Pyrimidine ribonucleoside catabolism in Pseudomonas fluorescens biotype A

The pyrimidine ribonucleosides uridine or cytidine were shown to serve as a source of nitrogen or carbon for the growth of Pseudomonas fluorescens strain A126. After incubation of either pyrimidine ribonucleoside with extracts of this strain, the resultant catabolic products were detected by thin-layer chromatography. It was found that pyrimidine ribonucleoside catabolism in this pseudomonad involved the enzymes nucleoside hydrolase and cytosine deaminase. The specific activities of both these enzymes could be influenced by the nitrogen or carbon source present in the medium.     

Degradation of pyrimidine ribonucleosides by Pseudomonas aeruginosa

Pyrimidine ribonucleoside degradation in the human pathogen Pseudomonas aeruginosa ATCC 15692 was investigated. Either uracil, cytosine, 5-methylcytosine, thymine, uridine or cytidine supported P. aeruginosa growth as a nitrogen source when glucose served as the carbon source. Using thin-layer chromatographic analysis, the enzymes nucleoside hydrolase and cytosine deaninase were shown to be active in ATCC 15692. Compared to (NH₄)₂SO₄-grown cells, nucleoside hydrolase activity in ATCC 15692 approximately doubled after growth on 5-methylcytosine as a nitrogen source while its cytosine deaminase activity increased several-fold after growth on the pyrimidine bases and ribonucleosides examined as nitrogen sources. Regulation at the level of protein synthesis by 5-methylcytosine was indicated for nucleoside hydrolase and cytosine deaminase in P. aeruginosa.     

Thymidine phosphorylating enzymes in the gonads of marine invertebrates

The activities of enzymes involved in the consecutive phosphorylation of thymidine were revealed in the gonad extracts of marine invertebrates. Along with thymidine kinase activity, thymidilate kinase activity was revealed in all the studied species; however, the specific activities of nucleoside and nucleotide kinases varied in different species of mollusks, sea stars and sea urchins. Thymidine and thymidilate kinases were isolated from the gonads of the scallop Mizuhopecten yessoensis and some of their enzymat properties were studied. The thymidine kinase of M. yessoensis catalyzed the phosphorylation of thymidine and deoxycytidine at a lesser rate, but didn’s use purine ribo-and deoxyribonucleosides or pyrimidine ribonucleosides as phosphate acceptors. The thymidilate kinase carried out both TMP and dCMP phosphorylation. As well as ATP, the enzymes of M. yessoensis were also able to use dATP, dGTP, GTP, UTP and CTP as donors of phosphate groups. The thymidine kinase activity was inhibited by TMP, TTP and dCTP.     

18O Labeled Nucleosides. 2. A General Method for the Synthesis of Specifically Labeled Pyrimidine Ribonucleosides1

Abstract

A facile method for the synthesis of highly enriched ¹⁸O labeled pyrimidine ribonucleosides is described using uridine as a model compound. The isotopic label may be selectively incorporated into the base moiety at O² or into the ribose portion of the molecule at the 5′ position. In addition, both positions may be labeled and this is the first report of a method for labeling of both the base and sugar moieties of pyrimidine ribonucleosides. The site and level of isotope incorporation may be determined mass spectrometrically.     

Why did the Fleming strain fail in penicillin industry?

Penicillin, discovered 75 years ago by Sir Alexander Fleming in Penicillium notatum, laid the foundations of modern antibiotic chemotherapy. Early work was carried out on the original Fleming strain, but it was later replaced by overproducing strains of Penicillium chrysogenum, which became the industrial penicillin producers. We show how a C(1357)-->T (A394V) change in the gene encoding PahA in P. chrysogenum may help to explain the drawback of P. notatum. PahA is a cytochrome P450 enzyme involved in the catabolism of phenylacetic acid (PA; a precursor of penicillin G). We expressed the pahA gene from P. notatum in P. chrysogenum obtaining transformants able to metabolize PA (P. chrysogenum does not), and observing penicillin production levels about fivefold lower than that of the parental strain. Our data thus show that a loss of function in P. chrysogenum PahA is directly related to penicillin overproduction, and support the historic choice of P. chrysogenum as the industrial producer of penicillin.     

