Expression systems and physiological control of promoter activity in bacteria

doi:10.1016/S1369-5274(98)80034-9

Current Opinion in Microbiology

Volume 1, Issue 3, June 1998, Pages 303-310

https://doi.org/10.1016/S1369-5274(98)80034-9 Get rights and content

Abstract

Promoter activity in vivo is not just dependent on the performance of the regulator/promoter pair which may predominantly control transcription initiation in response to a given signal, it also relies on overimposed mechanisms that connect the activity of individual promoters to the metabolic and energetic status of the bacterial cells. Such mechanisms—which frequently become limiting for biotechnological applications involving regulated promoters — include classic (i.e. cAMP/CRP-mediated) or alternative catabolite control checks, recruitment of protein intermediates of the phosphotransferase sugar transport system, coregulation through protein-induced DNA bending and the interplay of sigma factors during various growth stages.

References (71)

BH Kallipolitis et al.
Protein-protein communication: structural model of the repression complexes formed by CytR and the global regulator CRP
Cell
(1997)
J-H Kim et al.
Contacts between Bacillus subtilis catabolite regulatory protein CcpA and amyO target site
Nucleic Acids Res
(1997)
J Xu et al.
Activation of RpoS-dependent proP P2 transcription by the Fis protein in vitro
J Mol Biol
(1997)
A De Las Penas et al.
Sigma E is an essential sigma factor in Escherichia coli
J Bacteriol
(1997)
D Missiakas et al.
Modulation of the Escherichia coli sigmaE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins
Mol Microbiol
(1997)
S Marqués et al.
Role of σ^S in transcription from the positively controlled Pm promoter of the TOL plasmid of Pseudomonas putida
Mol Microbiol
(1995)
FJM Mojica et al.
In vivo supercolling of plasmid and chromosomal DNA in an Escherichia coli hns mutant
J Bacteriol
(1997)
A Kolb et al.
Transcriptional regulation by cAMP and its receptor protein
Ann Rev Biochem
(1993)
X Zhang et al.
Catabolite gene activator protein mutations affecting activity of the araBAD promoter
J Bacteriol
(1998)
J Pérez-Martin et al.
Clues and consequences of DNA bending in transcription
Ann Rev Microbiol
(1997)

M-J Lombardo et al.

Regulation of the Salmonella typhimurium pepT gene by cyclic AMP receptor protein (CRP) and FNR acting a hybrid CRP-FNR site

J Bacteriol

(1997)

G Sawers et al.

Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition

Mol Microbiol

(1997)

K Kimata et al.

cAMP receptor protein-cAMP plays a crucial role in glucose-lactose diauxie by activating the major glucose transporter gene in Escherichia coli

Proc Natl Acad Sci USA

(1997)

LJ Runyen-Janecky et al.

A divergently transcribed open reading frame is located upstream of the Pseudomonas aeruginosa vfr gene, a homolog of Escherichia coli crp

J Bacteriol

(1997)

AM Albus et al.

Vfr controls quorum sensing in Pseudomonas aeruginosa

J Bacteriol

(1997)

CH MacGregor et al.

The nucleotide sequence of the Pseudomonas aeruginosa pyr-crc-rph region and the purification of the crc gene product

J Bacteriol

(1996)

C Schleissner et al.

Catabolism of D-glucose by Pseudomonas putida U occurs via extracellular transformation in d-gluconic acid and induction of a specific gluconate transport system

Microbiology

(1997)

AE Sage et al.

A two-component response regulator, gltR, is required for glucose transport activity in Pseudomonas aeruginosa PAO1

J Bacteriol

(1996)

K Timmis et al.

Designing microorganisms for the treatment of toxic wastes

Annu Rev Microbiol

(1994)

I Cases et al.

Involvement of σ⁵⁴ in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter

Mol Microbiol

(1996)

WA Duetz et al.

Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation of chemostat culture

Appl Environ Microbiol

(1996)

C Sze et al.

Growth-phase dependent transcription of the σ⁵⁴-dependent Po promoter controlling the Pseudomonas-derived (methyl) phenol dmp operon of pVI150

J Bacteriol

(1996)

C Muller et al.

Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhIR

J Bacteriol

(1996)

WA Duetz et al.

Effect of growth rate, nutrient limitation and succinate on expression of TOL pathway enzymes in response to m-xylene in chemostat cultures of Pseudomonas putida (pWW0)

Microbiology

(1997)

SM McFall et al.

A tricarboxylic acid cycle intermediate regulating transcription of a chloroaromatic biodegradative pathway: fumarate-mediated repression of the clcABD operon

J Bacteriol

(1997)

JM Blatny et al.

Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon

Appl Environ Microbiol

(1997)

JM Blatny et al.

Improved broad-host-range RK2 vectors useful for high and low regulated gene expression levels in Gram-negative bacteria

Plasmid

(1997)

MH Saier et al.

The catabolite repressor/activator (Cra) protein or enteric bacteria

J Bacteriol

(1996)

A Mikulskis et al.

Regulation expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by Catabolite repressor Activator protein Cra

J Bacteriol

(1997)

M Crasnier-Mednansky et al.

Cra-mediated regulation of Escherichia coli adenylate cyclase

Microbiology

(1997)

MH Saier et al.

The bacterial phosphotransferase system: new frontiers 30 years later

Mol Microbiol

(1994)

PW Postma et al.

Phosphoenolpyruvate carbohydrate phosphotransferase system in bacteria

Microbiol Rev

(1993)

J Deutscher et al.

Regulation of carbon metabolism in Gram-positive bacteria by protein phosphorylation

Folia Microbiol

(1997)

MH Saier et al.

Catabolite repression and inducer control in Gram-positive bacteria

Microbiology

(1996)

BE Jones et al.

Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr

J Biol Chem

(1997)

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Expression systems and physiological control of promoter activity in bacteria

Abstract

Cell

Nucleic Acids Res

J Mol Biol

J Bacteriol

Mol Microbiol

Mol Microbiol

J Bacteriol

Transcriptional regulation by cAMP and its receptor protein

Ann Rev Biochem

Catabolite gene activator protein mutations affecting activity of the araBAD promoter

J Bacteriol

Clues and consequences of DNA bending in transcription

Ann Rev Microbiol

Regulation of the Salmonella typhimurium pepT gene by cyclic AMP receptor protein (CRP) and FNR acting a hybrid CRP-FNR site

J Bacteriol

Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition

Mol Microbiol

cAMP receptor protein-cAMP plays a crucial role in glucose-lactose diauxie by activating the major glucose transporter gene in Escherichia coli

Proc Natl Acad Sci USA

A divergently transcribed open reading frame is located upstream of the Pseudomonas aeruginosa vfr gene, a homolog of Escherichia coli crp

J Bacteriol

Vfr controls quorum sensing in Pseudomonas aeruginosa

J Bacteriol

The nucleotide sequence of the Pseudomonas aeruginosa pyr-crc-rph region and the purification of the crc gene product

J Bacteriol

Catabolism of D-glucose by Pseudomonas putida U occurs via extracellular transformation in d-gluconic acid and induction of a specific gluconate transport system

Microbiology

A two-component response regulator, gltR, is required for glucose transport activity in Pseudomonas aeruginosa PAO1

J Bacteriol

Designing microorganisms for the treatment of toxic wastes

Annu Rev Microbiol

Involvement of σ54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter

Mol Microbiol

Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation of chemostat culture

Appl Environ Microbiol

Growth-phase dependent transcription of the σ54-dependent Po promoter controlling the Pseudomonas-derived (methyl) phenol dmp operon of pVI150

J Bacteriol

Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhIR

J Bacteriol

Effect of growth rate, nutrient limitation and succinate on expression of TOL pathway enzymes in response to m-xylene in chemostat cultures of Pseudomonas putida (pWW0)

Microbiology

A tricarboxylic acid cycle intermediate regulating transcription of a chloroaromatic biodegradative pathway: fumarate-mediated repression of the clcABD operon

J Bacteriol

Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon

Appl Environ Microbiol

Improved broad-host-range RK2 vectors useful for high and low regulated gene expression levels in Gram-negative bacteria

Plasmid

The catabolite repressor/activator (Cra) protein or enteric bacteria

J Bacteriol

Regulation expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by Catabolite repressor Activator protein Cra

J Bacteriol

Cra-mediated regulation of Escherichia coli adenylate cyclase

Microbiology

The bacterial phosphotransferase system: new frontiers 30 years later

Mol Microbiol

Phosphoenolpyruvate carbohydrate phosphotransferase system in bacteria

Microbiol Rev

Regulation of carbon metabolism in Gram-positive bacteria by protein phosphorylation

Folia Microbiol

Catabolite repression and inducer control in Gram-positive bacteria

Microbiology

Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr

J Biol Chem

Involvement of σ⁵⁴ in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter

Growth-phase dependent transcription of the σ⁵⁴-dependent Po promoter controlling the Pseudomonas-derived (methyl) phenol dmp operon of pVI150