Ribosomal RNA and peptidyl-tRNA hydrolase: a peptide chain termination model for lambda bar RNA inhibition

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Regulation of protein synthesis by minigene expression

Peptidyl-tRNA hydrolase (Pth), an enzyme essential for Escherichia coli viability, scavenges peptidyl-tRNA released during abortive polypeptide chain elongation. Bacterial strains of E coli partially defective in Pth activity are unable to maintain bacteriophage lambda growth. Phage mutations that overcome the bacterial defect have been located to several regions in the lambda genome named bar. Plasmid constructs expressing just the bar region are toxic and cause a general arrest of protein synthesis in Pth-defective cells. Inspection of the nucleotide sequence from two bar regions reveals the short coding sequence AUG AUA Stop, spaced by an AT-rich segment from a Shine Dalgarno-like sequence (S-D). These sequences have been named minigenes. Base changes altering the putative S-D, the two sense codons, or the stop codon have been found to reduce Bar-toxicity. Transcripts containing bar function as mRNA. Upon expression in pth mutants, wild-type (bar+) transcripts are found associated with ribosomes. In addition, bar+ RNA forms ternary complexes with the 30S ribosomal subunit and the initiator tRNA and can be released upon run-off translation in the same way as an authentic mRNA. A cell free system for protein synthesis reproduces the in vivo effects: bar+ expression inhibits protein synthesis, bar+ RNA sequences are associated with ribosomes in the inhibited extracts, addition of purified Pth restores synthesis, and excess of tRNA(Lys), specific for the last sense codon in a mutant toxic minigene, prevents protein synthesis inhibition. Also, bar expression promotes association of methionine with ribosomes possibly in a translation complex. These results are consistent with a model proposing tRNA starvation to explain the behaviour of a pth mutant, thermosensitive for protein synthesis.

Inhibition of Escherichia coli protein synthesis by abortive translation of phage lambda minigenes

Escherichia coli mutants defective in peptidyl-tRNA hydrolase activity are unable to maintain bacteriophage lambda vegetative growth. Phage mutants, named bar, overcome the host limitation to support viral growth. Multicopy expression of lambda wild-type bar regions is deleterious to hydrolase-defective cells because it provokes arrest of protein synthesis. We noticed that the bar regions include minigenes whose transcripts would contain a Shine-Dalgarno-like sequence appropriately spaced for translation from a two codon open reading frame. To investigate the mechanism of bar inhibition, we asked if transcripts of the barI region function as mRNAs in their ribosomal interactions. We found that bar-containing RNA associates with ribosomes, forms ternary initiation complexes, yields a toeprint signal, and can be removed from ribosomes by run-off translation, as authentic mRNA. Since bar-containing RNA has the properties of a messenger, we propose that its translation leads to drop-off and accumulation of peptidyl-tRNA in pth-defective cells. Starvation of the tRNA(s) sequestered in pepidyl-tRNA(s) eventually causes inhibition of protein synthesis.

Molecular characterization of a genomic region in a Lactococcus bacteriophage that is involved in its sensitivity to the phage defense mechanism AbiA

A spontaneous mutant of the lactococcal phage phi31 that is insensitive to the phage defense mechanism AbiA was characterized in an effort to identify the phage factor(s) involved in sensitivity of phi31 to AbiA. A point mutation was localized in the genome of the AbiA-insensitive phage (phi31A) by heteroduplex analysis of a 9-kb region. The mutation (G to T) was within a 738-bp open reading frame (ORF245) and resulted in an arginine-to-leucine change in the predicted amino acid sequence of the protein. The mutant phi31A-ORF245 reduced the sensitivity of phi31 to AbiA when present in trans, indicating that the mutation in ORF245 is responsible for the AbiA insensitivity of phi31A. Transcription of ORF245 occurs early in the phage infection cycles of phi31 and phi31A and is unaffected by AbiA. Expansion of the phi31 sequence revealed ORF169 (immediately upstream of ORF245) and ORF71 (which ends 84 bp upstream of ORF169). Two inverted repeats lie within the 84-bp region between ORF71 and ORF169. Sequence analysis of an independently isolated AbiA-insensitive phage, phi31B, identified a mutation (G to A) in one of the inverted repeats. A 118-bp fragment from phi31, encompassing the 84-bp region between ORF71 and ORF169, eliminates AbiA activity against phi31 when present in trans, establishing a relationship between AbiA and this fragment. The study of this region of phage phi31 has identified an open reading frame (ORF245) and a 118-bp DNA fragment that interact with AbiA and are likely to be involved in the sensitivity of this phage to AbiA.

Incomplete entry of bacteriophage T7 DNA into F plasmid-containing Escherichia coli

The penetration of bacteriophage T7 DNA into F plasmid-containing Escherichia coli cells was determined by measuring Dam methylation of the entering genome. T7 strains that cannot productively infect F-containing cells fail to completely translocate their DNA into the cell before the infection aborts. The entry of the first 44% of the genome occurs normally in an F-containing cell, but the entry of the remainder is aberrant. Bypassing the normal mode of entry of the T7 genome by transfecting naked DNA into competent cells fails to suppress F exclusion of phage development. However, overexpression of various nontoxic T7 1.2 alleles from a high-copy-number plasmid or expression of T3 1.2 from a T7 genome allows phage growth in the presence of F.