Evidence that pheV, a gene for tRNAPhe of E. coli is transcribed from tandem promoters

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.

Human transcription factors IIIC2 , IIIC1 and a novel component IIIC0 fulfil different aspects of DNA binding to various pol III genes

Human transcription factor IIIC2 interacts with the TFIIIA-5S DNA complex and forms a ternary TFIIIA/IIIC2-5S DNA complex. Formation of this complex does not preclude simultaneous binding of TFIIIC2to the B-box sequence of a second template. This suggests that the domain(s) or subunit(s) required for indirect recognition of the 5S promoter by TFIIIC2 are different from those necessary for direct binding of TFIIIC2 to B-box-containing pol III promoters. Whereas TFIIIC2 is only required for transcription of the 'classical' pol III genes, TFIIIC1 is generally required for transcription of all pol III genes, including that of the U6 gene. The activity of TFIIIC1 strongly enhances specific binding of basal pol III factors TFIIIA, TFIIIC2 and the PSE binding protein (PBP) to their cognate promoter elements and it acts independently of the corresponding termination regions. Moreover, we characterize an activity, TFIIIC0, purified from phosphocellulose fraction C, which shows strong DNase I protection of the termination region of several pol III genes and which is functionally and chromatographically distinct from TFIIIC1 and TFIIIC2.

The growth defect in Escherichia coli deficient in peptidyl-tRNA hydrolase is due to starvation for Lys-tRNA(Lys)

The existence of a conditional lethal temperature-sensitive mutant affecting peptidyl-tRNA hydrolase in Escherichia coli suggests that this enzyme is essential to cell survival. We report here the isolation of both chromosomal and multicopy suppressors of this mutant in pth, the gene encoding the hydrolase. In one case, the cloned gene responsible for suppression is shown to be lysV, one of three genes encoding the unique lysine acceptor tRNA; 10 other cloned tRNA genes are without effect. Overexpression of lysV leading to a 2- to 3-fold increase in tRNA(Lys) concentration overcomes the shortage of peptidyl-tRNA hydrolase activity in the cell at non-permissive temperature. Conversely, in pth, supN double mutants, where the tRNA(Lys) concentration is reduced due to the conversion of lysV to an ochre suppressor (supN), the thermosensitivity of the initial pth mutant becomes accentuated. Thus, cells carrying both mutations show practically no growth at 39 degrees C, a temperature at which the pth mutant grows almost normally. Growth of the double mutant is restored by the expression of lysV from a plasmid. These results indicate that the limitation of growth in mutants of E.coli deficient in Pth is due to the sequestration of tRNA(Lys) as peptidyl-tRNA. This is consistent with previous observations that this tRNA is particularly prone to premature dissociation from the ribosome.

In vivo deuteration of transfer RNAs: overexpression and large-scale purification of deuterated specific tRNAs

Structural investigations of tRNA complexes using NMR or neutron scattering often require deuterated specific tRNAs. Those tRNAs are needed in large quantities and in highly purified and biologically active form. Fully deuterated tRNAs can be prepared from cells grown in deuterated minimal medium, but tRNA content under this conditions is low, due to regulation of tRNA biosynthesis in response to the slow growth of cells. Here we describe the large-scale preparation of two deuterated tRNA species, namely D-tRNAPhe and D-tRNAfMet (the method is also applicable for other tRNAs). Using overexpression constructs, the yield of specific deuterated tRNAs is improved by a factor of two to ten, depending on the tRNA and growth condition tested. The tRNAs are purified using a combination of classical chromatography on an anion exchange DEAE column with reversed phase preparative HPLC. Purification yields nearly homogenous deuterated tRNAs with a chargeability of 1400-1500 pmol amino acid/A260 unit. The deuterated tRNAs are of excellent biological activity.

