A new ribosomal protein locus in Escherichia coli: the gene for protein S6 maps at 97 min

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.

Characterization of the gene rimK responsible for the addition of glutamic acid residues to the C-terminus of ribosomal protein S6 in Escherichia coli K12

Ribosomal protein S6 of wild-type strains of Escherichia coli contains up to six glutamic acid residues at its C-terminus. The first two residues are encoded by the structural gene for this protein (rpsF) and the rest are added post-translationally. Mutants deficient in this modification were isolated and characterized genetically and biochemically. The S6 protein in these mutants appeared to contain only two glutamic acid residues at the C-terminus as expected. The mutated gene was termed rimK and was mapped at 18.7 min between cmlA and aroA. The rimK gene was cloned into a cosmid vector and its nucleotide sequence determined. Analysis of the transcriptional and translational products of this gene indicates that it encodes a protein with an Mr of 31.5 kDa and that it forms an operon with a gene encoding a 24 kDa protein. An rpsF mutant containing a Glu to Lys replacement in the second residue from the C-terminus of protein S6 was isolated. The S6 protein of this mutant was apparently inaccessible to the RimK modification system. This indicates that the RimK modification system requires the wild-type amino acid sequence at least in the C-terminal region of ribosomal protein S6.

Gene rpmF for ribosomal protein L32 and gene rimJ for a ribosomal protein acetylating enzyme are located near pyrC (23.4 min) in Escherichia coli

An Escherichia coli mutant harbouring altered ribosomal protein L32 has been isolated and genetically characterized. The mutation leading to this alteration (rpmF) and the temperature-sensitive mutation (ts-1517) present in the same strain were found to map near pyrC (23.4 min), being cotransducible not only with pyrC but also with fabD, flaT and purB in P1 phage mediated transductions. Furthermore, we found that the gene rimJ, which encodes an enzyme that acetylates the N-terminal alanine of protein S5 and the temperature-sensitive mutation, ts-386, present in the rimJ mutant strain (Cumberlidge and Isono 1979) also mapped in this region. Thus, the order of genes is deduced to be: ts-386-pyrC-ts-1517-rimJ-flaT-fabD-rpmF-purB+ ++.

DNA sequence and complementation analysis of a mutation in the rplX gene from Escherichia coli leading to loss of ribosomal protein L24

A mutation in Escherichia coli leads to the loss of ribosomal protein L24, severely impaired growth, and a temperature-sensitive phenotype. The mutation was shown to be in rplX, the gene for protein L24, and was due to the alteration of an AAA codon to a TAA stop codon at position 61 in rplX that resulted in a 20-amino acid peptide instead of the 104 amino acids of wild-type L24 protein. rplX genes from three temperature-resistant and fast growing pseudorevertants of the mutant were cloned and sequenced. They were found to have different base substitutions in the TAA codon, resulting in the reappearance of a full-sized protein L24 moiety. Complementation of the slow growth in trans could be achieved with several plasmids containing at least the spc promoter and intact L14 and L24 genes. Plasmids containing genes distal to rplX could further stimulate growth, and the wild type arose when the entire spc operon and the alpha operon were present. In all cases, protein L24 was expressed by the plasmids. Therefore, slow growth could be explained by polarity extending to the alpha operon. However, temperature sensitivity could not be complemented by any of the plasmids in trans, although we found that this phenotype was caused by the mutation in the rplX gene.

Ribosomal protein modification in Escherichia coli. III. Studies of mutants lacking an acetylase activity specific for protein L12

Among mutants of E. coli selected for temperature-sensitive growth, four were found to possess alterations in ribosomal proteins L7/L12. Of these, three apparently lack protein L7, the acetylated form of protein L12. Genetic analyses have revealed that the mutation responsible for this alteration maps at a locus around 34 min of the current E. coli genetic map, which is clearly different from the location for the structural gene for protein L7/L12 which is situated at 89 min. Hence, the gene affected in these mutants was termed rimL. Tryptic and thermolysin fingerprints of the protein L12 purified from the rimL mutants showed a profile indistinguishable from that of wild-type protein. It was found that the assayed in vitro, in the high-speed supernatant prepared from mutant cells. These results indicated that the three mutants contain mutations in the gene rimL codes for an acetylating enzyme specific for ribosomal protein L12.

Isolation and characterization of specialized transducing lambda phages carrying ribosomal protein genes of Escherichia coli

Specialized transducing lambda phages have been isolated which carry the regions of the Escherichia coli chromosome containing the gene or gene-clusters for ribosomal proteins (r-proteins) S1, S6-S18-L9, S16-L19, and L28-L33. To investigate whether these phages also carry the genes for r-proteins S9, L13, L20, L31 and L34 whose gene locations are not known, cells irradiated with UV light were infected with these phages and the r-proteins synthesized were analyzed by two-dimensional gel electrophoresis. However, no synthesis of these r-proteins was stimulated, indicating that their genes are not located in the neighborhood of any of the above-mentioned genes or gene clusters. It was found that proteins S6 and S18 synthesized in the cells irradiated with UV light were not modified under these conditions in which no concomitant ribosome assembly took place.

