Genetic and physical location of the Escherichia coli rap locus, which is essential for growth of bacteriophage lambda.

The Escherichia coli rap mutant does not support the growth of bacteriophage lambda (D. Henderson and J. Weil, Virology 71:546-559, 1976). We located the rap site at 26 min in the E. coli genetic map and determined the gene order fadR-rap-supF-trp from our transduction experiments. Plasmid pHO1 harbors a 5.6-kilobase-pair segment of the E. coli chromosome which contains the pth gene (B. Hove-Jensen, Mol. Gen. Genet. 201:269-276, 1985). This plasmid complemented rap bacteria, suggesting that it carries the dominant allele rap+. Subcloning experiments reduced the rap-complementing segment to 1.5 kilobase pairs. This segment still contained pth; thus, both loci are tightly linked. The lit mutations that inhibit phage T4 growth in E. coli are located nearby at 25 min (W. Cooley, K. Sirotkin, R. Green, and L. Snyder, J. Bacteriol. 140:83-91, 1979). We showed that rap and lit mutations are phenotypically and genetically different.     

The lit gene product which blocks bacteriophage T4 late gene expression is a membrane protein encoded by a cryptic DNA element, e14.

Escherichia coli lit(Con) mutations cause a severe inhibition of gene expression late in infection by bacteriophage T4 owing to the overproduction of one, and possibly two, proteins (C. Kao, E. Gumbs, and L. Snyder, J. Bacteriol. 169:1232-1238, 1987). One or both of these proteins interact, either directly or indirectly, with a short sequence about one-quarter of the way into the major capsid protein gene of T4, and the inhibition occurs when this late gene of the virus is expressed. In this report we show that lit(Con) mutations are up-promoter mutations in the cryptic DNA element e14 and that only one of the proteins, gplit, of about 34 kilodaltons, is required for the inhibition. We have sequenced the lit gene and the surrounding regions. From the sequence, and from cell fractionation studies, we conclude that gplit is an inner membrane protein. Since the assembly of T4 heads is thought to occur on the inner face of the inner membrane, we propose that gplit interferes with a normal regulation which coordinates the synthesis of proteins and the assembly of T4 heads.     

Cloning and characterization of the Escherichia coli lit gene, which blocks bacteriophage T4 late gene expression.

Escherichia coli lit mutations inhibit gene expression late in infection by bacteriophage T4. We cloned the lit gene from wild-type E. coli and three independent lit mutants. We present evidence that lit mutations [renamed lit(Con) mutations] cause overproduction of the lit gene product and that overproduction of this product causes the inhibition of gene expression. We also present evidence that the lit gene product is nonessential for E. coli growth, although the gene is common to most E. coli K-12 strains.     

Characterization of the Escherichia coli F factor traY gene product and its binding sites.

The traY gene product (TraYp) from the Escherichia coli F factor has previously been purified and shown to bind a DNA fragment containing the F plasmid oriT region (E. E. Lahue and S. W. Matson, J. Bacteriol. 172:1385-1391, 1990). To determine the precise nucleotide sequence bound by TraYp, DNase I footprinting was performed. The TraYp-binding site is near, but not coincident with, the site that is nicked to initiate conjugative DNA transfer. In addition, a second TraYp binding site, which is coincident with the mRNA start site at the traYI promoter, is described. The Kd for each binding site was determined by a gel mobility shift assay. TraYp exhibits a fivefold higher affinity for the oriT binding site compared with the traYI promoter binding site. Hydrodynamic studies were performed to show that TraYp is a monomer in solution under the conditions used in DNA binding assays. Early genetic experiments implicated the traY gene product in the site- and strand-specific endonuclease activity that nicks at oriT (R. Everett and N. Willetts, J. Mol. Biol. 136:129-150, 1980; S. McIntire and N. Willetts, Mol. Gen. Genet. 178:165-172, 1980). As this activity has recently been ascribed to helicase I, it was of interest to see whether TraYp had any effect on this reaction. Addition of TraYp to nicking reactions catalyzed by helicase I showed no effect on the rate or efficiency of oriT nicking. Roles for TraYp in conjugative DNA transfer and a possible mode of binding to DNA are discussed.     

Inositol monophosphatase activity from the Escherichia coli suhB gene product.

The suhB gene is located at 55 min on the Escherichia coli chromosome and encodes a protein of 268 amino acids. Mutant alleles of suhB have been isolated as extragenic suppressors for the protein secretion mutation (secY24), the heat shock response mutation (rpoH15), and the DNA synthesis mutation (dnaB121) (K. Shiba, K. Ito, and T. Yura, J. Bacteriol. 160:696-701, 1984; R. Yano, H. Nagai, K. Shiba, and T. Yura, J. Bacteriol. 172:2124-2130, 1990; S. Chang, D. Ng, L. Baird, and C. Georgopoulos, J. Biol. Chem. 266:3654-3660, 1991). These mutant alleles of suhB cause cold-sensitive cell growth, indicating that the suhB gene is essential at low temperatures. Little work has been done, however, to elucidate the role of the product of suhB in a normal cell and the suppression mechanisms of the suhB mutations in the aforementioned mutants. The sequence similarity shared between the suhB gene product and mammalian inositol monophosphatase has prompted us to test the inositol monophosphatase activity of the suhB gene product. We report here that the purified SuhB protein showed inositol monophosphatase activity. The kinetic parameters of SuhB inositol monophosphatase (Km = 0.071 mM; Vmax = 12.3 mumol/min per mg) are similar to those of mammalian inositol monophosphatase. The ssyA3 and suhB2 mutations, which were isolated as extragenic suppressors for secY24 and rpoH15, respectively, had a DNA insertion at the 5' proximal region of the suhB gene, and the amount of SuhB protein within mutant cells decreased. The possible role of suhB in E. coli is discussed.     

