Regulation of Benzoate Degradation inAcinetobacter sp. Strain ADP1 by BenM, a LysR-Type Transcriptional Activator

ABSTRACT In Acinetobacter sp. strain ADP1, benzoate degradation requires the ben genes for converting benzoate to catechol and the cat genes for degrading catechol. Here we describe a novel transcriptional activator, BenM, that regulates the chromosomalben and cat genes. BenM is homologous to CatM, a LysR-type transcriptional activator of the cat genes. Unusual regulatory features of this system include the abilities of both BenM and CatM to recognize the same inducer,cis,cis-muconate, and to regulate some of the same genes, such as catA and catB. Unlike CatM, BenM responded to benzoate. Benzoate together withcis,cis-muconate increased the BenM-dependent expression of the benABCDE operon synergistically. CatM was not required for this synergism, nor did CatM regulate the expression of a chromosomal benA::lacZtranscriptional fusion. BenM-mediated regulation differs significantly from that of the TOL plasmid-encoded conversion of benzoate to catechol in pseudomonads. The benM gene is immediately upstream of, and divergently transcribed from, benA, and a possible DNA binding site for BenM was identified between the two coding regions. Two mutations in the predicted operator/promoter region renderedben gene expression either constitutive or inducible bycis,cis-muconate but not benzoate. Mutants lacking BenM, CatM, or both of these regulators degraded aromatic compounds at different rates, and the levels of intermediary metabolites that accumulated depended on the genetic background. These studies indicated that BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. In a catM-disrupted strain, BenM was able to induce higher levels of catA expression thancatB expression.

[1]  A. Bairoch,et al.  Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases , 1991, Journal of bacteriology.

[2]  R. H. Olsen,et al.  Regulation of tfdCDEF by tfdR of the 2,4-dichlorophenoxyacetic acid degradation plasmid pJP4 , 1990, Journal of bacteriology.

[3]  Hilla Peretz,et al.  Ju n 20 03 Schrödinger ’ s Cat : The rules of engagement , 2003 .

[4]  E. Neidle,et al.  Characterization of Acinetobacter calcoaceticus catM, a repressor gene homologous in sequence to transcriptional activator genes , 1989, Journal of bacteriology.

[5]  M. Schell Molecular biology of the LysR family of transcriptional regulators. , 1993, Annual review of microbiology.

[6]  E. Kitsiou,et al.  Distribution of CD1A‐positive langerhans cells and lymphocyte subsets in transitional cell carcinoma of the urinary bladder. An immunohistological study on frozen sections , 1995, The Journal of pathology.

[7]  V. de Lorenzo,et al.  Cross talk between catabolic pathways in Pseudomonas putida: XylS-dependent and -independent activation of the TOL meta operon requires the same cis-acting sequences within the Pm promoter , 1994, Journal of bacteriology.

[8]  P. Chapman,et al.  Characterization of Pseudomonas putida mutants unable to catabolize benzoate: cloning and characterization of Pseudomonas genes involved in benzoate catabolism and isolation of a chromosomal DNA fragment able to substitute for xylS in activation of the TOL lower-pathway promoter , 1992, Journal of bacteriology.

[9]  W. Lotz,et al.  Construction of a lacZ-kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. , 1989, Gene.

[10]  C. A. Fewson,et al.  The Biology of Acinetobacter , 1991, Federation of European Microbiological Societies Symposium Series.

[11]  E. Neidle,et al.  Evolution of Genes for the β-Ketoadipate Pathway in Acinetobacter Calcoaceticus , 1991 .

[12]  D. Kobayashi,et al.  Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. , 1988, Gene.

[13]  G N Murshudov,et al.  The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. , 1997, Structure.

[14]  V. de Lorenzo,et al.  Effector Specificity Mutants of the Transcriptional Activator NahR of Naphthalene Degrading Pseudomonas Define Protein Sites Involved in Binding of Aromatic Inducers* , 1997, Journal of Biological Chemistry.