Catabolism of the methyl derivatives of adenosine and cytidine in staphylococci.

Products of 1-methyladenosine, 2'-O-methyladenosine, 2'-O-methylcytidine, and 5-methylcytidine catabolism by resting cells of Staphylococcus aureus and Staphylococcus intermedius were chromatographically separated. The methyl group in 1-methyladenosine protected the adenosine derivative from deamination by S. intermedius but it did not protect N-glycosidic bond from cleavage by S. intermedius and S. aureus. The methyl group in 2'-O-methyladenosine and 2'-O-methylcytidine protected the N-glycosidic bond from cleavage by S. aureus and S. intermedius but it did not protect the adenosine and cytidine derivatives from deamination by S. intermedius. 5-Methylcytidine was converted by the common route in which 5-methylcytidine was first deaminated to ribothymidine which was cleaved to yield thymine. S. intermedius deaminated the purine and pyrimidine ribonucleosides adenosine, 2'-O-methyladenosine, cytidine, and 5-methylcytidine. Pyrimidine ribonucleosides (cytidine, 5-methyl-cytidine) were deaminated only slowly and purine ribonucleosides (adenosine, 2'-O-methyladenosine) not at all by S. aureus.     

Biosynthesis of Deoxyribonucleotides in Ochromonas malhamensis

SYNOPSIS. Uniformly ¹⁴C-labeled pyrimidine ribonucleosides and orotic-6-¹⁴C acid were fed to growing cultures of Ochromonas malhamensis and the radioactivity appearing in RNA and DNA was determined. The carbon skeletons of uridine and cytidine were incorporated intact into all of the pyrimidine nucleotides from RNA and DNA. Incorporation of radioactivity into the purine nucleotides was negligible. The evidence supports the conclusion that deoxyribonucleotide biosynthesis in this organism proceeds via a pathway involving the direct reduction of the corresponding ribonucleosides or ribonucleotides. An important role for a trans-N-deoxyribosylase in deoxyribonucleotide biosynthesis here appears to be ruled out.     

Improved method to prepare RNA-free DNA from mammalian cells

To isolate DNA for nucleoside analog incorporation studies, many investigators use RNase A to remove RNA from total cellular nucleic acid. We observed persistence of ribonucleotides from RNA in nucleic acid samples treated with RNase A alone. Although incubation of [5-³H]uridine-labeled nucleic acid with 50 μg/ml RNase A decreased tritium by 97%, HPLC analysis of the resulting DNA preparation digested to nucleosides revealed high levels of ribonucleosides. Increasing RNase A 10-fold (500 μg/ml) effected only a 1.7-fold reduction in ribonucleosides. Overall, the level of ribonucleosides was one-fourth that of the deoxynucleosides, primarily due to the high levels of guanosine. It was hypothesized that the ribonucleosides originated from guanosine-rich tracts of RNA since RNase A cuts preferentially 3′ to pyrimidine monophosphates and to some extent after AMP. The addition of 0.05 μg/ml RNase T1, which preferentially cleaves RNA 3′ to GMP, decreased total ribonucleosides by nearly 20-fold. In conclusion, we have developed a rapid method which removes greater then 99% of cellular RNA from nucleic acid extracts and a reversed-phase HPLC procedure that detects RNA contamination more sensitively than [5-³H]uridine labeling. These methods are useful for the determination of analog incorporation into DNA, especially for agents which incorporate into both DNA and RNA.     

