Gene-protein index of Escherichia coli K-12

Participation of the dnaK and dnaJ gene products in phosphorylation of glutaminyl-tRNA synthetase and threonyl-tRNA synthetase of Escherichia coli K-12

The heat shock proteins DnaK and DnaJ of Escherichia coli participate in phosphorylation of both glutaminyl-tRNA synthetase and threonyl-tRNA synthetase. When cellular proteins extracted from the dnaK7(Ts) and dnaJ259(Ts) mutant cells labeled with 32Pi at 42 degrees C were analyzed by two-dimensional gel electrophoresis, no phosphorylation of these proteins was observed when they were compared with those from wild-type cells.

Further evidence for overlapping transcriptional units in an Escherichia coli cell envelope-cell division gene cluster: DNA sequence and transcriptional organization of the ddl ftsQ region

A 1.2-kilobase-pair BamHI fragment from a cell envelope-cell division gene cluster of Escherichia coli containing ddl and part of ftsQ was cloned and sequenced, and the sequence was interpreted with the aid of genetic complementation and promoter fusion data for the region. Both ddl and ftsQ were transcribed in the same direction (clockwise on the genetic map). ddl was shown to be capable of independent expression from a promoter of its own, and a promoter was identified within the ddl structural gene. The structural gene of ddl consisted of 918 nucleotides, encoding a 306-residue polypeptide of molecular weight 32,840; the synthesis of a protein of this molecular weight was shown to be directed from the 1.2-kilobase-pair BamHI fragment in minicells. Analysis of the DNA sequence further showed that the termination codon of ddl is separated from the initiation codon of ftsQ by one base, which suggests that these two genes may be translationally coupled when transcription is initiated upstream of ddl. This represents a second instance of potential translational coupling within this gene cluster and also indicates that the ddl and ftsQ transcriptional units must overlap (as has been reported earlier for ftsQ and ftsA and for ftsA and ftsZ).

Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene

In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons.

Expression of the Escherichia coli pfkA gene in Alcaligenes eutrophus and in other gram-negative bacteria

The Escherichia coli pfkA gene has been cloned in the non-self-transmissible vector pVK101 from hybrid plasmids obtained from the Clarke and Carbon clone bank, resulting in the plasmids pAS300 and pAS100; the latter plasmid also encoded the E. coli tpi gene. These plasmids were transferred by conjugation to mutants of Alcaligenes eutrophus which are unable to grow on fructose and gluconate due to lack of 2-keto-3-deoxy-6-phosphogluconate aldolase activity. These transconjugants recovered the ability to grow on fructose and harbored pAS100 or pAS300. After growth on fructose, the transconjugants contained phosphofructokinase at specific activities between 0.73 and 1.83 U/mg of protein, indicating that the E. coli pfkA gene is readily expressed in A. eutrophus and that the utilization of fructose occurs via the Embden-Meyerhof pathway instead of the Entner-Doudoroff pathway. In contrast, transconjugants of the wild type of A. eutrophus, which are potentially able to catabolize fructose via both pathways, grew at a decreased rate on fructose and during growth on fructose did not stably maintain pAS100 or pAS300. Indications for a glycolytic futile cycling of fructose 6-phosphate and fructose 1,6-bisphosphate are discussed. Plasmid pA 100 was also transferred to 14 different species of gram-negative bacteria. The pfkA gene was expressed in most of these species. In addition, most transconjugants of these strains and of A. eutrophus exhibited higher specific activities of triosephosphate isomerase than did the corresponding parent strains.

Proteins of Escherichia coli come in sizes that are multiples of 14 kDa: domain concepts and evolutionary implications

Initial attempts to correlate the distribution of gene density (number of gene loci per unit length on the linkage map) with the distribution of lengths of coding sequences have led to the observation that 46% of approximately 1000 sampled proteins in Escherichia coli have molecular masses of n X 14,000 +/- 2500 daltons (n = 1, 2, ...). This clustering around multiples of 14,000 contrasts with the 36% one would expect in these ranges if the sizes were uniformly distributed. The entire distribution is well fit by a sum of normal or lognormal distributions located at multiples of 14,000, which suggests that the percentage of E. coli proteins governed by the underlying sizing mechanism is much greater than 50%. Clustering of protein molecular sizes around multiples of a unit size also is suggested by the distribution of well-characterized HeLa cell proteins. The distribution of gene lengths for E. coli suggests regular clustering, which implies that the clustering of protein molecular masses is not an artifact of the molecular mass measurement by gel electrophoresis. These observations suggest the existence of a fundamental structural unit. The rather uniform size of this structural unit (without any apparent sequence homology) suggests that a general principle such as geometrical or physical optimization at the DNA or protein level is responsible. This suggestion is discussed in relation to experimental evidence for the domain structure of proteins and to existing hypotheses that attempt to account for these domains. Microevolution would appear to be accommodated by incremental changes within this fundamental unit, whereas macroevolution would appear to involve "quantum" changes to the next stable size of protein.

