Protein synthesis in vitro by Micrococcus luteus

Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis

Escherichia coli ribosomal protein S1 is required for the translation initiation of messenger RNAs, in particular when their Shine-Dalgarno sequence is degenerated. Closely related forms of the protein, composed of the same number of domains (six), are found in all Gram-negative bacteria. More distant proteins, generally formed of fewer domains, have been identified, by sequence similarities, in Gram-positive bacteria and are also termed 'S1 proteins'. However in the absence of functional information, it is generally difficult to ascertain their relationship with Gram-negative S1. In this article, we report the solution structure of the fourth and sixth domains of the E. coli protein S1 and show that it is possible to characterize their beta-barrel by a consensus sequence that allows a precise identification of all domains in Gram-negative and Gram-positive S1 proteins. In addition, we show that it is possible to discriminate between five domain types corresponding to the domains 1, 2, 3, 4-5 and 6 of E. coli S1 on the basis of their sequence. This enabled us to identify the nature of the domains present in Gram-positive proteins and, subsequently, to probe the filiations between all forms of S1.

Unnatural RNA display libraries

Combinatorial peptide and protein libraries have now been developed to accommodate unnatural amino acids in a genetically encoded format via in vitro nonsense and sense suppression. General translation features and specific regioselective and stereoselective properties of the ribosome endow these libraries with a broad chemical diversity. Alternatively, amino acid residues can be chemically derivatized post-translationally to add preferred functionality to the encoded peptide. All of these efforts are advancing combinatorial peptide and protein libraries for enhanced ligands against biological targets of interest.

Exploiting unassigned codons in Micrococcus luteus for tRNA-based amino acid mutagenesis

An alternative to suppression of stop codons for the biosynthetic insertion of non-natural amino acids has been developed. Micrococcus luteus , a Gram-positive bacterium, is incapable of translating at least two codons. One of these unused codons was inserted in a gene to act as a nonsense site. An aminoacylated tRNA was synthesized which was complementary to this codon. The gene containing the missing codon was expressed in vitro in a M.luteus transcription/translation system. Read-through of the missing codon occurred only when the complementary tRNA was included. The results demonstrate that M.luteus can be used for incorporation of amino acids via synthetically prepared aminoacylated tRNAs. The use of a M. luteus translation system provides a method for incorporation of non-natural amino acids which avoids the use of stop codons.

Dual translational start motif evolutionarily conserved in the holin gene of Bacillus subtilis phage phi 29

Holins represent phage encoded lysis functions required for transit of the phage murein hydrolases to the periplasm. The Lambda S, phage 21 S, and P22 13 holin genes contain a dual translational start motif, beginning with Met1-Lys2-X-Met3. In all cases both start codons at the 5' end of the respective holin gene are utilized. The resulting polypeptides have opposing functions, with the longer product acting as an inhibitor of the shorter one. The 131-codon gene 14 of Bacillus subtilis phage phi 29 encodes the holin function, whereas the downstream gene 15 codes for a lysozyme. phi 29 Gene 14 begins with Met1-Lys2-Met3. Here, we present in vitro and in vivo evidence for the expression of two protein 14 species consisting of 129 and 131 amino acids, respectively. These data suggest that the lysis control mechanism based on two holin species, which has been shown to be operational in the temperature Escherichia coli phages Lambda and 21, and in the Salmonella typhimurium phage P22, is evolutionarily conserved in the lytic B. subtilis phage phi 29.

The effect of ribosomal protein S1 from Escherichia coli and Micrococcus luteus on protein synthesis in vitro by E. coli and Bacillus subtilis

We have designed a set of nine plasmids containing the Bacillus pumilis cat gene with one of three Shine-Dalgarno (SD) sequences (weak, strong or stronger) and one of three initiation codons (AUG, GUG or UUG). These constructions have been used to determine the effect of ribosomal protein S1, SD and initiation codon sequences and Escherichia coli ribosomal protein S1 on translation in vitro by E. coli and B. subtilis ribosomes. Translation of these nine constructions was determined with three types of ribosomes: E. coli containing ribosomal protein S1, E. coli depleted of S1, and B. subtilis which is naturally free of S1. E. coli ribosomes were able to translate all nine transcripts with variable efficiencies. B. subtilis and S1-depleted E. coli ribosomes were similar to each other and differed from non-depleted E. coli ribosomes in that they required strong or stronger SD sequences and were unable to translate any of the weak transcripts. Addition of S1 from either E. coli or Micrococcus luteus, a Gram-positive bacterium, enabled S1-depleted E. coli ribosomes to translate mRNAs with weak SD sequences but had no effect on B. subtilis ribosomes. AUG was the preferred initiation codon for all ribosome types; however, B. subtilis ribosomes showed greater tolerance for the non-AUG codons than either type of E. coli ribosome. The presence of a strong or stronger SD sequence increased the efficiency by which E. coli ribosomes could utilize non-AUG codons.(ABSTRACT TRUNCATED AT 250 WORDS)