Triazole double-headed ribonucleosides as inhibitors of eosinophil derived neurotoxin

Eosinophil derived neurotoxin (EDN) is an eosinophil secretion protein and a member of the Ribonuclease A (RNase A) superfamily involved in the immune response system and inflammatory disorders. The pathological actions of EDN are strongly dependent on the enzymatic activity and therefore, it is of significant interest to discover potent and specific inhibitors of EDN. In this framework we have assessed the inhibitory potency of triazole double-headed ribonucleosides. We present here an efficient method for the heterologous production and purification of EDN together with the synthesis of nucleosides and their biochemical evaluation in RNase A and EDN. Two groups of double-headed nucleosides were synthesized by the attachment of a purine or a pyrimidine base, through a triazole group at the 3′-C position of a pyrimidine or a purine ribonucleoside, respectively. Based on previous data with mononucleosides these compounds were expected to improve the inhibitory potency for RNase A and specificity for EDN. Kinetics data revealed that despite the rational, all but one, double-headed ribonucleosides were less potent than the respective mononucleosides while they were also more specific for ribonuclease A than for EDN. Compound 11c (9-[3′-[4-[(cytosine-1-yl)methyl]-1,2,3-triazol-1-yl]-β-d-ribofuranosyl]adenine) displayed a stronger preference for EDN than for ribonuclease A and a K_i value of 58 μM. This is the first time that an inhibitor is reported to have a better potency for EDN than for RNase A. The crystal structure of EDN–11c complex reveals the structural basis of its potency and selectivity providing important guidelines for future structure-based inhibitor design efforts.     

Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA

Nucleotides are important for RNA and DNA synthesis and, despite a de novo synthesis by bacteria, uptake systems are crucial. Streptococcus pneumoniae, a facultative human pathogen, produces a surface-exposed nucleoside-binding protein, PnrA, as part of an ABC transporter system. Here we demonstrate the binding affinity of PnrA to nucleosides adenosine, guanosine, cytidine, thymidine and uridine by microscale thermophoresis and indicate the consumption of adenosine and guanosine by ¹H NMR spectroscopy. In a series of five crystal structures we revealed the PnrA structure and provide insights into how PnrA can bind purine and pyrimidine ribonucleosides but with preference for purine ribonucleosides. Crystal structures of PnrA:nucleoside complexes unveil a clear pattern of interactions in which both the N- and C- domains of PnrA contribute. The ribose moiety is strongly recognized through a conserved network of H-bond interactions, while plasticity in loop 27–36 is essential to bind purine- or pyrimidine-based nucleosides.Further, we deciphered the role of PnrA in pneumococcal fitness in infection experiments. Phagocytosis experiments did not show a clear difference in phagocytosis between PnrA-deficient and wild-type pneumococci. In the acute pneumonia infection model the deficiency of PnrA attenuated moderately virulence of the mutant, which is indicated by a delay in the development of severe lung infections. Importantly, we confirmed the loss of fitness in co-infections, where the wild-type out-competed the pnrA-mutant. In conclusion, we present the PnrA structure in complex with individual nucleosides and show that the consumption of adenosine and guanosine under infection conditions is required for virulence.     

Isolation and characterization of pyrimidine auxotrophs, and molecular cloning of the pyrE gene from the hyperthermophilic archaeon Pyrococcus abyssi

Uracil auxotrophic mutants of the hyperthermophilic archaeon Pyrococcus abyssi were isolated by screening for resistance to 5-fluoro-orotic acid (5-FOA). Wild-type strains were unable to grow on medium containing 5-FOA, whereas mutants grew normally. Enzymatic assays of extracts from wild-type P. abyssi and from pyrimidine auxotrophs demonstrated that the mutants are deficient in orotate phosphoribosyltransferase (PyrE) and/or orotidine-5′-monophosphate decarboxylase (PyrF) activity. The pyrE gene of wild-type P. abyssi and one of its mutant derivatives were cloned and sequenced. This pyrE gene could serve as selectable marker for the development of gene manipulation systems in archaeal hyperthermophiles.     

