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

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

Background

Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects.

Results

We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N α acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal N α acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM.

Conclusions

Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3676-8) contains supplementary material, which is available to authorized users.

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.

The nucleotide sequence of an Escherichia coli chromosomal region containing the genes for ribosomal proteins S6, S18, L9 and an open reading frame

The DNA sequence of a cluster of genes for ribosomal proteins S6 (rpsF), S18 (rpsR) and L9 (rplI), and of their surrounding regions was determined. The order of the genes was established as promoter-rpsF-rpsR-rplI. There is a 315 bp open reading frame that begins seven nucleotides after the end of rpsF and ends immediately before rpsR. Based on the data of insertional mutagenesis experiments with transposon gamma delta, we concluded that these genes probably form an operon. The amino acid sequence deduced from the nucleotide sequence of the genes agrees completely with the published amino acid sequence data for protein S6, but there are discrepancies in the case of proteins S18 and L9. The C-terminus of protein S6 was deduced to end with two Glu residues, suggesting that the other Glu residues previously found in this protein are added post-translationally as has been predicted (Reeh and Pedersen 1979). A possible secondary structure in the leader sequence as well as a possible transcriptional terminator after rplI were noticed in the sequence.

Suppressors of the secY24 mutation: identification and characterization of additional ssy genes in Escherichia coli

We previously reported (Shiba et al., J. Bacteriol. 160:696-701, 1984) the isolation and characterization of the mutation (ssy) that suppresses the protein export defect due to the secY24(Ts) mutation and causes cold-sensitive growth of Escherichia coli. This report describes more systematic isolation of ssy mutations. Among temperature-resistant revertants of the secY24 mutant, 65 mutants were found to be cold sensitive. These cold-sensitive mutations have been classified by genetic mapping. Twenty-two mutations fell into the ssyA class previously described. The remaining mutations were located at five new loci: ssyB at 9.5 min between tsx and lon; ssyD around 3 min; ssyE at 72.5 min near secY; ssyF at 20.5 min within rpsA; and ssyG at 69.0 min near argG. Two predominant classes, ssyA and ssyB, are probably affected in protein synthesis at the elongation step, whereas the ssyF mutant contained an altered form of ribosomal protein S1 (the gene product of rpsA). These cold-sensitive ssy mutations which suppress secY24 may define genes whose function is somehow involved in the secY-dependent protein secretion mechanism. However, the existence of multiple suppressor loci makes it unlikely that all of these genes specify additional components of the export machinery. A delicate balance may exist between the systems for synthesizing and exporting proteins.

The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways

Sub-cloning experiments aimed at precisely locating the E. coli aroA gene, which encodes the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate synthase, showed that in certain constructions, which remain capable of complementing an auxotrophic aroA mutation, expression of aroA is reduced. DNA sequence analysis revealed that a sequence approx. 1200 base pairs (bp) upstream of aroA is necessary for its expression. An open reading frame was identified in this region which encodes a protein of 362 amino acids with a calculated Mr of 39,834 and which ends 70 bp before the start of the aroA coding sequence. This gene has been identified as serC, the structural gene for 3-phosphoserine aminotransferase, an enzyme of the serine biosynthetic pathway. Both genes are expressed as a polycistronic message which is transcribed from a promotor located 58 bp upstream of serC. Evidence is presented which confirms that the aroA and serC genes constitute an operon which has the novel feature of encoding enzymes from two different amino acid biosynthetic pathways.

Comparative studies on the structural gene for the ribosomal protein S1 in ten bacterial species

By applying the Southern blot technique we compared the structural gene rpsA for ribosomal protein S1 and its preceding sequence from Escherichia coli with nine other bacterial species. We found high homology among the structural genes of E. coli and other gram-negative but not gram-positive bacteria. In contrast, the regulatory sequence preceding the structural gene was not highly conserved among the organisms studied. Cloning and DNA sequence analysis of a 1.2 kb fragment coding for most of the structural gene for S1 from Providencia localized some strongly conserved parts of the DNA sequence, despite the fact that the codon usage showed considerable divergence from that of E. coli.

Cloning and nucleotide sequencing of the genes for ribosomal proteins S9 (rpsI) and L13 (rplM) of Escherichia coli

The genes for the ribosomal proteins S9 (rpsI) and L13 (rplM) of Escherichia coli have been cloned into a lambda phage vector termed L47.1. The two genes were identified by infecting UV-light irradiated cells with the resultant phages and analyzing the protein products by two-dimensional gel electrophoresis. Suitable DNA fragments of the isolate were cloned subsequently into M13 phage vectors and their nucleotide sequence was determined by the dideoxy method. It is evident that the two genes form a transcriptional unit, the rplM gene being promoter-proximal. There is a typical signal sequence for transcriptional termination after the rpsI gene. The codon usage pattern in the two genes is similar to other ribosomal protein genes of E. coli.

