PaeExo IX: a unique deoxyribonuclease from Pseudomonas aeruginosa active in the presence of EDTA.

A new deoxyribonuclease, PaeExo IX, has been purified to electrophoretic homogeneity from extracts of Pseudomonas aeruginosa strain PAO. This enzyme, which is active in the presence of EDTA, is equally efficient in hydrolyzing native and heart-denatured DNA to acid-s-luble products. The enzyme is partially or totally inhibited by the presence of several divalent cations. The active protein has a molecular weight of 1.6 +/- 0.1 x 10(5) and is composed of two nonidentical polypeptides with molecular weights of 78,000 and 69,000.     

Ribonucleotide reductase from Escherichia coli: demonstration of a highly active form of the enzyme.

Ribonucleotide reductase from Escherichia coli consists of two nonidentical subunits, proteins B1 and B2. The activity of the enzyme in crude extracts prepared from mechanically disrupted bacteria is very low. Enzyme activity is stimulated 5 to 10-fold by addition of an excess of either subunit. Concentrated extracts from cells lysed gently on Cellophane discs (Schaller et al.) contained 10 to 20-fold higher activity than extracts from mechanically disrupted cells. This activity was not further stimulated by either B1 or B2. The system is suitable for complementation tests for the analysis of temperature-sensitive mutants affecting the ribonucleotide reductase system. Concentrated high-speed supernatants from E. coli treated with lysozyme (Wickner et al.) also contained a high ribonucleotide reductase activity, which was stimulated slightly or not at all by addition of B1 and B2. This active form of the enzyme was unstable and could not be purified. The results suggest that the intracellular form of the enzyme consists of a tight complex of proteins B1 and B2, possibly stabilized by other intracellular structures.     

Josephin domain-containing proteins from a variety of species are active de-ubiquitination enzymes

The neurodegenerative disease spinocerebellar ataxia type 3 (SCA3) is caused by the presence of an extended polyglutamine stretch (polyQ) in the unstructured C-terminus of the human ataxin-3 (AT3) protein. The structured N-terminal Josephin domain (JD) of AT3 is conserved within a novel family of potential ubiquitin proteases, the JD-containing proteins, which are sub-divided into two groups termed ataxins and Josephins. These AT3 orthologs are encoded by the genomes of organisms ranging from Plasmodium falciparum to humans, with most species possessing more than one homolog. While Josephins consist of JDs alone, ataxins contain additional functional domains that may influence their enzyme activity. Here, we show that the enzyme activity of human AT3 (hAT3) is not affected by the length of polyQ in its C-terminus, even when it is in the range associated with SCA3. We also show that JDs of all human proteins with homology to AT3 and its homologs from various species possess de-ubiquitination activity. These results establish JD-containing proteins as a novel family of active de-ubiquitination enzymes with wide phylogenic distribution.     

Variance reduction by simultaneous multi-exponential analysis of data sets from different experiments

The analysis of experimental data from the photocycle of bacteriorhodopsin (bR) as sums of exponentials has accumulated a large amount of information on its kinetics which is still controversial. One reason for ambiguous results can be found in the inherent instabilities connected with the fitting of noisy data by sums of exponentials. Nevertheless, there are strategies to optimize the experiments and the data analysis by a proper combination of well known techniques. This paper describes an applicable approach based on the correct weighting of the data, a separation of the linear and the non-linear parameters in the process of the least squares approximation, and a statistical analysis applying the correlation matrix, the determinant of Fisher's information matrix, and the variance of the parameters as a measure of the reliability of the results. In addition, the confidence regions for the linear approximation of the non-linear model are compared with confidence regions for the true non-linear model. Evaluation techniques and rules for an optimum experimental design are mainly exemplified by the analysis of numerically generated model data with increasing complexity. The estimation of the number of exponentials significant for the interpretation of a given set of data is demonstrated by using records from eight absorption and photocurrent experiments on the photocycle of bacteriorhodopsin. Offprint requests to: K.-H. Müller     

Arginine decarboxylase from a Pseudomonas species.

