1
|
Kabata H, Aramaki H, Shimamoto N. Single-molecule evidence for a chemical ratchet in binding between the cam repressor and its operator. NANOSCALE 2022; 14:13315-13323. [PMID: 36065798 DOI: 10.1039/d2nr03454a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The affinity for regulator-operator binding on DNA sometimes depends on the length of the DNA harboring the operator, which is known as the antenna effect. One-dimensional diffusion along DNA has been suggested to be the cause, but this may contradict the binding affinity independent of the reaction pathways, which is derived from the detailed balance of the reaction at equilibrium. Recently, the chemical ratchet was proposed to solve this contradiction by suggesting a stationary state containing microscopic non-equilibrium. In a single-molecule observation, P. putida CamR molecules associate with their operator via one-dimensional diffusion along the DNA, while they mostly dissociated from the operator without the diffusion. Consistently, the observed overall association rate was dependent on the DNA length, while the overall dissociation rate was not, leading to an antenna effect. E. coli RNA polymerase did not show this behavior, and thus it is a specific property of a protein. The bipartite interaction domains containing the helix-turn-helix motif are speculated to be one of the possible causes. The biological significance of the chemical ratchet and a model for its microscopic mechanism are also discussed.
Collapse
Affiliation(s)
- Hiroyuki Kabata
- National Institute of Genetics, and Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
| | - Hironori Aramaki
- Department of Molecular and Life Science, Faculty of Pharmacy, Daiichi University of Pharmacy, 22-1 Tamagawa-cho, Minami-ku, Fukuoka, 815-8511, Japan
| | - Nobuo Shimamoto
- National Institute of Genetics, and Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
| |
Collapse
|
2
|
The TetR Family Repressor HpaR Negatively Regulates the Catabolism of 5-Hydroxypicolinic Acid in Alcaligenes faecalis JQ135 by Binding to Two Unique DNA Sequences in the Promoter of hpa Operon. Appl Environ Microbiol 2022; 88:e0239021. [PMID: 35138929 DOI: 10.1128/aem.02390-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5-Hydroxypicolinic acid (5HPA), an important natural pyridine derivative, is microbially degraded in the environment. Previously, a gene cluster hpa responsible for 5HPA degradation has been identified in Alcaligenes faecalis JQ135. However, the transcription regulation mechanism of the hpa cluster is still unknown. In this study, the transcription start site and promoter of hpa operon was identified. Quantitative reverse transcription-PCR and promoter activity analysis indicated that the transcription of hpa operon was negatively regulated by a TetR family regulator HpaR, whereas the transcription of hpaR itself was not regulated by HpaR. Electrophoretic mobility shift assay and DNase I footprinting revealed that HpaR bound to two DNA sequences, covering -35 region and -10 region, respectively, in the promoter region of hpa operon. Interestingly, the two binding sequences are partial-palindromic with 3-4 mismatches, and are complementary with each other. 5HPA acted as a ligand of HpaR preventing HpaR from binding to promoter region thus derepressing the transcription of hpa operon. The study revealed that HpaR binds to two unique complementary sequences of the promoter of hpa operon to negatively regulate the catabolism of 5HPA. IMPORTANCE This study revealed that the transcription of hpa operon was negatively regulated by a TetR family regulator HpaR. The binding of HpaR to the promoter of hpa operon has the following unique features: (1) HpaR has two independent binding sites in the promoter of the hpa operon, covering -35 region and -10 region, respectively. (2) the palindrome sequences of the two binding sites are complementary with each other. (3) both of the two binding sites include a 10-nt partial palindrome sequences with 3-4 mismatches. This study provides new insights into the binding features of the TetR family regulator with DNA sequences.
