Bacterial transcriptional regulators for degradation pathways of aromatic compounds

Abstract

Human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals. The interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons. In addition, regulation of catabolic pathway expression has attracted the interest of numerous different groups, and several catabolic pathway regulators have been exemplary for understanding transcription control mechanisms. More recently, information about regulatory systems has been used to construct whole-cell living bioreporters that are used to measure the quality of the aqueous, soil, and air environment. The topic of biodegradation is relatively coherent, and this review presents a coherent overview of the regulatory systems involved in the transcriptional control of catabolic pathways. This review summarizes the different regulatory systems involved in biodegradation pathways of aromatic compounds linking them to other known protein families. Specific attention has been paid to describing the genetic organization of the regulatory genes, promoters, and target operon(s) and to discussing present knowledge about signaling molecules, DNA binding properties, and operator characteristics, and evidence from regulatory mutants. For each regulator family, this information is combined with recently obtained protein structural information to arrive at a possible mechanism of transcription activation. This demonstrates the diversity of control mechanisms existing in catabolic pathways.

FIG. 1.

Typical examples of the genetic organization of pathways for degradation of aromatic compounds. The regulatory genes are indicated in grey. (A) The tfd operons of R. eutropha JMP134(pJP4). The LysR-type transcription regulator TfdR/S regulates the tfdA, tfdC, and tfdD_II promoters. (B) The ben and cat operons of Acinetobacter sp. strain ADP1. benM and catM code for LysR-type transcription regulators, which act on four promoters: benP, benA, catA, and catB. (C) The pca and pob clusters of Acinetobacter sp. strain ADP1. The genes pcaU and pobR code for IclR-type regulators, acting on the pcaI and pobA promoters. (D) The hpa cluster of E. coli with HpaA as the XylS/AraC-type regulator. (E) The xyl operons for toluene degradation present on the TOL plasmid of P. putida mt2. XylR is the NtrC-type regulator acting on P_u and P_s, whereas XylS is the exemplar for the XylS/AraC family and acts on the P_m promoter. (F) The paa cluster in E. coli strain W, with the GntR-type regulator PaaX regulating the paaA promoter. (G) The aph cluster in C. testosteroni strain TA441, encoding the aphS (GntR-type) and aphR (XylR-type) regulators. (H) The cym and cmt clusters in P. putida F1 with the TetR-type regulator cymR. (I) The tod cluster of P. putida DOT-T1 with the two-component regulatory system todST. Straight arrows represent transcripts produced after specific regulatory action of the indicated regulator. Parabolic arrows point to the site of action of a specific regulator in cases when multiple regulators are involved. Hooked arrows indicate specific promoter names, where necessary.

FIG. 2.

Schematic domain organization of the different regulator families. The domain containing the HTH DNA binding motif is indicated in black. The domain bound by the chemical inducer is indicated in white.

FIG. 3.

Tetrameric structure of CbnR in side (A) and top (B) views (155). Subunits A, B, P, and Q are shown in yellow, magenta, cyan, and green, respectively. The symmetry axis in the molecule is shown as a red arrow. The location of the coiled-coil linkers (see the text) and DNA binding domains (DBD) are indicated, which would impose a 60°C bending angle on the binding site on the DNA. Reprinted from reference with permission from the publisher and from the authors.

FIG. 4.

Schematic steps in transcription activation by LysR-type transcription regulators. (A) Two subunits of the regulator tetramer binds to the RBS and two other subunits bind to the ABS present on the −35 promoter region. (B and C) In the presence of an inducer, the regulatory protein shifts its interaction on the ABS to −42. By interacting with the α-CTD domain of the RNAP, it directs this to bind a so-called UP-DNA sequence motif, which is located between the RBS and ABS (B). This increases the binding affinity of RNAP for the promoter and initiates transcription (C). mRNA is drawn as a zig-zagged arrow.

FIG. 5.

IclR dimer and tetramer arrangements as derived from the crystal structure (275). (A) The dimer interface is formed exclusively between the two HTH DNA binding domains. Monomers are colored red or green. (B) The tetramer viewed from the top is composed of two asymmetric dimers shown in four different colors: red and green for one asymmetric unit, and yellow and magenta for the other. The tetramer interface is formed exclusively between signal binding domains. Reprinted from reference with permission from the publisher and from the authors.

FIG. 6.

Structures of the Rob-micF and the MarA-mar DNA complex (114). The structurally similar N-terminal DNA binding domains of Rob and MarA are colored orange, and the unique C-terminal domain of Rob is shaded blue. (A) The N-terminal HTH motif of Rob contacting bases of the binding site. (B) MarA and the induced bend on its DNA binding site. Both HTH modules are situated in adjacent major-groove surfaces on one side of the DNA. Reprinted from reference with permission from the publisher and from the authors.

FIG. 7.

Structure of the FadR-DNA complex (273). The paired recognition helices are in the major groove, and the two wings are within the flanking minor grooves. Note that the DNA is bent toward the FadR protein, leaving a slight contraction in the major groove as a result. Reprinted from reference with permission from the publisher and from the authors.

FIG. 8.

Two modes of repression by GntR-type regulators. (A) The repressor bound to the −10 promoter region impairs RNA polymerase binding. (B) Binding of an inducer abolishes DNA binding upon which RNA polymerase can start transcription. (C) Repressor bound between the transcription and translation start site impairs open-complex formation. (D) Binding of the inducer to the repressor abolishes DNA binding activity. Regulatory proteins are shown as ellipsoids.

FIG. 9.

The structure of the DNA binding domain of the MarR dimer (4). One subunit is in grey, and the second is coloured. The first six N-terminal residues of MarR are not included in the structure. The α1- and α5-helices are the linkers between the central domain and the N- and C-terminal part of the protein. The central domain contains the α4-helix, expected to be the recognition helix of the DNA binding motif. Reprinted from reference with permission from the publisher and from the authors.

FIG. 10.

Crystal structures of NtrC1^AC and NtrC1^C (123). (A) Dimer solution structure of NtrC1^AC. The monomers are colored gray and gold. The GAFTGA and β-hairpin loops of the central ATPase domain are colored blue and green, respectively. ADP and the catalytic arginine residue (R293) are shown in a ball-and-stick representation. R293 cannot contact ADP in the dimer. (B) Heptameric structure of A-domain-deleted NtrC^C. The top view (left) illustrates how the protomers (labeled A to G) pack to a heptamer. GAFTGA loops (blue) and β-hairpin (green) point toward the central pore in the heptamer. The side view is also shown (right). Reprinted from reference with permission from the publisher and from the authors.

FIG. 11.

Schematic mode of activation of XylR/DmpR-type regulators. (A) The inactive regulator dimer binds its inducer, which results in a protein conformation change. (B) Binding of ATP triggers multimerization to a hexamer (or heptamer). (C) ATP hydrolysis coupled to correct interaction with RNA polymerase triggers transcription activation. (D) Dissociation of the hexamer to a dimer on ATP hydrolysis and dissociation of the inducer. The stages during which the DNA is contacted are not shown.