Evolution in biosynthetic pathways: two enzymes catalyzing consecutive steps in methionine biosynthesis originate from a common ancestor and possess a similar regulatory region

The metC gene of Escherichia coli K-12 was cloned and the nucleotide sequence of the metC gene and its flanking regions was determined. The translation initiation codon was identified by sequencing the NH2-terminal part of beta-cystathionase, the MetC gene product. The metC gene (1185 nucleotides) encodes a protein having 395 amino acid residues. The 5' noncoding region was found to contain a "Met box" homologous to sequences suggestive of operator structures upstream from other methionine genes that are controlled by the product of the pleiotropic regulatory metJ gene. The deduced amino acid sequence of beta-cystathionase showed extensive homology with that of the MetB protein (cystathionine gamma-synthase) that catalyzes the preceding step in methionine biosynthesis. The homology strongly suggests that the structural genes for the MetB and MetC proteins evolved from a common ancestral gene.

Identification and antigenic characterization of virulence-associated, plasmid-coded proteins of Shigella spp. and enteroinvasive Escherichia coli

Seven plasmid-coded polypeptides, designated a through g, were identified by two-dimensional nonequilibrium pH gradient electrophoresis of radiolabeled extracts from minicells of virulent Shigella flexneri serotypes 2a and 5 and enteroinvasive Escherichia coli O143. These polypeptides were deemed to be products of 140-megadalton (MDa) virulence-associated plasmids because they were not synthesized in minicells which were not harboring a 140-MDa plasmid or in minicells which were carrying an F lac plasmid of the same incompatibility group. Synthesis of these polypeptides was repressed in minicells incubated at 30 degrees C and in minicells isolated from a noninvasive opaque colonial variant, even though these strains harbored a 140-MDa plasmid. Enriched fractions of polypeptides b, c, and d were obtained from S. flexneri serotype 5 by preparative isoelectric focusing, and polyclonal rabbit antisera recognizing each polypeptide were raised. These antisera were able to detect cross-reacting plasmid-coded polypeptide antigens in S. flexneri serotype 3, Shigella sonnei, and enteroinvasive E. coli O143. In addition, Western blots of minicell extracts from S. flexneri serotype 5 or E. coli O143 indicated that plasmid-coded polypeptides a through d were recognized by convalescent antiserum from a monkey infected with S. flexneri serotype 2a.

Cloning of the Escherichia coli gene for the stringent starvation protein

In order to clone the Escherichia coli gene for the stringent starvation protein (SSP), we determined its N-terminal sequence as well as the sequence of two peptide fragments obtained by cyanogen bromide cleavage of the protein. We then chemically synthesized four sets of oligodeoxyribonucleotide mixtures that represented possible codon combinations for parts of these amino acid sequences. The synthetic oligonucleotides were labelled with 32P at their 5'-termini and used as hybridization probes to detect DNA fragments containing the complementary sequences. Genomic Southern hybridization of E. coli chromosomal DNA gave up to ten DNA fragments hybridizing with each probe but only a few hybridized with two or more of the probes. The latter fragments were cloned in pBR322. By determining partial base sequences with a rapid method and examining proteins encoded by the DNA fragments, we were able to show that we had isolated a clone containing the complete SSP structural gene.

Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase

An oligodeoxynucleotide specific for a pentapeptide sequence corresponding to amino acid residues 32 through 36 of Escherichia coli malate dehydrogenase was chemically synthesized and used to identify the mdh gene on plasmid pLC32-38 from the Clarke-Carbon recombinant library. Cells transformed with this plasmid exhibited a 10-fold increase in malate dehydrogenase activity. A 1.2-kilobase PvuII fragment which hybridized with the oligodeoxynucleotide probe was subcloned, and the identity of the mdh structural gene was confirmed by partial nucleotide sequence analysis. The expression of the mdh gene, as measured by both Northern blotting and enzyme assays, was found to vary over a 20-fold range with different culture conditions.

Heat shock stress in Bacteroides fragilis

The response to heat shock was investigated in the obligate anaerobe Bacteroides fragilis. The cells responded quickly to stress and synthesised seven heat shock proteins immediately upon exposure to heat. The apparent molecular weights of the seven proteins differed from the apparent molecular weights of the proteins induced by UV irradiation, O2 and H2O2. Heat shock did not induce phage reactivation whereas UV irradiation, O2 and H2O2 did induce phage reactivation systems. Ethanol did not elicit the heat shock response. Two heat resistant B. fragilis mutants were isolated. Both mutants lost the ability to synthesise the same two heat shock proteins. It is concluded that the heat shock response and the responses to UV irradiation, O2 and H2O2 represent two independent groups of stress responses in B. fragilis.