An arginine decarboxylase has been isolated from a Pseudomonas species. The enzyme is constitutive and did not appear to be repressed by a variety of carbon sources. After an approximately 40-fold purification, the enzyme appeared more similar in its properties to the Escherichia coli biosynthetic arginine decarboxylase than to the E. coli inducible (biodegradative) enzyme. The Pseudomonas arginine decarboxylase exhibited a pH optimum of 8.1 and an absolute requirement of Mg2+ and pyridoxal phosphate, and was inhibited significantly at lower Mg2+ concentrations by the polyamines putrescine, spermidine, and cadaverine. The Km for L-arginine was about 0.25 mM at pH 8.1 AND 7.2. The enzyme was completely inhibited by p-chloromercuribenzoate. The inhibition was prevented by dithiothreitol, a feature that suggests the involvement of an -SH group. Of a variety of labeled amino acids tested, only L-arginine, but not D-arginine was decarboxylated. D-Arginine was a potent inhibitor of arginine decarboxylase with a Ki of 3.2 muM.     

Allantoin racemase: a new enzyme from Pseudomonas species.

1. Allantoin racemase is a novel enzyme which catalyzes the conversion of S(+)-and R(minus)-allantoin into the racemate. 2. The enzyme is present in Pseudomonas testosteroni, Pseudomonas putida and five biotypes of Pseudomonas fluorescens, but absent in a number of other Pseudomonas species. 3. The enzyme of Ps. testosteroni was purified 133-fold and exposes optimal activity at pH 8.0-8.2 and 50 degrees C. The enzyme is stable on heating for 15 min at 70 degrees C. 4. The enzyme appeared to be specific for the optical isomers of allantoin and no cofactors are involved in the reaction. 5. The optical aspecificity of allantoinase of Proteus rettgeri was reaffirmed.     

A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species

Comparative genomic analysis has revolutionized our ability to predict the metabolic subsystems that occur in newly sequenced genomes, and to explore the functional roles of the set of genes within each subsystem. These computational predictions can considerably reduce the volume of experimental studies required to assess basic metabolic properties of multiple bacterial species. However, experimental validations are still required to resolve the apparent inconsistencies in the predictions by multiple resources. Here, we present combined computational-experimental analyses on eight completely sequenced Pseudomonas species. Comparative pathway analyses reveal that several pathways within the Pseudomonas species show high plasticity and versatility. Potential bypasses in 11 metabolic pathways were identified. We further confirmed the presence of the enzyme O-acetyl homoserine (thiol) lyase (EC: 2.5.1.49) in P. syringae pv. tomato that revealed inconsistent annotations in KEGG and in the recently published SYSTOMONAS database. These analyses connect and integrate systematic data generation, computational data interpretation, and experimental validation and represent a synergistic and powerful means for conducting biological research.     

Mmebrane phosphatase and active transport in red cells from different species

The K⁺-dependent phosphatase activity from red cell membranes from different mammalian species shows a close relationship with both the rate of active potassium influx and (Na⁺ + K⁺)-dependent ATPase activity. This finding supports the view that membrane phosphatase activity is related to the cation transport system.     

Ribonucleotide reductase modularity: Atypical duplication of the ATP-cone domain in Pseudomonas aeruginosa