[15]  S. Henikoff,et al.  Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida , 1993, Journal of bacteriology.

[16]  E. Neidle,et al.  Cloning and expression in Escherichia coli of Acinetobacter calcoaceticus genes for benzoate degradation , 1987, Journal of bacteriology.

[17]  Caroline S. Harwood,et al.  THE β-KETOADIPATE PATHWAY AND THE BIOLOGY OF SELF-IDENTITY , 1996 .

[18]  E. Juni,et al.  Transformation of Acinetobacter calco-aceticus (Bacterium anitratum) , 1969, Journal of bacteriology.

[19]  A. Bairoch,et al.  cis-diol dehydrogenases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily. , 1992, European journal of biochemistry.

[20]  A. L. Campbell,et al.  Directed introduction of DNA cleavage sites to produce a high-resolution genetic and physical map of the Acinetobacter sp. strain ADP1 (BD413UE) chromosome. , 1997, Microbiology.

[21]  V. de Lorenzo,et al.  Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. , 1994, Microbiological reviews.

[22]  E. Neidle,et al.  Cloning and expression of Acinetobacter calcoaceticus catBCDE genes in Pseudomonas putida and Escherichia coli , 1986, Journal of bacteriology.

[23]  Cánovas Jl,et al.  Regulation of the enzymes of the beta-ketoadipate pathway in Moraxella calcoacetica. 1. General aspects. , 1967 .

[24]  S. Kaplan,et al.  prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacter sphaeroides , 1994, Journal of bacteriology.

[25]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[26]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[27]  L. N. Ornston,et al.  Recovery of DNA from the Acinetobacter calcoaceticus chromosome by gap repair , 1990, Journal of bacteriology.

[28]  E. Neidle,et al.  Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon source utilization by Acinetobacter calcoaceticus , 1996, Journal of bacteriology.

[29]  J. Ramos,et al.  The XylS/AraC family of regulators. , 1993, Nucleic acids research.

[30]  Jeffrey H. Miller Experiments in molecular genetics , 1972 .

[31]  R. Stanier,et al.  Regulation of the Enzymes of the β‐Ketoadipate Pathway in Moraxella calcoacetica , 1968 .

[32]  H. Krisch,et al.  In vitro insertional mutagenesis with a selectable DNA fragment. , 1984, Gene.

[33]  E. Neidle,et al.  benK encodes a hydrophobic permease-like protein involved in benzoate degradation by Acinetobacter sp. strain ADP1 , 1997, Journal of bacteriology.

[34]  A. Pühler,et al.  A Broad Host Range Mobilization System for In Vivo Genetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria , 1983, Bio/Technology.

[35]  A. Bairoch,et al.  Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases , 1991, Journal of bacteriology.

[36]  E. Neidle,et al.  [20] Catechol and chlorocatechol 1,2-Dioxygenases , 1990 .

[37]  M. Schell,et al.  catM encodes a LysR-type transcriptional activator regulating catechol degradation in Acinetobacter calcoaceticus , 1995, Journal of bacteriology.

[38]  A. Chakrabarty,et al.  Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family , 1990, Journal of bacteriology.

[39]  C. Yanisch-Perron,et al.  Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. , 1985, Gene.

[40]  L. N. Ornston,et al.  Copyright � 1995, American Society for Microbiology Discontinuities in the Evolution of Pseudomonas putida cat Genes† , 1994 .

[41]  P. Williams,et al.  Spontaneous deletions in the TOL plasmid pWW20 which give rise to the B3 regulatory mutants of Pseudomonas putida MT20. , 1982, Journal of general microbiology.

[42]  E. Neidle,et al.  Catechol and chlorocatechol 1,2-dioxygenases. , 1990, Methods in enzymology.

[43]  W. D. de Vos,et al.  Characterization of the Pseudomonas sp. strain P51 gene tcbR, a LysR-type transcriptional activator of the tcbCDEF chlorocatechol oxidative operon, and analysis of the regulatory region , 1991, Journal of bacteriology.