Gene density over the chromosome of Escherichia coli: frequency distribution, spatial clustering, and symmetry

Published studies of gene density (the number of genetic loci per unit of length on the linkage map) for Escherichia coli report a nonrandom frequency distribution and indicate notable symmetry in spatial clustering of gene density. We reexamined these results and found that gene density is a random variable with a frequency distribution that is lognormal. That is, the logarithm of gene density is a normally distributed random variable. Furthermore, comparison of the observed E. coli map and computer-generated random maps showed that symmetries in the spatial clustering of gene density are not exceptional; these features arise naturally among genes (or loci) whose density has this frequency distribution. These results are discussed along with other related examples that illustrate the emerging importance of statistical inference in molecular genetics.

Host DNA replication forks are not preferred targets for bacteriophage Mu transposition

Bacteriophage Mu DNA integration in Escherichia coli strains infected after alignment of chromosomal replication was analyzed by a sandwich hybridization assay. The results indicated that Mu integrated into chromosomal segments at various distances from oriC with similar kinetics. In an extension of these studies, various Hfr strains were infected after alignment of chromosomal replication, and Mu transposition was shut down early after infection. The positions of integrated Mu copies were inferred from the transfer kinetics of Mu to an F- strain. Our analysis indicated that the location of Mu DNA in the host chromosome was not dependent on the positions of host replication forks at the time of infection. However, the procedure for aligning chromosomal replication affected DNA transfer by various Hfr strains differently, and this effect could account for prior results suggesting preferential integration of Mu at host replication forks.

Cloning and nucleotide sequence of the trxA gene of Escherichia coli K-12

The Escherichia coli K-12 trxA gene, the gene encoding thioredoxin, has been cloned and sequenced. The DNA sequence includes 280 base pairs upstream and 46 base pairs downstream of the coding region. The downstream sequence contains the -35 region of the promoter of the rho gene. Northern analysis of the trxA mRNA and S1 nuclease mapping indicate the presence of two promoters for the trxA gene. Initiation from either promoter results in an mRNA containing two potential translation initiation codons, one of which could initiate synthesis of a protein 18 amino acids longer than the mature trxA gene product. The 3' end of the gene, including the last eight codons, contains a stable stem-loop structure (delta G = -12.9 kcal) typical of a rho-independent transcription termination signal.

The seleno-polypeptide of formic dehydrogenase (formate hydrogen-lyase linked) from Escherichia coli: genetic analysis

The site of integration of phage M mu d (Ap lac) in mutant M9s which leads to deficiency of formic dehydrogenase (benzylviologen-linked) activity was determined. It was shown that the phage had inserted into the gene for the seleno-polypeptide of the enzyme (80 kd) leading to the formation of a truncated peptide (60 kd) still able to incorporate Se. Synthesis of the truncated polypeptide is subject to the same regulatory signals as that of the wild-type enzyme. The formation of the 110 kd seleno-polypeptide, which is a constituent component of the formic dehydrogenase from the formate-nitrate respiratory pathway, is unimpaired in mutant M9s. The location of the gene for the 80 kd seleno-polypeptide was mapped at 92.4 min of the Escherichia coli chromosome.

Duplication of Escherichia coli during inhibition of net phospholipid synthesis

In Escherichia coli BB26-36, the inhibition of net phospholipid synthesis during glycerol starvation affected cell duplication in a manner that was similar in some respects to that observed during the inhibition of protein synthesis. Ongoing rounds of chromosome replication continued, and cells in the D period divided. The initiation of new rounds of chromosome replication and division of cells in the C period were inhibited. Unlike the inhibition of protein synthesis, however, the accumulation of initiation potential in dnaA and dnaC mutants at the nonpermissive temperature was not affected by the inhibition of phospholipid synthesis. Furthermore, proteins synthesized during the inhibition of phospholipid synthesis can be utilized later for division. The results are consistent with a dual requirement for protein and phospholipid synthesis for both the inauguration of new rounds of chromosome replication and the initiation of septum formation. Once initiated, both processes progress to completion independent of continuous phospholipid and protein synthesis.