The opportunistic pathogen Pseudomonas aeruginosa, which causes serious nosocomial infections, is a gamma-proteobacterium that can live in many different environments. Interestingly P. aeruginosa encodes three ribonucleotide reductases (RNRs) that all differ from other well known RNRs. The RNR enzymes are central for de novo synthesis of deoxyribonucleotides and essential to all living cells. The RNR of this study (class Ia) is a complex of the NrdA protein harboring the active site and the allosteric sites and the NrdB protein harboring a tyrosyl radical necessary to initiate catalysis. P. aeruginosa NrdA contains an atypical duplication of the N-terminal ATP-cone, an allosteric domain that can bind either ATP or dATP and regulates the overall enzyme activity. Here we characterized the wild type NrdA and two truncated NrdA variants with precise N-terminal deletions. The N-terminal ATP-cone (ATP-c1) is allosterically functional, whereas the internal ATP-cone lacks allosteric activity. The P. aeruginosa NrdB is also atypical with an unusually short lived tyrosyl radical, which is efficiently regenerated in presence of oxygen as the iron ions remain tightly bound to the protein. The P. aeruginosa wild type NrdA and NrdB proteins form an extraordinarily tight complex with a suggested alpha4beta4 composition. An alpha2beta2 composition is suggested for the complex of truncated NrdA (lacking ATP-c1) and wild type NrdB. Duplication or triplication of the ATP-cone is found in some other bacterial class Ia RNRs. We suggest that protein modularity built on the common catalytic core of all RNRs plays an important role in class diversification within the RNR family.     

Vertebrate opsins belonging to different classes vary in constitutively active properties resulting from salt-bridge mutations

Vertebrate opsins are classified into one of five classes on the basis of amino acid similarity. These classes are short wavelength sensitive 1 and 2 (SWS1, SWS2), medium/long wavelength sensitive (M/LWS), and rod opsin like 1 and 2 (RH1, RH2). In bovine rod opsin (RH1), two critical amino acids form a salt bridge in the apoprotein that maintains the opsin in an inactive state. These residues are K296, which functions as the chromophore binding site, and E113, which functions as the counterion to the protonated Schiff base. Corresponding residues in each of the other vertebrate opsin classes are believed to play similar roles. Previous reports have demonstrated that mutations in these critical residues result in constitutive activation of transducin by RH1 class opsins in the absence of chromophore. Additionally, recent reports have shown that an E113Q mutation in SWS1 opsin is constitutively active. Here we ask if the other classes of vertebrate opsins maintain activation characteristics similar to that of bovine RH1 opsin. We approach this question by making the corresponding substitutions which disrupt the K296/E113 salt bridge in opsins belonging to the other vertebrate opsin classes. The mutant opsins are tested for their ability to constitutively activate bovine transducin. We demonstrate that mutations disrupting this key salt bridge produce constitutive activation in all classes. However, the mutant opsins differ in their ability to be quenched in the dark state by the addition of chromophore as well as in their level of constitutive activation. The differences in constitutive activation profiles suggest that structural differences exist among the opsin classes that may translate into a difference in activation properties.     

Enzymes responsible for chlorate reduction by Pseudomonas sp. are different from those used for perchlorate reduction by Azospira sp

Pseudomonas sp. PDA is an unusual bacterium due to its ability to respire using chlorate under aerobic conditions. The chlorate reductase produced by PDA was shown to be intrinsically different from the enzyme responsible for chlorate and perchlorate [(per)chlorate] reduction produced by Azospira sp. KJ based on subunit composition and other enzyme properties. The perchlorate reductase from strain KJ appeared to have two subunits (100 and 40 kDa) while the chlorate reductase from PDA had three subunits (60, 48, and 27 kDa). N-terminal amino acid sequencing of the 100 kDa protein from strain KJ showed a 77% similarity with the perchlorate reductase alpha subunit from another perchlorate-respiring bacterium, Dechloromonas agitata, while the N-terminus amino acid sequence of the 60 kDa protein from strain PDA did not show a similarity to previously isolated chlorate or perchlorate reductases.     

Chromium reduction in Pseudomonas putida.

Reduction of hexavalent chromium (chromate) to less-toxic trivalent chromium was studied by using cell suspensions and cell-free supernatant fluids from Pseudomonas putida PRS2000. Chromate reductase activity was associated with soluble protein and not with the membrane fraction. The crude enzyme activity was heat labile and showed a Km of 40 microM CrO4(2-). Neither sulfate nor nitrate affected chromate reduction either in vitro or with intact cells.     

New species of pathogenic Pseudomonas isolated from citrus in Tunisia: Proposal of Pseudomonas kairouanensis sp. nov. and Pseudomonas nabeulensis sp. nov.