Collapse
|
3
|
Zaide G, Elia U, Cohen-Gihon I, Israeli M, Rotem S, Israeli O, Ehrlich S, Cohen H, Lazar S, Beth-Din A, Shafferman A, Zvi A, Cohen O, Chitlaru T. Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. Microorganisms 2020; 8:microorganisms8121896. [PMID: 33265965 PMCID: PMC7760947 DOI: 10.3390/microorganisms8121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
Collapse
|
4
|
Roth S, Funk I, Hofer M, Sieber V. Chemoenzymatic Synthesis of a Novel Borneol-Based Polyester. CHEMSUSCHEM 2017; 10:3574-3580. [PMID: 28772002 DOI: 10.1002/cssc.201701146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Terpenes are a class of natural compounds that have recently moved into the focus as a bio-based resource for chemical production, owing to their abundance, their mostly cyclic structures, and the presence of olefin or single hydroxy groups. To apply this raw material in new industrial fields, a second hydroxy group is inserted into borneol by cytochrome P450cam (CYP101) enzymes in a whole-cell catalytic biotransformation with Pseudomonas putida KT2440. Next, a semi-continuous batch system was developed to produce 5-exo-hydroxyborneol with a final concentration of 0.54 g L-1 . The bifunctional terpene was then used for the synthesis of a bio-based polyester by a solvent-free polycondensation reaction. The resulting polymer showed a glass transition temperature of around 70 °C and a molecular weight in the range of 2000-4000 g mol-1 (Mw ). These results show that whole-cell catalytic biotransformation of terpenes could lead to bio-based, higher-functionalized monomers, which might be basic raw materials for different fields of application, such as biopolymers.
Collapse
Affiliation(s)
- Steffen Roth
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Irina Funk
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Michael Hofer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Bio, Electro and Chemocatalysis BioCat, Straubing Branch, Schulgasse 11a, 94315, Straubing, Germany
| | - Volker Sieber
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Bio, Electro and Chemocatalysis BioCat, Straubing Branch, Schulgasse 11a, 94315, Straubing, Germany
| |
Collapse
|
5
|
Aramaki H, Kabata H, Takeda S, Itou H, Nakayama H, Shimamoto N. Formation of repressor-inducer-operator ternary complex: negative cooperativity of d-camphor binding to CamR. Genes Cells 2011; 16:1200-7. [DOI: 10.1111/j.1365-2443.2011.01563.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
6
|
Vargas P, Felipe A, Michán C, Gallegos MT. Induction of Pseudomonas syringae pv. tomato DC3000 MexAB-OprM multidrug efflux pump by flavonoids is mediated by the repressor PmeR. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1207-19. [PMID: 21649511 DOI: 10.1094/mpmi-03-11-0077] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this study, we have analyzed the expression of the Pseudomonas syringae pv. tomato DC3000 mexAB-oprM efflux pump operon and of the regulatory gene pmeR, and we have investigated the role of the PmeR protein on transcription from both promoters. We demonstrate that mexAB-oprM and pmeR are expressed in vivo at a relatively high and moderate basal level, respectively, which, in both cases, increases in the presence of different flavonoids and other compounds, such as butyl and methylparaben. We show that PmeR is the local repressor of the mexAB-oprM promoter and is able to regulate its own expression. The mechanism for this regulation includes binding to a pseudopalindromic operator site which overlaps both mexAB-oprM and pmeR promoters. We have also proven that flavonoids are able to interact with PmeR and induce a conformational change that interferes with the DNA binding ability of PmeR, thereby modulating mexAB-oprM and pmeR expression. Finally, we demonstrate by in vivo experiments that the PmeR/MexAB-OprM system contributes to the colonization of tomato plants. These results provide new insight into a transcriptional regulator and a transport system that play essential roles in the ability of P. syringae pv. tomato DC3000 to resist the action of flavonoids produced by the host.
Collapse
Affiliation(s)
- Paola Vargas
- Department of Soil Microbiology and Symbiotic System, Estación Experimental del Zaidin, Granada, Spain
| | | | | | | |
Collapse
|
7
|
Yamamoto M, Ueda A, Kudo M, Matsuo Y, Fukushima J, Nakae T, Kaneko T, Ishigatsubo Y. Role of MexZ and PA5471 in transcriptional regulation of mexXY in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2009; 155:3312-3321. [PMID: 19589837 DOI: 10.1099/mic.0.028993-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
MexXY, a drug efflux pump in Pseudomonas aeruginosa, confers resistance to aminoglycoside antibiotics. We recently reported that MexZ binds to the promoter region of the mexXY operon. Electrophoretic mobility shift assay (EMSA) using recombinant MexZ and oligonucleotide probes prepared from the intergenic region between mexZ and mexX revealed that MexZ binds to a 20 bp palindromic sequence. Culture of P. aeruginosa in the presence of tetracycline induced higher levels of MexX and MexZ, as measured by immunoblotting and EMSA, than in the absence of antibiotics. When MexZ was expressed by a mexZ expression plasmid, the plasmid-borne MexZ repressed drug-induced MexX production, further confirming that MexZ acts as a repressor of the mexXY operon. PA5471 protein has been reported to be essential for drug-induced MexXY production. Similarly to that report, we observed that plasmid-borne PA5471 induced both MexX and MexZ production in PAO1 cells. Interestingly, interaction between MexZ and PA5471 was observed in a yeast two-hybrid assay. Furthermore, EMSA and in vitro transcription assays revealed that interaction between PA5471 and MexZ reduced MexZ DNA-binding ability, leading to mexXY transcription. These findings contribute to the understanding of the molecular mechanisms underlying the transcriptional regulation of mexZ and mexXY by drug-induced PA5471 expression.
