Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of <i>Pseudomonas putida</i> KT2440 and their counterparts in <i>Pseudomonas aeruginosa</i> PA01

Martínez-Bueno, Manuel; Tobes, Raquel; Rey, Manuel; Ramos, Juan L.

doi:10.1046/j.1462-2920.2002.00371.x

Cited by 90 publications

(89 citation statements)

References 62 publications

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“…The involvement of these regulatory systems in the expression of siderophore receptors provides an additional level of regulation, enabling P. aeruginosa to respond to the presence of siderophores in the environment as well as to levels of intracellular iron. This seems to be an important issue for environmental bacteria, as other species of Pseudomonas also contain large numbers of ECF sigma factors (37,56). In agreement with that, a genome-wide analysis of TonB-dependent receptors involved in regulatory pathways has indicated that these signaling systems are commonly found in several environmental bacteria but are only seldom present in dedicated human and animal pathogens (30).…”

Section: Discussionmentioning

confidence: 57%

The Heterologous Siderophores Ferrioxamine B and Ferrichrome Activate Signaling Pathways inPseudomonas aeruginosa

et al. 2006

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Pseudomonas aeruginosa secretes two siderophores, pyoverdine and pyochelin, under iron-limiting conditions. These siderophores are recognized at the cell surface by specific outer membrane receptors, also known as TonB-dependent receptors. In addition, this bacterium is also able to incorporate many heterologous siderophores of bacterial or fungal origin, which is reflected by the presence of 32 additional genes encoding putative TonB-dependent receptors. In this work, we have used a proteomic approach to identify the inducing conditions for P. aeruginosa TonB-dependent receptors. In total, 11 of these receptors could be discerned under various conditions. Two of them are only produced in the presence of the hydroxamate siderophores ferrioxamine B and ferrichrome. Regulation of their synthesis is affected by both iron and the presence of a cognate siderophore. Analysis of the P. aeruginosa genome showed that both receptor genes are located next to a regulatory locus encoding an extracytoplasmic function sigma factor and a transmembrane sensor. The involvement of this putative regulatory locus in the specific induction of the ferrioxamine B and ferrichrome receptors has been demonstrated. These results show that P. aeruginosa has evolved multiple specific regulatory systems to allow the regulation of TonB-dependent receptors.In most environments, the amount of free iron (approximately 10 Ϫ9 M) is below the concentration required by most microorganisms for growth (49). To fulfill their requirements for iron, bacteria have developed several strategies, including (i) the reduction of ferric to ferrous ions, (ii) the direct acquisition of iron from host proteins, (iii) the secretion of highaffinity iron-chelating compounds, called siderophores, and (iv) the uptake of heterologous siderophores (23). The transport of (heterologous) siderophores and heme/hemophores through the outer membranes of gram-negative bacteria is an energy-dependent process that needs the function of the ExbBExbD-TonB system. This system transduces the proton-motive force of the cytoplasmic membrane to the high-affinity outer membrane receptors, which are therefore also known as TonBdependent receptors (48). The synthesis of siderophores and their transport systems is negatively regulated by the Fur repressor protein (18). In addition, some siderophore transport systems are also positively regulated by the presence of their cognate siderophores (12). This level of regulation often involves extracytoplasmic function (ECF) sigma factors (56). The ECF family of sigma factors constitutes a group of environmentally responsive transcriptional factors of the RpoD ( 70 ) family that control a wide range of bacterial functions (39). The ECF factors involved in the regulation of iron uptake systems have been classified as the iron starvation class of sigma factors (35). One well-studied example is ferric dicitrate uptake by Escherichia coli (10

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Section: Discussionmentioning

confidence: 57%

The Heterologous Siderophores Ferrioxamine B and Ferrichrome Activate Signaling Pathways inPseudomonas aeruginosa

et al. 2006

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“…This in turn correlates with the fact that many members of the TetR family are found among microbes with abundant extracytoplasmic function sigma factors (52,227,236,277,444).…”

Section: Identification Of Tetr Family Members In Dna and Protein Datmentioning

confidence: 88%

“…Table 3 shows that members of the TetR family were detected in 144 microbial genomes belonging to 80 genera and 113 species of gram-positive and ␣-, ␤-, and ␥-proteobacteria, cyanobacteria, and archaea, indicating wide taxonomic distribution. We have found that proteins of the TetR family are encoded both in chromosomes and in plasmids, and the mobility of the latter elements could be a source of the spread of genes in this family via horizontal transfer (147, 383), as is also the case with catabolic genes (77,160,236,410,426), antimicrobial resistance determinants (20,100,124), and 16S rRNA genes (347).…”