Identification of the pheS5 mutation, which causes thermosensitivity of Escherichia coli mutant NP37

The pheS5 mutation responsible for the thermosensitive phenylalanyl-tRNA synthetase of the classical Escherichia coli NP37 was cloned by a recombination event and identified by DNA sequence analysis. The mutation was subsequently verified by direct sequencing of amplified NP37 DNA generated by an asymmetric polymerase chain reaction. The resulting amino acid exchange, Gly-98 to Asp-98 in the phenylalanyl-tRNA synthetase alpha subunit, might cause subunit disaggregation due to electrostatic repulsion.

Mutants of pheV in Escherichia coli affecting control by attenuation of the pheS, T and pheA operons. Two distinct mechanisms for de-attenuation

Two mutants of pheV, a gene coding for tRNA(Phe) in Escherichia coli, were previously isolated because they affect attenuator control of the pheS, T operon when the mutant pheV genes are carried by the plasmid pBR322. We show that the two mutants (A44 and A46) affect attenuator control by different mechanisms. The effect of mutant A44 on pheS, T expression can be progressively decreased by overproduction of Phe-tRNA synthetase, consistent with the mutant tRNA acting as a competitive inhibitor of the enzyme. By contrast, the effect on attenuation of mutant A46 increases with overproduction of Phe-tRNA synthetase, indicating that the mutant must be charged to affect attenuation; we propose that this mutant affects translation directly and causes derepression by competing with wild-type tRNA in translation of the attenuator region leader peptide. Mutant A46 but not mutant A44 leads to further de-attenuation in a miaA background. The presence of two different mechanisms for de-attenuation is further indicated by the finding that a second attenuator controlled by Phe codon translation, from the pheA operon, is affected quite differently by the mutant tRNAs. Finally, experiments involving the introduction of the mutations A44 and A46 into an amber suppressor derived from tRNA(Phe) suggest that both species can function in protein synthesis but with reduced efficiency; mutant A46 is less efficient than mutant A44, consistent with a defect in elongation.

Evidence that there are only two tRNA(Phe) genes in Escherichia coli

pheV, one of the genes that code for tRNA(Phe), was deleted from the chromosome of a strain of Escherichia coli K-12. As a consequence of this mutation, expression of pheA, the gene for chorismate mutase P-prephenate dehydratase, the first enzyme in the terminal pathway of phenylalanine biosynthesis, was derepressed. Similar derepression of pheA has been reported in pheR mutants of E. coli K-12 (J. Gowrishankar and J. Pittard, J. Bacteriol. 150:1130-1137, 1982). Attempts to introduce a pheR mutation into the delta pheV strain failed under circumstances suggesting that this combination of mutations is lethal. Southern blot analysis of pheV+ and delta pheV strains indicated that there are only two tRNA(Phe) genes in E. coli. It is recommended that the names pheU and pheV be retained for these genes.

Human transcription factor IIIC contains a polypeptide of 55 kDa specifically binding to Pol III genes

Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fractions of hTFIIIC by SDS PAGE, electrotransfer to nitrocellulose, renaturation of proteins and their subsequent binding to the VAI gene, (ii) recovery and renaturation of proteins from SDS gels and identification of a fraction of hTFIIIC with a molecular mass less than 68 kDa, which specifically binds to VAI DNA, (iii) correlating the differential binding activity of the renatured 55 kDa component of hTFIIIC to mutated Pol III promoters with the ability of the entire factor to form functional transcription complexes thereon, and finally by (iv) specific crosslinking of the 55 kDa DNA binding component of hTFIIIC to the photoaffinity labeled B-box promoter sequence of the VAI gene.

Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase gene and a tRNA operon in Escherichia coli. Transcriptional and post-transcriptional regulation of gltX, valU and alaW

The transcription of the gltX gene encoding the glutamyl-tRNA synthetase and of the adjacent valU and alaW tRNA operons of Escherichia coli K-12 has been studied. The alaW operon containing two tRNA(GGCAla) genes, is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon, containing three tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN) genes, is adjacent to gltX and is transcribed from the opposite strand. Its only promoter is upstream from the gltX promoters. The gltX gene transcript is monocistronic and its transcription initiates at three promoters, P1, P2 and P3. The transcripts from one or more of these promoters are processed by RNase E to generate two major species of gltX mRNA, which are stable and whose relative abundance varies with growth conditions. The stability of gltX mRNA decreases in an RNase E- strain and its level increases with growth rate about three times more than that of the glutamyl-tRNA synthetase. The 5' region of these mRNAs can adopt a stable secondary structure (close to the ribosome binding site) that is similar to the anticodon and part of the dihydroU stems and loops of tRNA(Glu), and which might be involved in translational regulation of GluRS synthesis. The gltX and valU promoters share the same AT-rich and bent upstream region, whose position coincides with the position of the upstream activating sequences of tRNA and rRNA promoters to which they are similar. This suggests that gltX and valU share transcriptional regulatory mechanisms.

Linkage map of Escherichia coli K-12, edition 8

The linkage map of Escherichia coli K-12 depicts the arrangement of genes on the circular chromosome of this organism. The basic units of the map are minutes, determined by the time-of-entry of markers from Hfr into F- strains in interrupted-conjugation experiments. The time-of-entry distances have been refined over the years by determination of the frequency of cotransduction of loci in transduction experiments utilizing bacteriophage P1, which transduces segments of DNA approximately 2 min in length. In recent years, the relative positions of many genes have been determined even more precisely by physical techniques, including the mapping of restriction fragments and the sequencing of many small regions of the chromosome. On the whole, the agreement between results obtained by genetic and physical methods has been remarkably good considering the different levels of accuracy to be expected of the methods used. There are now few regions of the map whose length is still in some doubt. In some regions, genetic experiments utilizing different mutant strains give different map distances. In other regions, the genetic markers available have not been close enough to give accurate cotransduction data. The chromosome is now known to contain several inserted elements apparently derived from lambdoid phages and other sources. The nature of the region in which the termination of replication of the chromosome occurs is now known to be much more complex than the picture given in the previous map. The present map is based upon the published literature through June of 1988. There are now 1,403 loci placed on the linkage group, which may represent between one-third and one-half of the genes in this organism.

Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12

By using a set of 476 ordered DNA clones (in lambda phage vector) that covers the entire chromosome of Escherichia coli K12, we have made an exhaustive survey of tRNA genes in the E. coli genome. Ultraviolet-irradiated bacteria were separately infected with each of the 476 clones and the RNA molecules produced upon infection were labeled with 32P. The labeled tRNAs were separated by gel electrophoresis and then characterized by fingerprinting analysis. Fifty-nine of the 476 clones produced tRNAs, including adjacent overlapping ones that share the same tRNA genes. The products of all the previously mapped tRNA genes (about 60, to date) were detected according to their expected positions, and 19 more tRNA genes were newly elucidated. These new tRNA genes were identified by sequencing the DNA from relevant regions of the clones; the DNA sequences were scanned for the stretches that could be folded into the familiar cloverleaf structure and the transcription units were deduced by predicting the promoters and terminators. The total complement of the tRNA genes in E. coli K12 was 78 for 45 tRNA (or 41 anticodon) species, distributed in 40 different transcription units throughout the chromosome. In addition, a gene for selenocysteine tRNA was detected by hybridization and mapped to a specific DNA segment. A comprehensive tRNA gene map of E. coli was constructed, including the selenocysteine tRNA gene. All the tRNA genes encode the 3' CCA, and in several cases the terminal 19 nucleotides (including the 3' CCA) of a tRNA gene is repeated several times. Finally, in the present study the sites for a long inversion (approx. 800 x 10(3) base-pairs, around the oriC region) in Kohara's library was determined to be within the 23 S-5 S regions in rrnD and rrnE, revealing the exchange of combinations of spacer and distal tRNA genes between these two ribosomal RNA operons.

Genetic mapping of pheV, an Escherichia coli gene for tRNA(Phe)

We report the physical and genetic mapping of pheV, an Escherichia coli gene for phenylalanine tRNA, to 64 min on the chromosomal map in the near vicinity of speC coding for ornithine decarboxylase.

Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA

The overall structure of transfer RNA is optimized for its various functions by a series of unique post-transcriptional nucleotide modifications. Since many of these modifications are conserved from prokaryotes through higher eukaryotes, it has been proposed that most modified nucleotides serve to optimize the ability of the tRNA to accurately interact with other components of the protein synthesizing machinery. When a cloned synthetic Escherichia coli tRNAPhe gene was transfected into a bacterial host that carried a defective phenylalanine tRNA-synthetase gene, tRNAPhe was overexpressed by 11-fold. As a result of this overexpression, an undermodified tRNAPhe species was produced that lacked only N6-(delta 2-isopentenyl)-2-methylthioadenosine (ms2i6A), a hypermodified nucleotide found immediately 3' to the anticodon of all major E. coli tRNAs that read UNN codons. To investigate the role of ms2i6A in E. coli tRNA, we compared the aminoacylation kinetics and in vitro codon-reading properties of the ms2i6A-lacking and normal fully modified tRNAPhe species. The results of these experiments indicate that while ms2i6A is not required for normal aminoacylation of tRNAPhe, its presence stabilizes codon-anticodon interaction and thereby prevents misreading of the genetic code.

Mutants affecting tRNA(Phe) from Escherichia coli. Studies of the suppression of thermosensitive phenylalanyl-tRNA synthetase

Four mutants of pheV, a gene coding for tRNA(Phe) in Escherichia coli, share the characteristic that when carried in the plasmid pBR322, they lose the capacity of wild-type pheV to complement the thermosensitive defect in a mutant of phenylalanyl-tRNA synthetase. One of these mutants, leading to the change C2----U2 in tRNA(Phe), is expressed about 10-fold lower in transformed cells than wild-type pheV. This mutant, unlike the remaining three (G15----A15, G44----A44, m7G46----A46), can recover the capacity to complement thermosensitivity when carried in a plasmid of higher copy number. The other three mutants, even when expressed at a similar level, remain unable to complement thermosensitivity. A study of charging kinetics suggests that the loss of complementation associated with these mutants is due to an altered interaction with phenylalanyl-tRNA synthetase. The mutant gene pheV (U2), when carried in pBR322, can also recover the capacity to complement thermosensitivity through a second-site mutation outside the tRNA structural gene, in the discriminator region. This mutation, C(-6)----T(-6), restores expression of the mutant U2 to about the level of wild-type tRNA(Phe).

Mutations that reduce expression from the P2 promoter of the Escherichia coli galactose operon

We describe the isolation and characterisation of twelve different mutations that reduce gene expression from the galP2 promoter, starting with a gal regulatory region with a mutation that inactivated galP1, the cAMP-CRP-dependent promoter. Seven of the new mutations reduce the initiation of transcription at P2 whereas the others reduce translation initiation of the first gal operon gene, galE. Two of the mutations affecting translation fall in the galE initiation codon and the Shine-Dalgarno sequence. Mutations that allow the formation of a stem-loop structure in the messenger including this sequence also reduce translation. A deletion of 11 bp, upstream of the Shine-Dalgarno sequence, almost totally prevents translation. Although none of the point mutations that reduced transcription initiation at P2 fall in the -35 region, we repeatedly isolated insertions in this zone. The point mutations all fell around the -10 region: the strongest effects were found with mutations that altered the sequence away from the consensus that has been established for Escherichia coli promoters. The effects of the two strongest P2 mutations were investigated in the absence of the P1 mutation used for their isolation. One mutation, a T:A to C:G transition at -12, inactivates both P2 and P1. In contrast the other, a T:A to G:C transversion at -19, specifically inactivates P2, but leaves P1 partially active even in the absence of cAMP-CRP. The implications of this are discussed in the context of how cAMP-CRP controls the balance between transcription from P2 and P1 at the gal operon regulatory region.