Genetic fine structure of the pyrE region containing the genes for ribosomal proteins L28 and L33 in Escherichia coli

Temperature-sensitive mutants harbouring alterations in ribosomal proteins L28 and L33 have been isolated and used in mapping the genes coding for the two proteins. It was found that they mapped very close to each other and near pyrE at 80.7 min on the E. coli genetic map. The genes affected by the mutations have been concluded to be the structural genes for proteins L28 (rpmB) and L33 (rpmG) by constructing merodiploids heterozygous for pyrE and for the two ribosomal proteins. Various transduction studies with P1kc phages indicate the gene order in this region to be (rpmB, rpmG)-pyrE-spoT-gltC.

Ribosomal protein modification in Escherichia coli. II. Studies of a mutant lacking the N-terminal acetylation of protein S18

A mutant of Escherichia coli K12 has been isolated which shows an alteration in the ribosomal protein S18. Genetic analyses have revealed that the mutation causing this alteration maps at 99.3 min of the E. coli genetic map, between dnaC and deo. This indicated that the mutation has occurred in a gene different from the structural gene for this protein which has been located at 94 min. From the N-terminal amino acid sequence analysis it is concluded that the mutation has resulted in loss of the N-terminal acetyl group of this protein. The gene which is affected in this mutant is termed rimI that most likely specifies an enzyme acetylating the N-terminal alanine of protein S18. The mutation does not affect the acetylation of two other ribosomal proteins, S5 and L12, both of which are known to be acetylated in wild-type E. coli K12.

The gene for ribosomal protein L25 (rplY) maps at 47.3 min near nalA in Escherichia coli K-12

A temperature sensitive mutant, termed JE1306, derived from Escherichia coli strain PA3092 was found to have an alteration in the ribosomal protein L25. Crosses with various Hfr strains and transductions with P1 kc phage have revealed that the mutation maps at 47.3 min between nalA and fpk, in a region where no ribosomal protein gene has so far been located. The gene affected by this mutation is most probably the structural gene for protein L25 (rplY), because a strain heteromerozygous for the region shows both wild type and mutant forms of protein L25.

Post-translational modification of Escherichia coli ribosomal protein S6

Escherichia coli has multiple forms of ribosomal protein S6, differing in number of glutamyl resideus at the C-terminal end. Three forms are revealed when crude cell extracts are fractionated by a two-dimensional gel electrophoresis technique. Pulse-chase experiments show that the shortest and most alkaline form of S6 is the first to appear. In about one doubling time this form reaches equilibrium with the two other forms of S6, implicating the existence of an enzyme, which adds glutamic acid residues to S6. We show that the relative levels of these three S6 forms are not affected by the growth rate of the culture.

Genes encoding ribosomal proteins S16 and L19 form a gene cluster at 56.4 min in Escherichia coli

A mutant of Escherichia coli which was isolated for temperature-sensitive growth was found to harbour a structural alterations in protein S16 (Isolo et al., 1978). The mutation was localized by matings with various Hfr strains and by Plkc-mediated transduction. The results showed that it mapped very close to the gene coding for L19 protein which has been placed at 56.4 min (Kitakawa and Isono, 1977), indicating that it most likely forms a new ribosomal protein-gene cluster.

Mapping by interspecies transformation experiments of several ribosomal protein genes near the replication origin of Bacillus subtilis chromosome

Bacillus subtilis 168 was transformed with DNAs from B. amyloliquefaciens K or B. licheniformis IAM 11054. These two species show a considerable difference in ribosomal proteins from B. subtilis. Analyses of the transformants indicated that the genes for 16 proteins, S3, S5, S8, S12, S17, S19, BL1, BL5, BL6, BL8, BL14, BL16, BL17, BL22, BL23 and BL25 are located in the cysA-str-spc region on B. subtilis chromosome. The genes for 10 proteins, S4, S6, S13, S16, S20, BL15, BL18, BL20, BL24 and BL28 could not be found in this region in the present experiments.

Genetic studies of the ribosomal proteins in Escherichia coli. XI. Mapping of the genes for L21, L27, S15 and S21 by using hybrid bacteria and over-production of these proteins in the merodiploid strains

E. coli episomes which cover argG region were transferred to S. marcescens and ribosomal proteins (r-proteins) from these hybrid strains were analyzed by two-dimensional (2D) polyacrylamide gel electrophoresis. Three E. coli r-proteins L21, L27 and S15 could be detected in the ribosomes from the hybrid strains. The relative rate of synthesis of the individual r-proteins were determined for E. coli merodiploid strains harboring these episomes. Over-production of three r-proteins L21, L27 and S21 (but not S15) was observed in the merodiploid strains.