Synthesis of 6-Aza- & 6-Methyl-pyrimidine Ribonucleoside Phosphoramidites and Their Incorporation in Hammerhead Ribozymes

Abstract

The synthesis of phosphoramidites of 6-modified pyrimidine ribonucleosides and their incorporation into hammerhead ribozymes and influence on nuclease stability and catalytic activity is described.     

Purine metabolism in the bloodstream forms of trypanosoma gambiense and Trypanosoma rhodesiense

Bloodstream forms of Trypanosoma brucie gambiense and Trypanosoma brucei rhodesiense are incapable of de novo purine synthesis. Purine bases are converted directly to ribonucleotides and with the exception of guanine, are stable. Guanine is incorporated directly into ribonucleotides and also deaminated to xanthine. Purine ribonucleosides are hydrolyzed rapidly; these reactions may limit their incorporation since purine bases label the nucleotide pools more efficiently than do ribonucleosides. The apparent order of salvage efficiency for ribonucleosides is adenosine>inosine>guanosine>xanthosine for both organisms. T. b. gambiense salvages purine bases in the same order, while T. b. rhodesiense salvages purine bases in the order hypoxanthine>adenine>guanine>xanthine.     

Characterization of the lys2 gene of Penicillium chrysogenum encoding α-aminoadipic acid reductase

A DNA fragment containing a gene homologous to LYS2 gene of Saccharomyces cerevisiae was cloned from a genomic DNA library of Penicillium chrysogenum AS-P-78. It encodes a protein of 1409 amino acids (Mr^ 154?859) with strong similarity to the S.?cerevisiae (49.9% identity) Schizosaccharomycespombe (51.3% identity) and Candida albicans (48.12% identity) α-aminoadipate reductases and a lesser degree of identity to the amino acid-activating domains of the non-ribosomal peptide synthetases, including the α-aminoadipate-activating domain of the α-aminoadipyl-cysteinyl-valine synthetase of P. chrysogenum (12.4% identical amino acids). The lys2 gene contained one intron in the 5′-region and other in the 3′-region, as shown by comparing the nucleotide sequences of the cDNA and genomic DNA, and was transcribed as a 4.7-kb monocistronic mRNA. The lys2 gene was localized on chromosome III (7.5?Mb) in P. chrysogenum AS-P-78 and on chromosome IV (5.6 Mb) in strain P2, whereas the penicillin gene cluster is known to be located in chromosome I in both strains. The lys2-encoded protein is a member of the aminoacyladenylate-forming enzyme family with a reductase domain in its C-terminal region.     

Catabolism of lysine in Penicillium chrysogenum leads to formation of 2-aminoadipic acid, a precursor of penicillin biosynthesis.

Penicillium chrysogenum L2, a lysine auxotroph blocked in the early steps of the lysine pathway before 2-aminoadipic acid, was able to synthesize penicillin when supplemented with lysine. The amount of penicillin produced increased as the level of lysine in the media was increased. The same results were observed in resting-cell systems. Catabolism of [U-14C]lysine by resting cells and batch cultures of P. chrysogenum L2 resulted in the formation of labeled saccharopine and 2-aminoadipic acid. Formation of [14C]saccharopine was also observed in vitro when cell extracts of P. chrysogenum L2 and Wis 54-1255 were used. Saccharopine dehydrogenase and saccharopine reductase activities were found in cell extracts of P. chrysogenum, which indicates that lysine catabolism may proceed by reversal of the two last steps of the lysine biosynthetic pathway. In addition, a high lysine:2-ketoglutarate-6-aminotransferase activity, which converts lysine into piperideine-6-carboxylic acid, was found in cell extracts of P. chrysogenum. These results suggest that lysine is catabolized to 2-aminoadipic acid in P. chrysogenum by two different pathways. The relative contribution of lysine catabolism in providing 2-aminoadipic acid for penicillin production is discussed.     

