title: Autoregulator protein PhaR for biosynthesis of polyhydroxybutyrate [P(3HB)] possibly has two separate domains that bind to the target DNA and P(3HB): Functional mapping of amino acid residues responsible for DNA binding.
abstract: PhaR from Paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (PhaP) and PhaR itself, both of which are components of polyhydroxyalkanoate (PHA) granules (A. Maehara, S. Taguchi, T. Nishiyama, T. Yamane, and Y. Doi, J. Bacteriol. 184:3992-4002, 2002). PhaR is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, PHA polyester. In this study, by using a quartz crystal microbalance, we obtained direct evidence that PhaR binds to the target DNA and poly[(R)-3-hydroxybutyrate] [P(3HB)], one of the PHAs, at the same time. To identify the PhaR amino acid residues responsible for DNA binding, deletion and PCR-mediated random point mutation experiments were carried out with the gene encoding the PhaR protein. PhaR point mutants with decreased DNA-binding abilities were efficiently screened by an in vivo monitoring assay system coupled with gene expression of green fluorescent protein in Escherichia coli. DNA-binding abilities of the wild-type and mutants of recombinant PhaR expressed in E. coli were evaluated using a gel shift assay and a surface plasmon resonance analysis. These experiments revealed that basic amino acids and a tyrosine in the N-terminal region, which is highly conserved among PhaR homologs, are responsible for DNA binding. However, most of the mutants with decreased DNA-binding abilities were unaffected in their ability to bind P(3HB), strongly suggesting that PhaR has two separate domains capable of binding to the target DNA and P(3HB).
authors.affiliation: Graduate School of Engineering, Hokkaido University, N13W8, Sapporo, Hokkaido 060-8628, Japan.
authors.forename: Miwa
authors.initials: M
authors.lastname: Yamada
authors.forename: Koichi
authors.initials: K
authors.lastname: Yamashita
authors.forename: Akiko
authors.initials: A
authors.lastname: Wakuda
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Ichimura
authors.forename: Akira
authors.initials: A
authors.lastname: Maehara
authors.forename: Michihisa
authors.initials: M
authors.lastname: Maeda
authors.forename: Seiichi
authors.initials: S
authors.lastname: Taguchi
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002942:Circular Dichroism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D005822:Genetic Vectors / Q000235:genetics; D006885:Hydroxybutyrates / Q000378:metabolism*; D008969:Molecular Sequence Data; D010231:Paracoccus denitrificans / Q000235:genetics / Q000378:metabolism*; D011091:Polyesters / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D000094122:Polyhydroxybutyrates
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D006885:Hydroxybutyrates; D011091:Polyesters; D012097:Repressor Proteins; C003182:poly-beta-hydroxybutyrate; D000094122:Polyhydroxybutyrates