crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli

Cossart, Pascale; Groisman, Eduardo A.; Serre, Marie-Claude; Casadaban, Malcolm J.; Gicquel-Sanzey, Brigitte

doi:10.1128/jb.167.2.639-646.1986

Cited by 34 publications

(16 citation statements)

References 51 publications

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“…It is generally believed that the overexpression of many TFs can be deleterious to the cells. For example, the maximum concentration for typical TFs in bacteria is not much more than Ϸ100 nM; even the global regulator Crp is present only at Ϸ1,500 nM (35). Thus, typical bacterial TFs tend to be at lower concentrations in vivo and tend to have smaller K d.…”

Section: Resultsmentioning

confidence: 99%

Nonlinear protein degradation and the function of genetic circuits

Buchler

Gerland

Hwa

2005

Proc. Natl. Acad. Sci. U.S.A.

159

170

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The functions of most genetic circuits require a sufficient degree of cooperativity in the circuit components. Although mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control, cooperativity from other processes involved in the operation of the circuits can also play important roles. In this work, we examine a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins. Ample experimental evidence suggests that protein subunits can degrade less rapidly when associated in multimeric complexes, an effect we refer to as ''cooperative stability.'' For dimeric transcription factors, this effect leads to a concentration-dependence in the degradation rate because monomers, which are predominant at low concentrations, will be more rapidly degraded. Thus, cooperative stability can effectively widen the accessible range of protein levels in vivo. Through theoretical analysis of two exemplary genetic circuits in bacteria, we show that such an increased range is important for the robust operation of genetic circuits as well as their evolvability. Our calculations demonstrate that a few-fold difference between the degradation rate of monomers and dimers can already enhance the function of these circuits substantially. We discuss molecular mechanisms of cooperative stability and their occurrence in natural or engineered systems. Our results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits.amplification ͉ dimerization ͉ bistability ͉ oscillation I t is widely recognized that controlled proteolysis, where the degradation of one protein depends on the presence of another protein in the cell, can play an important regulatory role in genetic circuits (1). Here, we examine another effect of proteolysis that does not involve such regulatory control, but can nevertheless impact the function of genetic circuits in important ways. It is a kinetic, cooperative effect predicated on the following two essential ingredients: (i) the fact that many proteins perform their physiological functions as dimers or higher-order oligomers, and (ii) the tendency for the oligomers to be more stable (to proteolysis) than their monomeric components. This effect, referred to below as ''cooperative stability,'' has been discussed previously in qualitative terms in the context of many well-studied examples in prokaryotes and eukaryotes (1, 2). For example, in the SOS response of Escherichia coli, UmuC degradation is rescued by oligomerization with UmuDЈ 2 (3). Additionally, in Saccharomyces cerevisiae, the dimerization of a1 and ␣2 reduced the degradation rate by as much as 15-fold (4). Possible molecular mechanisms that give rise to cooperative stability include enhanced thermal stability of proteins upon mutual association [because thermal instability correlates with the rate of degradation (5, 6)] and the burial of proteolytic recogni...

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Section: Resultsmentioning

confidence: 99%

Nonlinear protein degradation and the function of genetic circuits

Buchler

Gerland

Hwa

2005

Proc. Natl. Acad. Sci. U.S.A.

159

170

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“…Cross-reacting proteins have been detected by immunological tests in a great variety of gramnegative bacteria (3). The gene that encodes CAP (crp) has been cloned and sequenced in three enteric species, i.e., E. coli (1,5), Salmonella typhimurium (6), and Shigellaflexneri (6), and the respective sequences are nearly identical. An attempt to identify a cAMP-CAP regulatory control factor in X. campestris pv.…”

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confidence: 99%

A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity

et al. 1990

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A DNA fragment from Xanthomonas campestris pv. campestris that partially restored the carbohydrate fermentation pattern of a cya crp Escherichia coli strain was cloned and expressed in E. coli. The nucleotide sequence of this fragment revealed the presence of a 700-base-pair open reading frame that coded for a protein highly similar to the catabolite activation factor (CAP) of E. coli (accordingly named CLP for CAP-like protein). An X. campestris pv. campestris clp mutant was constructed by reverse genetics. This strain was not affected in the utilization of various carbon sources but had strongly reduced pathogenicity. Production of xanthan gum, pigment, and extracellular enzymes was either increased or decreased, suggesting that CLP plays a role in the regulation of phytopathogenicity.