Collapse
Affiliation(s)
- Masaki Yamamoto
- Department of Internal Medicine and Clinical Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsuhisa Ueda
- Department of Internal Medicine and Clinical Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Makoto Kudo
- Department of Internal Medicine and Clinical Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yasuhiro Matsuo
- Department of Internal Medicine and Clinical Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Jun Fukushima
- Department of Biotechnology, Akita Prefectural University, Akita 010-0195, Japan
| | - Taiji Nakae
- Antimicrobial Research Center, Kitasato Institute, Kitasato University, Sagamihara 228-8555, Japan
| | - Takeshi Kaneko
- Department of Pulmonary Medicine, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Yoshiaki Ishigatsubo
- Department of Internal Medicine and Clinical Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| |
Collapse
|
8
|
Lin J, Cagliero C, Guo B, Barton YW, Maurel MC, Payot S, Zhang Q. Bile salts modulate expression of the CmeABC multidrug efflux pump in Campylobacter jejuni. J Bacteriol 2005; 187:7417-24. [PMID: 16237025 PMCID: PMC1272998 DOI: 10.1128/jb.187.21.7417-7424.2005] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CmeABC, a multidrug efflux pump, is involved in the resistance of Campylobacter jejuni to a broad spectrum of antimicrobial agents and is essential for Campylobacter colonization in animal intestine by mediating bile resistance. Previously, we have shown that expression of this efflux pump is under the control of a transcriptional repressor named CmeR. Inactivation of CmeR or mutation in the cmeABC promoter (PcmeABC) region derepresses cmeABC, leading to overexpression of this efflux pump. However, it is unknown if the expression of cmeABC can be conditionally induced by the substrates it extrudes. In this study, we examined the expression of cmeABC in the presence of various antimicrobial compounds. Although the majority of the antimicrobials tested did not affect the expression of cmeABC, bile salts drastically elevated the expression of this efflux operon. The induction was observed with both conjugated and unconjugated bile salts and was in a dose- and time-dependent manner. Experiments using surface plasmon resonance demonstrated that bile salts inhibited the binding of CmeR to PcmeABC, suggesting that bile compounds are inducing ligands of CmeR. The interaction between bile salts and CmeR likely triggers conformational changes in CmeR, resulting in reduced binding affinity of CmeR to PcmeABC. Bile did not affect the transcription of cmeR, indicating that altered expression of cmeR is not a factor in bile-induced overexpression of cmeABC. In addition to the CmeR-dependent induction, some bile salts (e.g., taurocholate) also activated the expression of cmeABC by a CmeR-independent pathway. Consistent with the elevated production of CmeABC, the presence of bile salts in culture media resulted in increased resistance of Campylobacter to multiple antimicrobials. These findings reveal a new mechanism that modulates the expression of cmeABC and further support the notion that bile resistance is a natural function of CmeABC.
Collapse
Affiliation(s)
- Jun Lin
- Department of Veterinary Microbiology and Preventive Medicine, 1116 Veterinary Medicine Complex, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | | | | | |
Collapse
|
9
|
Maenaka K, Fukushi K, Aramaki H, Shirakihara Y. Expression, crystallization and preliminary diffraction studies of the Pseudomonas putida cytochrome P450cam operon repressor CamR. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:796-8. [PMID: 16511161 PMCID: PMC1952358 DOI: 10.1107/s1744309105023225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 07/21/2005] [Indexed: 11/10/2022]
Abstract
The Pseudomonas putida cam repressor (CamR) is a homodimeric protein that binds to the camO DNA operator to inhibit the transcription of the cytochrome P450cam operon camDCAB. CamR has two functional domains: a regulatory domain and a DNA-binding domain. The binding of the inducer D-camphor to the regulatory domain renders the DNA-binding domain unable to bind camO. Native CamR and its selenomethionyl derivative have been overproduced in Escherichia coli and purified. Native CamR was crystallized under the following conditions: (i) 12-14% PEG 4000, 50 mM Na PIPES, 0.1 M KCl, 1% glycerol pH 7.3 at 288 K with and without camphor and (ii) 1.6 M P(i), 50 mM Na PIPES, 2 mM camphor pH 6.7 at 278 K. The selenomethionyl derivative CamR did not crystallize under either of these conditions, but did crystallize using 12.5% PEG MME 550, 25 mM Na PIPES, 2.5 mM MgCl2 pH 7.3 at 298 K. Preliminary X-ray diffraction studies revealed the space group to be orthorhombic (P2(1)2(1)2), with unit-cell parameters a = 48.0, b = 73.3, c = 105.7 A. Native and selenomethionyl derivative data sets were collected to 3 A resolution at SPring-8 and the Photon Factory.
