-positive bacteria

Initiation factor-independent translation of mRNA derived from bacillus phage phi29 DNA occurs with translation systems derived from Bacillus subtilis or Escherichia coli. This is in sharp contrast to the strict dependence on ribosome salt wash fraction of E. coli ribosomes for the translation of T7 and other mRNAs derived from Gram-negative organisms.

Role of 16-S RNA in ribosome messenger recognition

The deoxyoctanuclotide (5'-3')d(A-A-G-G-A-G-G-T), which is complementary to the 3' end of 16-S RNA, inhibits the formation of the complex between the 30-S subunit and MS2 RNA described in the preceding paper. If the complex is preformed, the octanucleotide cannot prevent entry of the complex into the ribosome cycle upon supplementation with the components for protein synthesis. The subunit . MS2-RNA complex is unable to bind the octanucleotide. It is concluded that in the subunit . phage-RNA initiation precursor the 16-S terminus is base-paired with a complementary MS2 RNA sequence. Edeine, aurintricarboxylic acid and antibodies against ribosomal protein S1 prevent the association of phage RNA with 30-S subunits. These compounds do not, however, inhibit the binding of (5'-3')d(A-A-G-G-A-G-G-T) to 3-S subunits. It is concluded that formation of the complex between MS2 RNA and 30-S subunits does not depend solely on the Shine and Dalgarno base-paring reaction.

Metabolic stability of the two forms of initiation factor IF-3 in Escherichia coli during the growth cycle

Possible alteration in the ratio of the long and short forms of initiation factor IF-3 (FEBS Lett. 79, 264-275, 1977) during the growth cycle of Escherichia coli was examined. The ratio was found to remain unchanged between the exponential and stationary growth phases. Contrary to an earlier report (Eur. J. Biochem. 29, 319-325, 1972), the total amount of IF-3 relative to the ribosome content in stationary phase cells was essentially the same as in midlogarithmic phase cells. The activity of IF-3, assayed after its separation from other initiation factors by chromatography, was also the same in extracts from midlogarithmic and stationary phase cells. The data show that in Escherichia coli the ratio of IF-3/ribosome is maintained constant. The ribosomes themselves have been shown to retain virtually full activity in vitro during this transition indicating that growth-cycle-dependent biochemical modifications of the ribosome do not affect its protein synthetic capacity per se.

Identification of a temperature-sensitive asparaginyl-transfer ribonucleic acid synthetase mutant of Escherichia coli

A temperature-sensitive mutant of Escherichia coli K-12 isolated previously (H. Ohsawa and B. Maruo, J. Bacteriol. 127:1157-1166, 1976) was found to have an alteration in asparaginyl-transfer ribonucleic acid synthetase. This alteration can account for the temperature-sensitive phenotype of the mutant. No evidence was obtained to support the previous suggestion that ribosomal protein S1 is altered in this mutant. Combined with the previous genetic studies, we conclude that the newly defined genetic locus, asnS, for the asparaginyl-transfer ribonucleic acid synthetase maps near pyrD at 21 min on the E. coli chromosome.

Restoration by ribosomal protein S1 of the defective translation in a temperature-sensitive mutant of Escherichia coli K-12: characterization and genetic studies

A temperature-sensitive mutant of Escherichia coli was isolated that had a temperature-sensitive defect in ribosomal-wash protein(s) required for translation in vitro of E. coli endogenous messenger ribonucleic acid. It was found that 30S ribosomal protein S1 rescued the defect in the ribosomal-wash protein(s) of the mutant and that the complete restoration to the wild-type level was attained when 1 mol of protein S1 was added to 1 mol of 70S ribosome. The mutation, tss, causing such a defect was mapped at 21 min and was closely linked to the pyrD locus, the region of which was entirely different from that of the other genes coding for the many ribosomal proteins of E. coli. These results indicate that the gene specified by this mutation is involved in the function of the 30S ribosomal protein S1.

The specific role of ribosomal protein S1 in the recognition of native phage RNA

The previously reported requirement of ribosomal protein S1 for translation of phage RNA is now shown to be related to the involvement of the protein in initiation complex formation. The structure of the messenger RNA appears to be uniquely related to S1 function, since translation and initiation and midly unfolded phage RNA (by modification with formaldehyde) are independent of S1. It is proposed that S1 functions in conjunction with initiation factor IF-3 by recognizing and unfolding elements of the tertiary structure of phage RNA. A model is suggested for S1 function in both initiation of protein synthesis and initiation of phage RNA replication.

Lack of ribosomal protein S1 in Bacillus stearothermophilus

The 30S ribosomal subunit of Bacillus stearothermophilus migrated as a single band when electrophoresed on agarose-acrylamide composite gels. The addition of the ribosomal protein S1 purified from Escherichia coli resulted in the appearance of an additional band migrating more slowly; 14C-labeled S1 of E. coli was shown to be associated only with this form. Antibody against E. coli protein S1 did not crossreact with either the total 30S ribosomal proteins or the postribosomal supernatant from B. stearothermophilus. These results indicate that B. stearothermophilus lacks a protein equivalent to E. coli S1 and may explain our previous finding [Eur. J. Biochem. 56, 15-22 (1975) that E. coli S1 greatly stimulated the translation by B. stearothermophilus ribosomes of f2 phage RNA.