A collection of Pseudomonas strains was isolated in different regions of Tunisia in the period 2016–2017 from the fruits and leaves of Citrus sinensis cv. ‘Valencia Late’ and Citrus limon cv. ‘Eureka’ plants with symptoms of blast and black pit disease. A phylogenetic analysis of the housekeeping gene rpoD was used for strain identification at the species level. The results demonstrated the affiliation of these strains with the genus Pseudomonas and revealed the presence of 11 strains representing two putative new species in two monophyletic branches. These strains were analyzed morphologically and genotypically by multilocus sequence analyses of the rpoD, gyrB and 16S rRNA (rrs) gene sequences, and their phenotypic characteristics by API 20NE and Biolog GEN III. Plant pathogenic properties were confirmed on fruits and detached leaves of C. limon cv. ‘Eureka’. Fatty acids and WC MALDI-TOF MS major protein profiles were determined. The genomes of both representatives were sequenced. The average nucleotide index and genome-to-genome distance from KC12^T and E10B^T are below the cut-off established for a described species. These results support the conclusion that the strains KC12^T, KC17, KC20, KC22, KC24A, KC25 and KC26 represent a novel species of Pseudomonas, for which the name of Pseudomonas kairouanensis is proposed. The type strain is KC12^T (=CECT9766 and CFBP 8662). The strains E10B^T, E10AB, E10CB1 and Iy3BA represent another novel species of Pseudomonas for which the name of Pseudomonas nabeulensis is proposed; the type strain is E10B^T (=CECT9765 and CFBP 8661).     

Ribonucleotide reductase: Association of the regulatory subunit in the presence of allosteric effectors

Ribonucleotide reductase from Ehrlich tumor cells moves as a 9 S particle in sucrose gradient centrifugation. In the presence of ATP or dATP, but not dGTP, there is a loss of enzyme activity in the 9 S region. When a fraction from the 6 S region of the gradient or the reductase component not bound by blue-dextran Sepharose or ATP-agarose columns, is added to each gradient fraction, essentially full activity can be recovered, the major portion of which is in the 16–18 S region. The reductase subunit which is bound by blue-dextran Sepharose moves as a 6.5 S particle but ATP shifts this component to 16–18 S. These results indicate that ATP or dATP causes association of the nucleoside triphosphate-binding subunit and dissociation of the remainder of the enzyme from this aggregate.     

Ribonucleotide reduction and the possible role of cobalamin in evolution

The biological pathways of ribonucleotide reduction are briefly reviewed. The hypothesis is presented that reduction of ribonucleoside triphosphates to their deoxynucleotide analogs through the mediation of vitamin B12 or a similar corrinoid preceded and was necessary for the subsequent development of a DNA-type genome. There are two known biological systems for ribonucleotide reduction: (1) The ribonucleoside diphosphate reduction system which utilizes a nonheme iron ribonucleotide reductase enzyme, thioredoxin and its reductase, and NADPH. This enzyme complex is found in most bacteria, some higher organisms, and in all animals. (2) The ribonucleoside triphosphate reduction system which utilizes adenosyl cobalamin, ribonucleotide reductase and either thioredoxin or a disulfhydryl compound. The cobalamin-dependent reductase is restricted to a few species of bacteria and blue-gree algae. This system is considered more primitive than the iron reductase one based on their differences in distribution, components, and products.     

Selenate reduction by a Pseudomonas species: a new mode of anaerobic respiration

The high levels of selenium (selenate, selenite) in agricultural drainage water in the San Joaquin Valley of California, which have led to environmental problems, might be lowered if the selenate/selenite could be reduced to elemental insoluble selenium. Two organisms have been newly isolated which do this in anaerobic coculture. One, a strictly anaerobic, Gram-positive rod, reduces selenite to elemental selenium. The other, a Pseudomonas species, was shown to respire selenate to selenite. Cells grown anaerobically in Minimal Medium on acetate plus selenate oxidized 14C-acetate to 14CO2 with concomitant reduction of selenate to selenite and small amounts of elemental selenium.