Section: Identification Of Tetr Family Members In Dna and Protein Datmentioning

confidence: 99%

The TetR Family of Transcriptional Repressors

Ramos

Martínez-Bueno

Molina‐Henares

et al. 2005

Microbiol Mol Biol Rev

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976

1,133

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We have developed a general profile for the proteins of the TetR family of repressors. The stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix DNA binding motif and adjacent regions in the three-dimensional structures of TetR, QacR, CprB, and EthR, four family members for which the function and three-dimensional structure are known. We have detected a set of 2,353 nonredundant proteins belonging to this family by screening genome and protein databases with the TetR profile. Proteins of the TetR family have been found in 115 genera of gram-positive, α-, β-, and γ-proteobacteria, cyanobacteria, and archaea. The set of genes they regulate is known for 85 out of the 2,353 members of the family. These proteins are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which the family member is involved can be simple, as in TetR (i.e., TetR bound to the target operator represses tetA transcription and is released in the presence of tetracycline), or more complex, involving a series of regulatory cascades in which either the expression of the TetR family member is modulated by another regulator or the TetR family member triggers a cell response to react to environmental insults. Based on what has been learned from the cocrystals of TetR and QacR with their target operators and from their three-dimensional structures in the absence and in the presence of ligands, and based on multialignment analyses of the conserved stretch of 47 amino acids in the 2,353 TetR family members, two groups of residues have been identified. One group includes highly conserved positions involved in the proper orientation of the helix-turn-helix motif and hence seems to play a structural role. The other set of less conserved residues are involved in establishing contacts with the phosphate backbone and target bases in the operator. Information related to the TetR family of regulators has been updated in a database that can be accessed at www.bactregulators.org

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“…Comparisons with genome sequences of other bacteria reveal homologs of FecIRA whose encoding genes are arranged in the same order as fecIRA of E. coli (7). Particularly abundant are fecIRA homologs in Pseudomonas aeruginosa (46), Pseudomonas putida (34), Nitrosomonas europaea, and Bacteroides thetaiotaomicron, for which 10, 11, 15, and 23 fecIRA gene clusters, respectively, are predicted (V. Braun and S. Mahren, unpublished results). The E. coli fecIRA type of transmembrane transcriptional control thus seems to represent a paradigm of a large number of similar transcriptional control devices in many gram-negative bacteria.…”

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confidence: 96%

Defined Inactive FecA Derivatives Mutated in Functional Domains of the Outer Membrane Transport and Signaling Protein of Escherichia coli K-12

Sauter

Braun

2004

J Bacteriol

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The FecA outer membrane protein of Escherichia coli functions as a transporter of ferric citrate and as a signal receiver and signal transmitter for transcription initiation of the fec transport genes. Three FecA regions for which functional roles have been predicted from the crystal structures were mutagenized: (i) loops 7 and 8, which move upon binding of ferric citrate and close the entrance to the ferric citrate binding site; (ii) the dinuclear ferric citrate binding site; and (iii) the interface between the globular domain and the ␤-barrel. Deletion of loops 7 and 8 abolished FecA transport and induction activities. Deletion of loops 3 and 11 also inactivated FecA, whereas deletion of loops 9 and 10 largely retained FecA activities. The replacement of arginine residue R365 or R380 and glutamine Q570, which are predicted to serve as binding sites for the negatively charged dinuclear ferric citrate, with alanine resulted in inactive FecA, whereas the binding site mutant R438A retained approximately 50% of the FecA induction and transport activities. Residues R150, E541, and E587, conserved among energy-coupled outer membrane transporters, are predicted to form salt bridges between the globular domain and the ␤-barrel and to contribute to the fixation of the globular domain inside the ␤-barrel. Mutations E541A and E541R affected FecA induction and transport activity slightly, whereas mutations E587A and E587R more strongly reduced FecA activity. The double mutations R150A E541R and R150A E587R nearly abolished FecA activity. Apparently, the salt bridges are less important than the individual functions these residues seem to have for FecA activity. Comparison of the properties of the FecA, FhuA, FepA, and BtuB transporters indicates that although they have very similar crystal structures, the details of their functional mechanisms differ.

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Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01

Cited by 90 publications

References 62 publications

The Heterologous Siderophores Ferrioxamine B and Ferrichrome Activate Signaling Pathways inPseudomonas aeruginosa

The Heterologous Siderophores Ferrioxamine B and Ferrichrome Activate Signaling Pathways inPseudomonas aeruginosa

The TetR Family of Transcriptional Repressors

Defined Inactive FecA Derivatives Mutated in Functional Domains of the Outer Membrane Transport and Signaling Protein of Escherichia coli K-12

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