Expression and purification of nuclease-free protocatechuate 3,4-dioxygenase for prolonged single-molecule fluorescence imaging.

Single-molecule (SM) microscopy is a powerful tool capable of visualizing individual molecules and events in real time. SM imaging may rely on proteins or nucleic acids labelled with a fluorophore. Unfortunately photobleaching of fluorophores leads to irreversible loss of signal, impacting the collection of data from SM experiments. Trace amounts of dissolved oxygen (O2) are the main cause of photobleaching. Oxygen scavenging systems (OSS) have been developed that decrease dissolved O2. Commercial OSS enzyme preparations are frequently contaminated with nucleases that damage nucleic acid substrates. In this protocol, we purify highly active Pseudomonas putida protocatechuate 3,4-dioxygenase (PCD) without nuclease contaminations. Quantitation of Cy3 photostability revealed that PCD with its substrate protocatechuic acid (PCA) increased the fluorophore half-life 100-fold. This low cost purification method of recombinant PCD yields an enzyme superior to commercially available OSS that is effectively free of nuclease activity.

Role of Acinetobacter baylyi Crc in catabolite repression of enzymes for aromatic compound catabolism.

Here, we describe for the first time the Crc (catabolite repression control) protein from the soil bacterium Acinetobacter baylyi. Expression of A. baylyi crc varied according to the growth conditions. A strain with a disrupted crc gene showed the same growth as the wild type on a number of carbon sources. Carbon catabolite repression by acetate and succinate of protocatechuate 3,4-dioxygenase, the key enzyme of protocatechuate breakdown, was strongly reduced in the crc strain, whereas in the wild-type strain it underwent strong catabolite repression. This strong effect was not based on transcriptional regulation because the transcription pattern of the pca-qui operon (encoding protocatechuate 3,4-dioxygenase) did not reflect the derepression in the absence of Crc. pca-qui transcript abundance was slightly increased in the crc strain. Lack of Crc dramatically increased the mRNA stability of the pca-qui transcript (up to 14-fold), whereas two other transcripts (pobA and catA) remained unaffected. p-Hydroxybenzoate hydroxylase activity, encoded by pobA, was not significantly different in the absence of Crc, as protocatechuate 3,4-dioxygenase was. It is proposed that A. baylyi Crc is involved in the determination of the transcript stability of the pca-qui operon and thereby effects catabolite repression.

[Aromatic hydrocarbons as enzyme inducers of cleavage of the aromatic ring in Candida guilliermondii]. / Aromaticheskie uglevodorody kak induktory fermentov rasshchepleniia aromaticheskogo iadra u Candida guilliermondii.

Monocyclic and dicyclic aromatic hydrocarbons, toluene and 2-methylnaphthalene, can induce pyrocatechate-1,2-oxygenase in Candida guilliermondii BKM Y-916 cells. The enzyme is active at pH 7.0. The culture oxidizes toluene via benzoic acid by ortho-cleavage. The results indicate that Candida as an ecologo-trophic group of microorganisms can be involved, along with bacteria, in biodegradation of various aromatic hydrocarbons.

[Key Rhodococcus enzymes in the catabolism of aromatic compounds]. / Kliuchevye fermenty katabolizma aromaticheskikh soedinenii Rhodococcus.

The enzyme apparatus involved in the catabolism of aromatic compounds in rhodococci is characterized by the presence of pyrocatechase and protocatechoate-3,4-dioxygenase as principal enzymes cleaving the aromatic cycle. Metapyrocatechase was found in about 30% of the rhodococci. All the enzymes are inducible. The inductor of pyrocatechase seems to be cyc-cys-muconate, and that of protocatechase appears to be 3-oxoadipate. The metapyrocatechase of rhodococci, in contrast to that of Pseudomonas, is not induced by benzoate, p-toluylate, p-xylene and phenol. The activity of metapyrocatechase rises 20-50 times comparing to the basal level only in the presence of p-cresol. The enzyme has a relatively low activity in rhodococci (50-200 nmole per 1 min per 1 mg of protein), though a very high affinity for methylcatechols. The activity of metapyrocatechase with methylcatechols is 2-5 times as high as that with catechol as a substrate, whereas the activity of pyrocatechase with methylcatechols is two times as low as that with catechol as a substrate. Such additional substrates as acetate, glycerol or fumarate have no effect on the qualitative composition of the key enzymes involved in the degradation of aromatic compounds in Rhodococcus carollinus 172. Glucose represses the synthesis of enzymes cleaving the aromatic ring by 100%. Fumarate taken in a 5-fold excess inhibits the activity of catechol oxygenases by 40%; if it is taken in a 1000-fold excess, it inhibits the enzyme activity by 100%.

[Characteristics of the key enzyme regulation of peripheral p-xylene metabolism in Pseudomonas aeruginosa]. / Osobennosti reguliatsii kliuchevykh fermentov periferiinogo metabolizma p-ksilola u Pseudomonas aeruginosa.

The regulation of p-xylene methylhydroxylase, metapyrocatechase, pyrocatechase and protocatechoate-3,4-dioxygenase was studied in Pseudomonas aeruginosa 2x. Methylhydroxylase, the first enzyme of p-xylene oxidation, was shown to be synthesized in the strain in a constitutive manner and to be regulated at the level of the enzyme activity. Metapyrocatechase, protocatechase and pyrocatechase are inducible enzymes; these are repressed to a different extent by the end products of p-xylene oxidation. Metapyrocatechase has a broader substrate specificity as compared to pyrocatechase and is induced by a greater number of substrates, the affinity for different substrates depending on the structure of an inductor. Presumably, two isofunctional metapyrocatechases exist in P. aeruginosa 2 x.

Purification and properties of protocatechuate 3,4-dioxygenase from Chaetomium piluliferum induced with p-hydroxybenzoic acid.

1. Protocatechuate 3,4-dioxygenase (protocatechuate : oxygen 3,4-oxidoreductase, EC 1.13.11.3) was isolated from mycelium of Chaetomium piluliferum induced with p-hydroxybenzoic acid. The enzyme was purified about 80-fold by ammonium sulphate fractionation and DEAE-cellulose and Sephadex G-200 chromatography, and was homogeneous on polyacrylamide-gel electrophoresis. 2. The enzyme showed high substrate specificity; its pH optimum was 7.5-8.0, and molecula weight about 76 000 as determined by filtration on Sephadex G-200. The Michaelis constant for protocatechuic acid was 11.1 microM.

Phthalate metabolism in Pseudomonas testosteroni: accumulation of 4,5-dihydroxyphthalate by a mutant strain.

A mutant strain of Pseudomonas testosteroni blocked in phthalate catabolism converted phthalate into 4,5-dihydroxyphthalate. The latter compound was isolated, and its physical properties were determined. A stoichiometric conversion of the compound to protocatechuate was demonstrated spectrophotometrically with crude extracts of a protocatechuate 4,5-dioxygenase-deficient mutant. Therefore, phthalate is metabolized through 4,5-dihydroxyphthalate and protocatechuate, which is further degraded by protocatechuate 4,5-dioxygenase in P. testosteroni. By using several mutants blocked in phthalate catabolism, 4,5-dihydroxyphthalate decarboxylase was shown to be induced by phthalate. A simple spectrophotometric assay for the enzyme is also reported.