tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli

Effect of NusA protein on expression of the nusA,infB operon in E. coli

Protein and operon fusions between lacZ and various genes of the nusA,infB operon have been constructed on lambda bacteriophages and used to show that the operon is negatively regulated by the level of NusA protein. Overproducing NusA (but not IF2) from a multicopy plasmid reduces the level of beta-galactosidase from the fusions indicating repression of the operon. Introducing the lambda carrying the fusions into nusA mutant strains produces a higher level of beta-galactosidase-indicative of derepression of the operon. In particular, a larger form of the NusA protein which does not affect bacterial growth per se causes a derepression of the operon. As both protein and operon fusions respond equivalently, we conclude that the nusA protein is acting at the transcriptional level to regulate expression of the nusA, infB operon.

Structure and transcription of the tRNAPro1 gene from Escherichia coli

A 5 kbp DNA fragment containing the tRNAPro1 gene from Escherichia coli was cloned into Charon 21A phage and sequenced by the M13 DNA sequencing technique. When the cloned DNA fragment was used as a template for in vitro transcription with E. coli RNA polymerase, a tRNAPro1 precursor of 120 nucleotide residues was obtained. The tRNAPro1 gene transcribed as a single transcription unit was followed by two unusual repeating sequences, both of 108 bp. These two repeating sequences were separated by a 60 bp spacer sequence. The 5'-portion of each repeating sequence overlapped 19 bp of the 3'-terminal region of the tRNAPro1 gene just like the repeating sequences in the E. coli tRNATyr1 gene. A rho-independent termination was present in the first repeating unit.

Escherichia coli 6S RNA gene is part of a dual-function transcription unit

The gene coding for the metabolically stable 6S RNA of Escherichia coli has been cloned, sequenced, and partially characterized in expression analyses. The DNA sequence results confirm the accuracy of the previously established RNA sequence and, with genomic hybridization data, reveal that there is only one copy of the 6S DNA in the chromosome. Consistent with its relaxed mode of expression, the promoter region of the 6S RNA gene was found to lack the hypothetical GC-rich discriminator domain common to other stable RNA genes under stringent control. The sequence results also revealed the occurrence of a 540-base-pair open reading frame immediately downstream from the 6S RNA coding region. Results from the expression analyses show that the protein and RNA coding regions are cotranscribed in vitro and that the open reading frame is translated in vivo.

In vivo evidence that the nusA and infB genes of E. coli are part of the same multi-gene operon which encodes at least four proteins

Previous work has shown that the Escherichia coli nusA gene codes for a protein which regulates transcription termination. The 16.0-kb EcoRI DNA fragment that includes the nusA gene, codes for at least eight bacterial proteins of mol. wts. 48 000 (argG), 21 000 (p21), 64 000 (nusA), 120 000 (IF2 alpha)-(infB), 91 000 (IF2 beta)(infB), 15 000 (p15), 10 000 (rpsO) and 85 000 (pnp). We have constructed several deletion and fusion derivatives from this cloned DNA and examined in vivo the structure and expression of these genes. First, the promoter functional in vivo for the nusA gene was mapped at approximately 800 bp upstream of the nusA structural gene. Second, the synthesis of five proteins, p21, NusA, IF2 alpha, IF2 beta (and p15) proteins, was affected by the deletion of the nusA promoter. Third, these same five proteins were hyperproduced after fusion of the DNA fragment to the lambda pL promoter. In addition, subcloning experiments revealed that the p15 gene is expressed by the read-through transcription from the infB gene. These results lead us to conclude that the genes coding for the p21, NusA, InfB (IF2 alpha and IF2 beta), and p15 proteins form a single-transcriptional unit ('nusA-infB operon') in vivo and that rpsO and pnp genes do not belong to the same operon. The in vivo attenuation site of this operon is described.

Heat shock regulatory gene (htpR) of Escherichia coli is required for growth at high temperature but is dispensable at low temperature

Nonsense mutations affecting the positive regulatory gene (htpR) of heat shock response have been obtained in a strain of Escherichia coli carrying no suppressor. The mutants can grow only at temperatures below 34 degrees C-35 degrees C. Heat, ethanol, and coumermycin induce major heat shock proteins in the wild-type but not in the htpR mutants. In contrast, the level of heat shock proteins synthesized at low temperature is unaffected. The htpR gene product is thus required for induction of heat shock proteins by heat or other stresses but not for their "basal-level" synthesis. Nucleotide sequence has been determined for the wild-type and the mutant alleles of htpR. The coding region appears to consist of 852 nucleotide pairs that correspond to 284 amino acids. Sequences commonly considered as signals for transcriptional initiation and termination were found flanking the coding region. Within this region, six amber, one opal, and two missense mutations were identified; the nonsense mutations are scattered along the gene, some being very close to the presumed amino terminus. These results indicate that the absence of htpR gene product is directly responsible for the failure to respond to heat shock or other stresses and for the inability to grow at high temperature. We propose that htpR represents a new class of genes that are essential for growth only at high temperatures (greater than 35 degrees C). Implications of the sequence homologies found among htpR, rpoD, and nusA proteins are discussed.

The nucleotide sequence of the cloned nusA gene and its flanking region of Escherichia coli

The nucleotide sequence of the promoter-proximal portion of the nusA operon including the genes for tRNAMetf2, a 15 kilodalton protein and the initial portion of the nusA gene has been determined previously (1). Here, we report the sequence for the entire nusA gene and its flanking region. The open reading frame, consisting of 1,482 nucleotides, was identified as that of the nusA protein on the basis of agreement of the amino acid sequence deduced from the DNA sequence with the N-terminal sequence of the purified nusA protein. The molecular weight of 54,417 daltons calculated for the 494 amino acid polypeptide is significantly lower than that determined previously by SDS polyacrylamide gel analysis. The nusA gene is immediately followed by another open reading frame encoding a polypeptide of at least 22 amino acids, which was identified as the initial portion of the infB structural gene. In the spacer region of 24 base pairs between the nusA and infB structural genes there is no significant DNA sequence that fits the canonical transcriptional termination signal or promoter sequence. We suggest, therefore, that the genes for tRNAMetf2, a 15 kilodalton protein, the nusA protein and IF2 alpha, aligned in this order, are co-transcribed.

Conserved features of coordinately regulated E. coli promoters

E. coli promoters which are coordinately regulated in response to amino acid limitation contain conserved nucleotide sequences immediately 3' to -10 region. These sequences contain predominantly either GC or AT residues depending on whether the response is respectively negative or positive. Certain classes of promoters also contain conserved sequences upstream of the primary promoter. In tRNA genes these sequences could act as a secondary polymerase binding site.