Expression of the cloned uvrB gene of Escherichia coli: mode of transcription and orientation

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.

A physical map of the Escherichia coli bio operon

The endpoints of the Escherichia coli bio DNA insertions in 24 lambda bio transducing phage were mapped electron micrographically in heteroduplexes of the type lambda bio/lambda att2, which permit simultaneous measurement of the lambda deletion and bio insertion endpoints. A physical map of the bio operon was constructed and correlated with the genetic map, the molecular sizes of the bio gene products, and the restriction map. The order att lambda-bioA-pBopA-bioBFCD-uvrB was confirmed. The maximum size of the bio operon was estimated at 5.5 kb, and the locus was found to be fully saturated with genes. There appears to be little space between the bioA gene and att lambda, while bioD mapped within 0.7 kb from uvrB. The size of the uvrB locus was estimated not to exceed 2.6 kb.

Effect of lexA and ssb genes, present on a uvrA recombinant plasmid, on the UV survival of Escherichia coli K-12

The recombinant plasmid pJA01 contains, besides the uvrA gene, the genes lexA, ubiA and ssb. This plasmid does not fully complement a uvrA mutation in a Rec+ background. Plasmids which contain the uvrA and ssg genes, but not the lexA gene, show a higher but still only partial complementation. Full complementation achieved when the ssb gene us inactivated by insertion of Tn5. Furthermore, it appears that the presence of the ssb gene on a multicopy plasmid sensitizes wild-type cells to UV light. The effect of Ssb (single-strand DNA binding protein) overproduction on UV survival is discussed.

The structure and function of the regulatory elements of the Escherichia coli uvrB gene

The construction and properties of recombinant plasmids carrying the Escherichia coli uvrB gene, including its transcriptional- and translational regulatory elements, is reported. The DNA sequence of the region, which governs the expression of the uvrB gene, has been determined. Within this sequence two non-overlapping DNA segments match the model sequence for Escherichia coli promoters (1). The '-10 regions' and the '-35 regions' of the proposed uvrB promoters are, respectively, 5'TAAAAT (P1), 5'TATAAT (P2) and 5'TTGGCA (P1), 5'GTGATG (P2). The existence and the position of these promoters has been established by elimination of one promoter (P2), using molecular cloning procedures, by length measurements of in vitro synthesized 'run-off' transcripts and by protection of the uvrB regulatory region for S1 nuclease digestion using in vivo made RNA. Potential sites of interaction within the uvrB regulatory region with regulatory proteins, such as the LexA protein (2) and the UvrC protein (3) are discussed.

Relief of polarity caused by transposon Tn5: application in mapping a cloned region of the Escherichia coli uvrB locus essential for UV resistance

The structure and function of recombinant plasmid pNP5, which consists of vector pMB9 and a 2.5 kb EcoRI fragment harbouring the Escherichia coli uvrB gene, has been investigated. Insertional inactivation with the transposons Tn1 (Apr) or Tn5 (Kmr) has been used to determine the region on pNP5 DNA that is essential for UV resistance in uvrB deletion strains. This region spans approx. 1.8 kb and is separated by at least 280 bp from the pMB9 promoter to which it has been fused. Furthermore, a procedure is described to eliminate the polarity exerted by the transposon Tn5. A combination of in vitro digestion of pNP5::Tn5 DNA with restriction endonuclease XHoI, followed by ligation and subsequent in vivo propagation of the resulting plasmid DNA yields predominantly pNP5 molecules with a site-specific nonpolar mutation. The method allows an investigation of cloned complex genetic units, such as operons.

Tn5 mutagenesis of the enterochelin gene cluster of Escherichia coli

Three recombinant plasmids have been studied which collectively carry all the nine known genes of the enterochelin system of iron transport in Escherichia coli K-12. The genetic organization of these genes was studied using a combination of Tn5 mutagenesis, subcloning of restriction fragments and restriction mapping. The order of the genes was established as entD, fes, entF, fep, and entCAGBE and the nine genes were shown to be distributed across 26 kb of DNA. The results of these studies indicate that the genes are organized into at least six transcriptional units.

Transcription of bacteriophage Mu. II. Transcription of the repressor gene

Using pBR322 as a vector, three plasmids were constructed, pGP2, pGP3, and pGP7, containing respectively 5, 100, 700-950, and 1,000 base pairs derived from the immunity end of bacteriophage Mu. All three plasmids contain a functional repressor gene coding for a thermosensitive repressor. RNAs produced when the DNA of these plasmids was used as template in in vitro RNA synthesis, were analysed by hybridization to the DNA of several lambda pMu transducing phages. In spite of the differences in length of the Mu fragments all three plasmids show the same amount of Mu specific l-strand transcription. Since the repressor gene comprises at least 70% of the Mu fragments of pGP3 and pGP7, these results indicate that the repressor gene c of bacteriophage Mu is transcribed on the l-strand. Analysis of in vivo RNA from cells harboring the plasmids pGP2, pGP3, or pGP7 also indicates that the repressor gene of phage Mu is transcribed on the l-strand, as all Mu-specific RNA extracted from these cells at 28 degrees C hybridizes with the l-strand of the first 3,100 basepairs from the Mu immunity end.

Structure of a promotor on plasmid pMB9 derived from plasmid pSC101

The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment which contains the heptamer 5' TATGGTG (132-126) and the duodecamer 5' TGATGAACATCA (158-147). Based on commonalities with other promotors these DNA sequences probably function as, respectively, "binding site" and "recognition site". Furthermore, this fragment harbours a translation reading frame free of nonsense codons and at about 25 basepairs from the indicated heptamer a nucleotide sequence which meets with the requirements for initiation of translation. By heteroduplex mapping it was shown that the EcoRI-HindIII fragment has been derived from a region near or within the origin of replication of pSC101. The copynumber of plasmids containing the EcoRI-HindIII fragment is two-fold lower than that of plasmids lacking this fragment. This effect might be related to the original function of this fragment on plasmid pSC101.

Expression of the cloned uvrB gene of Escherichia coli: dependency on nonsense suppressors

Recombinant plasmid pNP5, consisting of plasmid pMB9 on which the uvrB gene is cloned, fully complements for the defects due to chromosomal uvrB mutations in the presence of the amber suppressor sup-6 or supF. Correndonuclease II activity was also completely restored in in UvrB strains containing both plasmid pNP5 and amber suppressor sup-6, as compared with the parental UvrB+ strain. It is shown that the amber mutation which interferes with the expression of the cloned uvrB gene is located outside this gene. Apparently, the amber mutation exerts a polar effect on uvrB expression that is relieved by sup-6 or supF. Introduction of a rho mutation into suppressor-free UvrB strains, harboring pNP5, did not relieve the polarity caused by the amber mutation.