Transcriptional organization of the rpsA operon of Escherichia coli

Three strong and two minor rpsA promoters were found by nuclease S1 mapping, promoter cloning and in vitro transcription. The longest transcript encodes a protein, located upstream from rpsA with a molecular weight of 25,000. The identity of this protein remains to be established. The other rpsA promoters are located within the gene for this 25 K protein. The rpsA leader region including the sequence of the 25 K protein and its promoter was DNA sequenced.

The purification of 5-enolpyruvylshikimate 3-phosphate synthase from an overproducing strain of Escherichia coli

The Escherichia coli aroA gene which codes for the enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSP synthase) has been cloned from the lambda-transducing bacteriophage lambda pserC. The gene has been located on a 4.7 kilobase pair PstI DNA fragment which has been inserted into the multiple copy plasmid pAT153. E. coli cells transformed with this recombinant plasmid overproduce EPSP synthase 100-fold. A simple method for the purification of homogeneous enzyme in milligram quantities has been devised. The resulting enzyme is indistinguishable from enzyme isolated from untransformed E. coli.

An amber mutation in the gene rpsA for ribosomal protein S1 in Escherichia coli

An amber mutation has been induced in the gene rpsA (which codes for ribosomal protein S1) of Escherichia coli K-12 strain in the presence of an amber suppressor (supD) and mutations sueA, sueB and sueC that additively enhance the efficiency of suppression. That the amber mutation has occurred in the gene rpsA was confirmed by complementation with a plasmid which carried the wild-type allele of rpsA. The mutation is lethal in the absence of an amber suppressor, indicating that ribosomal protein S1 is indispensable to E. coli.

Primary structure of Escherichia coli ribosomal protein S1 and of its gene rpsA

The primary structure of proteins S1, the largest protein component of the Escherichia coli ribosome, has been elucidated by determining the amino acid sequence of the protein (from E. coli MRE600) and the nucleotide sequence of the S1 gene (rpsA, of a K-12 strain). The two methods gave results in perfect agreement except of two positions where possible strain specific differences were found. Protein S1 (MRE600) is composed of 557 amino acid residues (no modified amino acids were detected) and has Mr 61,159. The DNA sequence for protein S1 (K-12) suggests 556 amino acid residues. A computer survey of the sequence revealed three regions in S1 with a high degree of internal homology. The ribosome binding domain of S1 (NH2 terminus) does not show any preponderance of basic amino acids. The two cysteine and the majority of tryptophan residues of S1 as well as two od the three homologous regions were located in its middle region which contains the nucleic acid binding domain. The pattern of degenerate codon usage in the S1 gene is nonrandom and similar to that reported for other ribosomal protein genes.

Cloning and the nucleotide sequence of the genes for Escherichia coli ribosomal proteins L28 (rpmB) and L33 (rpmG)

The specialized transducing bacteriophage lambda dpyrE DNA was used as a source of DNA to clone two ribosomal protein genes rpmB (L28) and rpmG (L33) on the cloning vehicle pACYC184. Using one of these plasmids, the nucleotide sequence of these two genes and their flanking regions were determined. The amino acid sequences of both proteins deduced from the nucleotide sequences match with the amino acid sequences previously determined, with one exception. The nucleotide sequences suggest that these two ribosomal protein genes are cotranstribed. There was no expression of the second gene of the operon, rpmG, in the absence of the 5' sequences adjacent to the first gene, rpmB. Observation of the structure of mRNA also strongly supports the idea that rpmB and rpmG are in a single transcription unit whose order is: rpmBp-rpmB-rpmG-rpmGt.

Cloning, restriction endonuclease mapping and post-transcriptional regulation of rpsA, the structural gene for ribosomal protein S1

Transducing lambda phages have been isolated that carry segments of the Escherichia coli chromosome in the aspC region, 20.5 min on the E. coli map. One of these phages, lambda aspC2, carries rpsA, the structural gene for the ribosomal protein S1. A three kilobase fragment from this phage, cloned into either the plasmid pACYC184 or the plasmid pBR322, was found to express S1. In cells carrying the rpsA gene on the high copy number plasmid pBR322 the rate of rpsA mRNA synthesis was increased 40-fold, whereas the rate of protein S1 synthesis was doubled, in comparison with these rates in an rpsA haploid.

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.