N-formyl-methionyl-sRNA and its relation to protein biosynthesis

In commemoration of completion of the genetic code, and in memory of Prof. Brian Clark

While we celebrate the 20th anniversary of the complete decoding of the genetic code, we should also commemorate Prof. Brian Clark for his remarkable contributions to this historic landmark in life sciences, as well as to the global collaboration on sciences. As an international citizen and a great scientist, Prof. Brian Clark will live for ever in the hearts of all his friends and students.

Partial purification and characterization of a formylmethionine deformylase from rat small intestine

A formylmethionine deformylase from rat small-intestinal mucosa has been isolated, characterized and partially purified. The enzyme catalyses the release of equimolar amounts of formate and the free amino acid. The deformylase was active against formylmethionine (Km 7.1 mM) and formylnorleucine, but showed reduced activity against formyl-leucine. It was inactive against a range of other polar and nonpolar formyl-amino acids and against formyl di- and tri-peptides. The Mr of the native enzyme was between 45,000 and 66,000, as determined by h.p.l.c. gel permeation. Further purification of the enzyme either by h.p.l.c. ion-exchange chromatography and concanavalin A-Sepharose or by isoelectric focusing yielded a preparation with one predominant band of Mr 50,000 on SDS/polyacrylamide-gel electrophoresis. Bacteria in the intestine present the host with substantial amounts of formylmethionine (fMet) from proteinase and carboxypeptidase digestion of bacterial formyl-peptides in the intestinal lumen. fMet (0.01-1.0 mM) inhibited translation of a test RNA from brome mosaic virus in vitro, indicating that it could have adverse effects on cellular metabolism. Gut epithelial fMet deformylase may be required for deformylation of this exogenous (bacterial) and also endogenous (mitochondrial) fMet.

The dihydrolipoyltransacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii. Molecular cloning and sequence analysis

The gene encoding the dihydrolipoyltransacetylase component (E2) of the pyruvate dehydrogenase complex from Azotobacter vinelandii has been cloned in Escherichia coli. A plasmid containing a 2.8-kbp insert of A. vinelandii chromosomal DNA was obtained and its nucleotide sequence determined. The gene comprises 1911 base pairs, 637 codons excluding the initiation codon GUG and stop codon UGA. It is preceded by the gene encoding the pyruvate dehydrogenase component (E1) of pyruvate dehydrogenase complex and by an intercistronic region of 11 base pairs containing a good ribosome binding site. The gene is followed downstream by a strong terminating sequence. The relative molecular mass (64913), amino acid composition and N-terminal sequence are in good agreement with information obtained from studies on the purified enzyme. Approximately the first half of the gene codes for the lipoyl domain. Three very homologous sequences are present, which are translated in three almost identical units, alternated with non-homologous regions which are very rich in alanyl and prolyl residues. The N-terminus of the catalytic domain is sited at residue 381. Between the lipoyl domain and the catalytic domain, a region of about 50 residues is found containing many charged amino acid residues. This region is characterized as a hinge region and is involved in the binding of the pyruvate dehydrogenase and lipoamide dehydrogenase components. The homology with the dihydrolipoyltransacetylase from E. coli is high: 50% amino acid residues are identical.

Evidence for the absence of the G-T-psi-C sequence from two mammalian initiator transfer RNAs

Analyses were performed on the purified initiator tRNA from rabbit liver to test for the presence of Psip and Tp in this molecule. Neither of these nucleotides could be detected after hydrolysis by piperidine, NaOH, or T2 RNase. Similarly digestion with venom phosphodiesterase plus phosphatase failed to release any pseudourdine or ribothymidine. Identical results were obtained with the initiator tRNA from sheep mammary gland. The absence of these nucleosides was confirmed by pancreatic and T1 RNase digestion of the rabbit-liver initiator tRNA. The classical G-T-Psi-C sequence was not detected in this molecule. An A-U-C-G sequence has been identified; it may possibly replace the G-T-Psi-C sequence.

N-formylseryl-transfer RNA

The reactions between serine and transfer RNA from baker's yeast and from Escherichia coli have been investigated. Results obtained from in vitro, in vivo, and chemical syntheses and from electrophoretic, chromatographic, and radioautographic analyses demonstrate that N-formylseryl-transfer RNA is formed in these systems.