Essential site for growth rate-dependent regulation within the Escherichia coli gnd structural gene

Expression of gnd of Escherichia coli, which encodes the hexose monophosphate shunt enzyme, 6-phosphogluconate dehydrogenase (6PGD; EC 1.1.1.44), is subject to growth rate-dependent regulation: the level of the enzyme is directly proportional to growth rate under a variety of growth conditions. Previous results obtained with strains carrying transcriptional fusions of gnd to the structural genes of the lactose operon suggested that the growth rate-dependent regulation of gnd expression is at the post-transcriptional level. To characterize the regulation further, we prepared with phage MudII a set of eight independent gnd-lac gene (protein) fusions. We showed through genetic analysis and DNA sequencing that each fusion joint was located within the 6PGD-coding sequence between the first and second base pair of a codon, the reading frame required for production of a hybrid 6PGD-beta-galactosidase. Strains harboring the gnd-lac fusion plasmids produced proteins whose mobility in a NaDodSO4/polyacrylamide gel agreed with the molecular weights predicted from the DNA sequence for the respective hybrid proteins. The level of beta-galactosidase was high and relatively growth rate-independent in the fusion whose fusion joint was at codon 48. The level of beta-galactosidase in the other seven fusion strains whose fusion joints were located further downstream in the 6PGD-coding sequence showed the same dependence on growth rate as 6PGD in a normal strain. beta-Galactosidase levels were not affected by the presence of a gnd+ gene in trans to any of the fusions. The results suggest that all sites necessary for growth rate-dependent regulation of 6PGD level lie in gnd upstream from codon 118 and that an essential site of negative control lies within the coding sequence, between codons 48 and 118.

Molecular cloning and primary structure of the Escherichia coli methionyl-tRNA synthetase gene

The intact metG gene was cloned in plasmid pBR322 from an F32 episomal gene library by complementation of a structural mutant, metG83. The Escherichia coli strain transformed with this plasmid (pX1) overproduced methionyl-tRNA synthetase 40-fold. Maxicell analysis showed that three major polypeptides with MrS of 76,000, 37,000, and 29,000 were expressed from pX1. The polypeptide with an Mr of 76,000 was identified as the product of metG on the basis of immunological studies and was indistinguishable from purified methionyl-tRNA synthetase. In addition, DNA-DNA hybridization studies demonstrated that the metG regions were homologous on the E. coli chromosome and on the F32 episome. DNA sequencing of 642 nucleotides was performed. It completes the partial metG sequence already published (D. G. Barker, J. P. Ebel, R. Jakes, and C. J. Bruton, Eur. J. Biochem. 127:449-451, 1982). Examination of the deduced primary structure of methionyl-tRNA synthetase excludes the occurrence of any significant repeated sequences. Finally, mapping of mutation metG83 by complementation experiments strongly suggests that the central part of methionyl-tRNA synthetase is involved in methionine recognition. This observation is discussed in the light of the known three-dimensional crystallographic structure.

Transcriptional organization within an Escherichia coli cell division gene cluster: direction of transcription of the cell separation gene envA

A cluster of at least 14 genes, each concerned with some aspect of cell envelope growth, morphogenesis, or function, is located at 2 min on the genetic map of Escherichia coli. We located the envA cell division gene and its promoter within the cluster and determined the direction of transcription of the gene by constructing fusions between its promoter and the galK coding sequence. In addition, we identified the promoter of a possible new gene lying between envA and the secA gene. We also present evidence from gene fusion studies which shows the direction of transcription of the ftsZ(sulB) division gene. The direction of transcription is the same for all three promoters and is the same as that of all other cluster genes for which this is known. We discuss the significance of this observation, together with the fact that every gene examined in sufficient detail within the cluster appears to have its own promoter and to be able to be expressed from isolated cloned fragments. Using a novel variable-copy plasmid vector, we demonstrate that the DNA fragment containing the envA gene is not stably maintained in multiple copies. The construction of two independent, nonoverlapping deletions allows us to conclude that the envA product itself is responsible for this effect.

lon gene product of Escherichia coli is a heat-shock protein

The product of the pleiotropic gene lon is a protein with protease activity and has been tentatively identified as protein H94.0 on the reference two-dimensional gel of Escherichia coli proteins. Purified Lon protease migrated with the prominent cellular protein H94.0 in E. coli K-12 strains. Peptide map patterns of Lon protease and H94.0 were identical. A mutant form of the protease had altered mobility during gel electrophoresis. An E. coli B/r strain that is known to be defective in Lon function contained no detectable H94.0 protein under normal growth conditions. Upon a shift to 42 degrees C, however, the Lon protease was induced to high levels in K-12 strains and a small amount of protein became detectable at the H94.0 location in strain B/r. Heat induction of Lon protease was dependent on the normal allele of the regulatory gene, htpR, establishing lon as a member of the high-temperature-production regulon of E. coli.

Identification of the purC gene product of Escherichia coli

The purC region of the Escherichia coli chromosome was isolated from in vivo-derived lambda transducing bacteriophages and cloned in high-copy-number plasmids. The product of the purC gene, phosphoribosylaminoimidazolesuccinocarboxamide synthetase, was identified as a protein with an Mr of ca. 27,000. The level of the protein is increased by more than 60-fold in strains carrying the gene on a high-copy-number plasmid. Purine addition represses the enzyme level in both plasmid- and non-plasmid-containing strains.