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“…The probability of cloning a gene will be affected by the Mini-Mu replicon clones are stable -enough to prepare plasmid DNA to be used for restriction digestion or DNA sequencing. The DNA sequences of the crp genes from Shigella flexneri and S. typhimurium have recently been determined from clones obtained by the mini-Mu replicon cloning system (12). A remarkable degree of conversation between the crp gene from these species and crp of E. coli K-12 was found.…”

Section: Discussionmentioning

confidence: 99%

Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons

Groisman¹,

Casadaban²

1987

J Bacteriol

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An in vivo cloning system that uses derivatives of the Escherichia coli bacteriophage Mu with plasmid replicons has been extended to five different species of the family Enterobacteriaceae. Mu and these mini-Mu replicon elements were introduced into strains of E. coli, Shigellaflexneri, Salmonella typhimurium, Citrobacter freundii, and Proteus mirabilis by infection, by transformation, or by conjugation with newly constructed broad-host-range plasmids containing insertions of these elements. Lysates from these cells, lysogenic for Mu and mini-Mu elements, were used to infect sensitive recipient strains of E. coli, S. typhimurium, and C. freundii. Drug-resistant transductants had mini-Mu replicon elements with inserts of different DNA sequences. All of the lysogens made could be induced to yield high phage titers, including those coming from strains that were resistant to Mu and Mu derivatives. Clones of 10 particular genes were isolated by their ability to complement specific mutations in the recipient strains, even in the presence of the E. coli K-12 restriction system. Some of the mini-Mu replicon elements used contained lac gene fusing segments and resulted in fusions of the lac operon to control regions in the cloned sequences.The cloning of DNA sequences responsible for a particular genetic trait has become a routine step in molecular biology. Although this is often done with in vitro recombinant DNA cloning procedures, in vivo methods have also been used. These include the isolation of lambdoid specialized transducing phages (35) and the generation of R-prime factors with transposable genetic elements (20,26). Cloning systems that use the transposable element bacteriophage Mu have been extensively used because of its high transposition frequency. They usually involve the use of conjugative plasmids or phage transduction to transfer the cloned segment to a new cell, away from the donor one which is usually killed by the disruptive effects of multiple transposition. Conjugation systems use either the full-length bacteriophage Mu (15,19,20), or mini-Mu derivatives (43, 44) that lack genes for Mu phage morphogenesis but that remain transposition proficient. Transduction cloning systems use mini-Mu elements to allow larger host DNA segments to be incorporated into the phage capsid, together with a helper phage to package the structures generated by the mini-Mu (24, 25). The presence of plasmid replicons in the mini-Mu elements allows the isolation of clones that have the DNA sequences on a plasmid (24,25).Bacteriophage Mu is a temperate phage with a broad host range. In addition to Escherichia coli K-12 and C, it can infect many strains of other members of the family Enterobacteriaceae, including Citrobacter freundii, Shigella sonnei, Shigella flexneri, Erwinia carotovora, Erwinia amylovora, Erwinia herbicola, Enterobacter cloacae, and Arizona species (42; our unpublished results). The wild-type Mu has two different host ranges, depending on the orientation of an invertable DNA segment with genes for two pairs ...

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crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli

Cited by 34 publications

References 51 publications

Nonlinear protein degradation and the function of genetic circuits

Nonlinear protein degradation and the function of genetic circuits

A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity

Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons

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