Circular organization of the DNA synthetic pathway in Caulobacter crescentus.

Genetic analysis of the cell cycle of Caulobacter crescentus has identified a DNA synthetic pathway and a cell division pathway (M. A. Osley and A. Newton, J. Mol. Biol. 138:109-128, 1980). The results presented here show that in double-shift experiments the function of the PC2076 gene product, which is required for the initiation of DNA synthesis, depends on completion of a late stage of chromosome replication in the previous cell cycle. These findings suggest a circular organization of steps in the DNA synthetic pathway in C. crescentus.     

Genetic analysis of gene 1.2 of bacteriophage T7: isolation of a mutant of Escherichia coli unable to support the growth of T7 gene 1.2 mutants.

The product of gene 1.2 of bacteriophage T7 is not required for the growth of T7 in wild-type Escherichia coli since deletion mutants lacking the entire gene 1.2 grow normally (Studier et al., J. Mol. Biol. 135:917-937, 1979). By using a T7 strain lacking gene 1.2, we have isolated a mutant of E. coli that was unable to support the growth of both point and deletion mutants defective in gene 1.2. The mutation, optA1, was located at approximately 3.6 min on the E. coli linkage map in the interval between dapD and tonA; optA1 was 92% cotransducible with dapD. By using the optA1 mutant, we have isolated six gene 1.2 point mutants of T7, all of which mapped between positions 15 and 16 on the T7 genetic map. These mutations have also been characterized by DNA sequence analysis, E. coli optA1 cells infected with T7 gene 1.2 mutants were defective in T7 DNA replication; early RNA and protein synthesis proceeded normally. The defect in T7 DNA replication is manifested by a premature cessation of DNA synthesis and degradation of the newly synthesized DNA. The defect was not observed in E. coli opt+ cells infected with T7 gene 1.2 mutants or in E. coli optA1 cells infected with wild-type T7 phage.     

Purification and properties of the bacteriophage T4 gene 31 protein required for prehead assembly.

A low molecular weight (approximately 16,000), early protein is characterized as the product of the essential T4 head assembly gene 31. This gene is known to be required to allow formation of any ordered head structure from the major T4 capsid protein, P23 (Laemmli, U.K., Beguin, F., and Gujer-Kellenberger, G. (1970) J. Mol. Biol. 47, 69-85). In wild type infection P31 synthesis ceases at late times; in contrast, P31 is overproduced in certain early or regulatory T4 mutant infections, particularly gene 55 mutant infections. P31 was purified preparatively from Escherichia coli infected with the latter mutant, but could only be obtained for the most part in modified form, possibly due to unusual sensitivity to a proteolytic activity. P31 is not cleaved in vivo during normal head assembly, nor does it become a part of the mature head or any ordered prehead structure as determined by an immunological assay using antiserum prepared against the purified protein. However P31 does appear to become a part of the unordered P23 aggregates (lumps) which accumulate when ordered P23 assembly is prevented. We cound find no evidence for P31 association with T4 DNA or the host membrane. Our experiments favor the hypothesis that P31 directly affects the aggregation state and solubility properties of P23.     

Accumulation of a murein-membrane attachment site fraction when cell division is blocked in lkyD and cha mutants of Salmonella typhimurium and Escherichia coli.

Membrane fractionation studies were performed on Salmonella typhimurium lkyD(Ts) and E. coli cha(Ts) mutants that appeared to be blocked at a late stage of the cell division cycle. In both cases growth of the mutant strains at nonpermissive temperatures was associated with accumulation of a characteristic cell envelope fraction (fraction OML) that contained inner membrane, murein, and outer membrane components. The isolated fraction corresponded in composition and bouyant density to a fraction from wild-type strains that had previously been suggested (M. H. Bayer, G. P. Costello, and M. E. Bayer, J. Bacteriol. 149:758-767, 1982; K. Ishidate, E. S. Creeger, J. Zrike, S. Deb, B. Glauner, T. J. MacAlister, and L. I. Rothfield, J. Biol. Chem. 261:428-443, 1986) to contain adhesion sites between inner membrane, murein, and outer membrane. The accumulation of OML in LkyD- and Cha- cells was prevented by treatments that blocked DNA synthesis. The effects of interference with DNA synthesis did not appear to involve the SOS response.     

The spacing of Escherichia coli DNA gyrase sites cleaved in vivo by treatment with oxolinic acid and sodium dodecyl sulfate

In an attempt to locate gyrase binding sites in a specific region of the chromosome of E. coli, we have reinvestigated gyrase-promoted cleavage of chromosomal DNA by oxolinic acid and sodium dodecyl sulfate. Contrary to a previous report suggesting the presence of one site every 100 kb of DNA (Snyder and Drlica, J. Mol. Biol. 131, 287-302), we found frequencies of one cleavage every 25 or 12 kb depending on the growth medium. A search for cleavage sites by Southern blot hybridization failed to reveal any binding site cleaved at a high frequency. These results suggest that the actual spacing of sites is much closer than that determined from the frequency of cleavage. Measurement of the average size of fragments containing defined DNA sequences indicated that the frequency of sites varies along the chromosome. The region located opposite to oriC carries relatively few sites.     

Primary structure of human salivary alpha-amylase gene

A recombinant clone which covers the human salivary alpha-amylase gene in a single insert has been isolated from a human genomic DNA library using a human salivary alpha-amylase cDNA as a probe. Restriction mapping and nucleotide (nt) sequence analysis revealed that this gene is approx. 10 kb long and is separated into eleven exons by ten introns. Its 5'-flanking region has some sequence homology with that of mouse salivary alpha-amylase gene [Schibler et al., J. Mol. Biol. 155 (1982) 247-266].