Collapse
Affiliation(s)
- Katsumi Maenaka
- Structural Biology Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Kouji Fukushi
- Structural Biology Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hironori Aramaki
- Department of Molecular Biology, Daiichi College of Pharmaceutical Sciences, Minami-ku, Fukuoka 815-8511, Japan
| | - Yasuo Shirakihara
- Structural Biology Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
10
|
Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R. The TetR family of transcriptional repressors. Microbiol Mol Biol Rev 2005; 69:326-56. [PMID: 15944459 PMCID: PMC1197418 DOI: 10.1128/mmbr.69.2.326-356.2005] [Citation(s) in RCA: 848] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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, alpha-, beta-, and gamma-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.
Collapse
Affiliation(s)
- Juan L Ramos
- Department of Plant Biochemistry and Molecular and Cellular Biology, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas, Granada, Spain.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Matsuo Y, Eda S, Gotoh N, Yoshihara E, Nakae T. MexZ-mediated regulation ofmexXYmultidrug efflux pump expression inPseudomonas aeruginosaby binding on themexZ-mexXintergenic DNA. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09732.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
12
|
Engohang-Ndong J, Baillat D, Aumercier M, Bellefontaine F, Besra GS, Locht C, Baulard AR. EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator. Mol Microbiol 2004; 51:175-88. [PMID: 14651620 DOI: 10.1046/j.1365-2958.2003.03809.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ethionamide (ETH) is an important second-line antitubercular drug used for the treatment of patients infected with multidrug-resistant Mycobacterium tuberculosis. Although ETH is a structural analogue of isoniazid, only little cross-resistance to these two drugs is observed among clinical isolates. Both isoniazid and ETH are pro-drugs that need to be activated by mycobacterial enzymes to exert their antimicrobial activity. We have recently identified two M. tuberculosis genes, Rv3854c (ethA) and Rv3855 (ethR), involved in resistance to ETH. ethA encodes a protein that belongs to the Flavin-containing monooxygenase family catalysing the activation of ETH. We show here that ethR, which encodes a repressor belonging to the TetR/CamR family of transcriptional regulators, negatively regulates the expression of ethA. By the insertion of the ethA promoter region upstream of the lacZ reporter gene, overexpression of ethR in trans was found to cause a strong inhibition of ethA expression, independently of the presence of ETH in the culture media. Electrophoretic mobility shift assays indicated that EthR interacts directly with the ethA promoter region. This interaction was confirmed by DNA footprinting analysis, which, in addition, identified the EthR-binding region. Unlike other TetR/CamR members, which typically bind 15 bp operators, EthR recognises an unusually long 55 bp region suggesting multimerization of the repressor on its operator. Identification by primer-extension of the ethA transcriptional start site indicated that it is located within the EthR-binding region. Taken together, bacterial two-hybrid experiments and gel filtration assays suggested a dimerization of EthR in the absence of its operator. In contrast, surface plasmon resonance analyses showed that eight EthR molecules bind cooperatively to the 55 bp operator, which represents a novel repression mechanism for a TetR/CamR member.
