Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12

Davies, Ian J.; Drabble, W. T.

doi:10.1099/00221287-142-9-2429

Cited by 25 publications

(43 citation statements)

References 26 publications

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“…Because GMP is a precursor for the synthesis of GTP, it follows that the rate of synthesis of GMP should be regulated according to the growth rate. Consistent with this, it has been shown that P guaB activity is subject to GRDC (8). The bestcharacterized promoter subject to GRDC that also contains an UP element is the rrnB P1 promoter, although the UP element plays no role in GRDC of this promoter (2,28).…”

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confidence: 68%

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Husnain

Thomas

2008

J Bacteriol

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The Escherichia coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P guaB is subject to growth rate-dependent control (GRDC). Here we show that the A؉T-rich sequence located between positions ؊59 and ؊38 relative to the guaB transcription start site stimulates transcription from P guaB ϳ8-to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase ␣ subunit for activity. Like the rrnB P1 UP element, the P guaB UP element contains two independently acting subsites located at positions ؊59 to ؊47 and ؊46 to ؊38 and can stimulate transcription when placed upstream of the lacP1 promoter. We reveal a novel role for the P guaB UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the guaB transcription start site. These sequences are required for down-regulation of P guaB activity at lower growth rates.Escherichia coli RNA polymerase (RNAP) is a multisubunit complex consisting of an ␣ subunit homodimer, single ␤, ␤Ј, and subunits, and one of several subunits (14). The ␣ subunit contains an N-terminal domain (␣NTD; residues 8 to 232) and a C-terminal domain (␣CTD; residues 249 to 329) (5, 21, 44). ␣NTD and ␣CTD are separated by a flexible linker that is at least 13 amino acids long (5,20,25). ␣CTD plays important roles in transcription activation by contacting a number of transcription factors (6, 18) or through interacting with an AϩT-rich DNA sequence referred to as the UP element (16).UP elements stimulate transcription by recruiting ␣CTD to DNA (32, 43). The best-studied UP element spans the region from Ϫ59 to Ϫ38 at the rrnB P1 promoter (16). The rrnB P1 UP element contains two domains, a ϳ9-bp proximal UP element subsite located at positions Ϫ46 to Ϫ38 and a ϳ13-bp distal UP element subsite located at positions Ϫ59 to Ϫ47. Each subsite functions independently by recruiting one ␣CTD (11). The amino acid residues in ␣CTD that comprise the 265 determinant, including residues V264, R265, N268, N294, G296, K298, and S299, interact with UP element and A-tract sequences by contacting the DNA backbone, and R265 makes additional contacts with bases in the minor groove (4, 32, 43). These residues are the most important for rrnB P1 UP element utilization both in vivo and in vitro (13, 35). In the absence of a strong distal UP element subsite, ␣CTD bound to a consensus or near-consensus proximal UP element subsite also makes productive contacts with region 4.2 of 70 that serve to stimulate transcription (7,35).The E. coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, which together constitute the guaBA operon. The guaB and guaA genes encode IMP dehydrogenase and GMP synthetase, respectively, and are required for the biosynthesis of GMP from IMP (22, 42). P guaB...

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confidence: 68%

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Husnain

Thomas

2008

J Bacteriol

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“…Proteins involved in glycolysis, as well as purine and pyrimidine biosynthesis, are downregulated independently of RelA. This is in contrast to E. coli, in which the transcription of some genes involved in purine and pyrimidine biosynthesis is repressed by the stringent response (19,87).…”

Section: Discussionmentioning

confidence: 99%

Bacillus subtilisfunctional genomics: global characterization of the stringent response by proteome and transcriptome analysis

et al. 2002

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The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches. Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences. According to their altered synthesis patterns in response to DL-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes. However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis. The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp. The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG). On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins. A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp.

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“…In addition, growth-dependent regulation by guanosine 3'5'-bisphosphate appears to be a major control for setting the levels of gua operon expression appropriate to the growth rate [47]. This stringent control is responsible for regulating production of guanine ribonucleotide precursors of rRNA and RNA, both major cell components.…”

Section: Discussionmentioning

confidence: 99%

Specific Binding of DnaA Protein to a DnaA Box in the GuaB Gene of Escherichia Coli K12

Tesfa-Selase

Drabble

1996

European Journal of Biochemistry

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Expression of the guaBA operon of Escherichia coli is regulated by the DNA replication-initiating protein, DnaA. Two DnaA boxes, which are potential binding sites for DnaA, are present in the gua operon. One box (with 819 match to the DnaA box consensus sequence) is at the gua promoter; the other box, which has a consensus sequence, is on the non-transcribed strand within the guaB coding region approximately 200 bp downstream of the initiation codon. The binding in vitro of purified DnaA protein to these boxes was investigated by filter retention and gel retardation analysis, and by deoxyribonuclease I footprinting, using restriction fragments of gua operon DNA. DnaA protein was shown to bind specifically only to the fragment carrying the consensus sequence DnaA box, and to protect this box from deoxyribonuclease I. Transcription termination resulting from the binding of DnaA to this box within the guaB gene explains repression by DnaA of the gua operon in vivo.Keywords: guaBA operon ; transcriptional control ; DnaA protein; Escherichia coli.In Escherichia coli, bidirectional DNA replication is initiated at a distinct region of the chromosome known as oriC (origin of chromosome replication). DnaA protein, the product of the dnaA gene, is essential for initiation of replication from oriC both in vivo [l] and in vitro [2]. DnaA binds to oriC specifically and cooperatively at 9-bp repeats (DnaA boxes of consensus sequence TTAT(C,)CA(C,)A [3]) present four times within the minimal origin region of 245 bp. After binding, DnaA organizes the assembly of the replisome complex by directing other proteins required for initiation and replication to this site [4, 51.In addition to being required for replication initiation, DnaA also acts as a repressor and/or terminator of transcription for several genes. One of the genes affected is the dnaA gene itself 16, 71. Other genes for which there is direct or circumstantial evidence for regulation by DnaA are mioC [8] [12], pros (drpA) [13], and nrdAB [14]. The products of most of these genes are concerned with the major macromolecular processes of replication and modification of DNA, transcription and translation. The dnaA gene is autoregulated by the binding of DnaA to a DnaA box located between its two promoters [6,[15][16][17]. Messer et al. [7] proposed that when DnaA binds to a second DnaA box, within the dnaAcoding region, it acts as a transcriptional terminator. Termination of transcription was shown to be orientation dependent [18]; a DnaA box located on the non-transcribed strand, which is orientated in the direction of transcription, is necessary for transcription termination.We have recently reported [19] that the guaBA operon, which is responsible for the production of the final two enzymes for guanine nucleotide biosynthesis, is regulated by DnaA protein. When the intracellular concentration of DnaA is increased (by induction of a multicopy plasmid carrying the dnaA gene fused to a tac promoter), expression of the gua operon is reduced. Decreasing the intracellular...

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Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12

Cited by 25 publications

References 26 publications

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Bacillus subtilisfunctional genomics: global characterization of the stringent response by proteome and transcriptome analysis

Specific Binding of DnaA Protein to a DnaA Box in the GuaB Gene of Escherichia Coli K12

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