Collapse
Affiliation(s)
- Jean Engohang-Ndong
- INSERM-U447, Institut de Biologie de Lille - Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 245, 59019 Lille Cedex, France
| | | | | | | | | | | | | |
Collapse
|
13
|
Trigui M, Pulvin S, Truffaut N, Thomas D, Poupin P. Molecular cloning, nucleotide sequencing and expression of genes encoding a cytochrome P450 system involved in secondary amine utilization in Mycobacterium sp. strain RP1. Res Microbiol 2004; 155:1-9. [PMID: 14759702 DOI: 10.1016/j.resmic.2003.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 09/12/2003] [Indexed: 11/18/2022]
Abstract
Mycobacterium sp. strain RP1 degrades morpholine, piperidine, and pyrrolidine and is able to use these compounds as the sole source of carbon, nitrogen, and energy. Cytochrome P450 (MorA) is involved in the biodegradation of these secondary amines. A 3.9-PstI genomic DNA fragment, containing the gene encoding MorA, was cloned and sequenced. Four open reading frames were detected on this DNA fragment. The first encoded a cytochrome P450 designated as MorA which was the second member of the CYP151 family and was named CYP151A2. The second open reading frame (morB) featured a [3Fe-4S] type of ferredoxin. A third gene (morC), exhibiting sequence identity to known reductases, and a fourth truncated gene encoding a putative glutamine reductase (orf1' ), were found downstream of morB. Recombinant MorA cytochrome P450 was purified to homogeneity from Escherichia coli. The purified enzyme was a monomeric soluble protein with an apparent Mr of about 45,000. CYP151A2 catalyzed the ring cleavage of the secondary amines and the Vmax/KMapp values indicated that pyrrolidine is the preferred substrate for this monooxygenase.
Collapse
Affiliation(s)
- Mohamed Trigui
- Laboratoire de Technologie Enzymatique, MR 6022 CNRS, Université de Technologie de Compiègne, BP 20529, 60205 Compiègne, France
| | | | | | | | | |
Collapse
|
14
|
Conlon KM, Humphreys H, O'Gara JP. icaR encodes a transcriptional repressor involved in environmental regulation of ica operon expression and biofilm formation in Staphylococcus epidermidis. J Bacteriol 2002; 184:4400-8. [PMID: 12142410 PMCID: PMC135245 DOI: 10.1128/jb.184.16.4400-4408.2002] [Citation(s) in RCA: 230] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilm formation in Staphylococcus epidermidis is dependent upon the ica operon-encoded polysaccharide intercellular adhesin, which is subject to phase-variable and environmental regulation. The icaR gene, located adjacent to the ica operon, appears to be a member of the tetR family of transcriptional regulators. In the reference strain RP62A, reversible inactivation of the ica operon by IS256 accounts for 25 to 33% of phase variants. In this study, icaA and icaR regulation were compared in RP62A and a biofilm-forming clinical isolate, CSF41498, in which IS256 is absent. Predictably, ica operon expression was detected only in wild-type CSF41498 and RP62A but not in non-IS256-generated phase variants. In contrast, the icaR gene was not expressed in RP62A phase variants but was expressed in CSF41498 variants. An icaR::Em(r) insertion mutation in CSF41498 resulted in an at least a 5.8-fold increase in ica operon expression but did not significantly alter regulation of the icaR gene itself. Activation of ica operon transcription by ethanol in CSF41498 was icaR dependent. In contrast, a small but significant induction of ica by NaCl and glucose (NaCl-glucose) was observed in the icaR::Em(r) mutant. In addition, transcription of the icaR gene itself was not significantly affected by NaCl-glucose but was repressed by ethanol. Expression of the ica operon was induced by ethanol or NaCl-glucose in phase variants of CSF41498 (icaR+) but not in RP62A variants (icaR deficient). These data indicate that icaR encodes a repressor of ica operon transcription required for ethanol but not NaCl-glucose activation of ica operon expression and biofilm formation.
Collapse
Affiliation(s)
- Kevin M Conlon
- Department of Microbiology, RCSI Education and Research Centre, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | | | | |
Collapse
|
15
|
Grkovic S, Brown MH, Schumacher MA, Brennan RG, Skurray RA. The staphylococcal QacR multidrug regulator binds a correctly spaced operator as a pair of dimers. J Bacteriol 2001; 183:7102-9. [PMID: 11717268 PMCID: PMC95558 DOI: 10.1128/jb.183.24.7102-7109.2001] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2001] [Accepted: 09/20/2001] [Indexed: 11/20/2022] Open
Abstract
Expression of the Staphylococcus aureus plasmid-encoded QacA multidrug transporter is regulated by the divergently encoded QacR repressor protein. To circumvent the formation of disulfide-bonded degradation products, site-directed mutagenesis to replace the two cysteine residues in wild-type QacR was undertaken. Analysis of a resultant cysteineless QacR derivative indicated that it retained full DNA-binding activities in vivo and in vitro and continued to be fully proficient for the mediation of induction of qacA expression in response to a range of structurally dissimilar multidrug transporter substrates. The cysteineless QacR protein was used in cross-linking and dynamic light-scattering experiments to show that its native form was a dimer, whereas gel filtration indicated that four QacR molecules bound per DNA operator site. The addition of inducing compounds led to the dissociation of the four operator-bound QacR molecules from the DNA as dimers. Binding of QacR dimers to DNA was found to be dependent on the correct spacing of the operator half-sites. A revised model proposed for the regulation of qacA expression by QacR features the unusual characteristic of one dimer of the regulatory protein binding to each operator half-site by a process that does not appear to require the prior self-assembly of QacR into tetramers.
Collapse
Affiliation(s)
- S Grkovic
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | | | | | | |
Collapse
|
16
|
Poupin P, Ducrocq V, Hallier-Soulier S, Truffaut N. Cloning and characterization of the genes encoding a cytochrome P450 (PipA) involved in piperidine and pyrrolidine utilization and its regulatory protein (PipR) in Mycobacterium smegmatis mc2155. J Bacteriol 1999; 181:3419-26. [PMID: 10348853 PMCID: PMC93808 DOI: 10.1128/jb.181.11.3419-3426.1999] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/1998] [Accepted: 04/06/1999] [Indexed: 11/20/2022] Open
Abstract
Transposon mutagenesis of Mycobacterium smegmatis mc2155 enabled the isolation of a mutant strain (called LGM1) altered in the regulation of piperidine and pyrrolidine utilization. The complete nucleotide sequence of the gene inactivated in mutant LGM1 was determined from the wild-type strain. This gene (pipR) encoded a member of the GntR family of bacterial regulatory proteins. An insertion element (IS1096), previously described for M. smegmatis, was detected downstream of the gene pipR. Three additional open reading frames were found downstream of IS1096. The first open reading frame (pipA) appeared to encode a protein identified as a cytochrome P450 enzyme. This gene is the first member of a new family, CYP151. By a gene replacement experiment, it was demonstrated that the cytochrome P450 pipA gene is required for piperidine and pyrrolidine utilization in M. smegmatis mc2155. Genes homologous to pipA were detected by hybridization in several, previously isolated, morpholine-degrading mycobacterial strains. A gene encoding a putative [3Fe-4S] ferredoxin (orf1) and a truncated gene encoding a putative glutamine synthetase (orf2') were found downstream of pipA.
Collapse
Affiliation(s)
- P Poupin
- Laboratoire de Génétique Microbienne, Université de Technologie de Compiègne, Centre de Recherches, 60205 Compiègne, France
| | | | | | | |
Collapse
|
17
|
Grkovic S, Brown MH, Roberts NJ, Paulsen IT, Skurray RA. QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. J Biol Chem 1998; 273:18665-73. [PMID: 9660841 DOI: 10.1074/jbc.273.29.18665] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Staphylococcus aureus QacA protein is a multidrug transporter that confers resistance to a broad range of antimicrobial agents via proton motive force-dependent efflux of the compounds. Primer extension analysis was performed to map the transcription start points of the qacA and divergently transcribed qacR mRNAs. Each gene utilized a single promoter element, the locations of which were confirmed by site-directed mutagenesis. Fusions of the qacA and qacR promoters to a chloramphenicol acetyl transferase reporter gene were used to demonstrate that QacR is a trans-acting repressor of qacA transcription that does not autoregulate its own expression. An inverted repeat overlapping the qacA transcription start site was shown to be the operator sequence for control of qacA gene expression. Removal of one half of the operator prevented QacR-mediated repression of the qacA promoter. Purified QacR protein bound specifically to this operator sequence in DNase I-footprinting experiments. Importantly, addition of diverse QacA substrates was shown to induce qacA expression in vivo, as well as inhibit binding of QacR to operator DNA in vitro, by using gel-mobility shift assays. QacR therefore appears to interact directly with structurally dissimilar inducing compounds that are substrates of the QacA multidrug efflux pump.
Collapse
Affiliation(s)
- S Grkovic
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | | | | | | |
Collapse
|
18
|
van der Werf MJ, de Bont JAM, Leak DJ. Opportunities in microbial biotransformation of monoterpenes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1997. [DOI: 10.1007/bfb0102065] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|