Degradation of pyrimidine ribonucleosides by Pseudomonas aeruginosa

Pyrimidine ribonucleoside degradation in the human pathogen Pseudomonas aeruginosa ATCC 15692 was investigated. Either uracil, cytosine, 5-methylcytosine, thymine, uridine or cytidine supported P. aeruginosa growth as a nitrogen source when glucose served as the carbon source. Using thin-layer chromatographic analysis, the enzymes nucleoside hydrolase and cytosine deaninase were shown to be active in ATCC 15692. Compared to (NH₄)₂SO₄-grown cells, nucleoside hydrolase activity in ATCC 15692 approximately doubled after growth on 5-methylcytosine as a nitrogen source while its cytosine deaminase activity increased several-fold after growth on the pyrimidine bases and ribonucleosides examined as nitrogen sources. Regulation at the level of protein synthesis by 5-methylcytosine was indicated for nucleoside hydrolase and cytosine deaminase in P. aeruginosa.     

Over-expression of <Emphasis Type="Italic">pcvA</Emphasis> involved in vesicle–vacuolar fusion affects the conidiation and penicillin production in <Emphasis Type="Italic">Penicillium chrysogenum</Emphasis>

Rab GTPase is required for vesicle–vacuolar fusion during the vacuolar biogenesis in fungi. Rab GTPase-encoding gene, pcvA, was cloned from Penicillium chrysogenum: it contained five introns and its predicted protein contained the conserved Rab GTPase domain involved in GTP-binding and hydrolysis. Over-expression of pcvA significantly stimulated the vesicle–vacuolar fusion but repressed the conidiation and decreased conidial tolerance against thermal stress. Penicillin production was decreased in the pcvA over-expressed strain suggesting that pcvA is involved in vesicle–vacuolar fusion participates in the penicillin biosynthesis in P. chrysogenum.     

Carbohydrases of the rumen ciliate Epidinium ecaudatum (Crawley). Hydrolysis of plant hemicellulose fractions and beta-linked glucose polymers

1. Cell-free extracts from Epidinium ecaudatum (Crawley) hydrolysed the three hemicellulose fractions of pasture plants, but at different rates. 2. All of the constituent monosaccharides are released from the hemicellulose fractions, galactose and uronic acids being liberated at much slower rates than pentoses. 3. An arabinofuranosidase, which removes arabinose from highly branched arabinoxylan before the xylan chain can be hydrolysed, was isolated free from other pentosanases. 4. A xylanase hydrolysing xylan (by random cleavage) and xylodextrins of degree of polymerization (D.P.) > 3 to xylotriose and xylobiose was isolated free from other pentosanases. 5. A separate xylodextrinase hydrolysing (by random cleavage) xylodextrins of D.P. > 2 to xylobiose and xylose was also obtained; this enzyme did not hydrolyse xylan or xylobiose and the original extracts themselves possessed very weak xylobiase activity. 6. The epidinial extracts hydrolysed laminaribiose, laminarin, lichenin and cellodextrins of D.P. < 7 rapidly, cellobiose and gentiobiose slowly but cellulose not at all. 7. Polysaccharide glucose associated with plant linear B hemicellulose was liberated with cellobiose and possibly laminaribiose as intermediates. 8. The cellodextrinase hydrolysed cellopentaose initially to cellobiose plus cellotriose and is a distinctly different enzyme from the xylanase and xylodextrinase. 9. Extracts from Entodinium species and Eremoplastron bovis also hydrolysed all three types of plant hemicellose.     

Induction of phosphoribomutase in Bacillus cereus growing on nucleosides

In this paper we show that phosphoribomutase is induced in Bacillus cereus by the same metabolizable purine and pyrimidine ribonucleosides previously shown to induce the purine nucleoside phosphorylase (Tozzi, M.G., Sgarrella, F. and Ipata, P.L. (1981) Biochim. Biophys. Acta 678, 460–466). The mutase allows ribose 1-phosphate formed from nucleosides to be utilized by the cell through the pentose cycle, upon transformation to ribose 5-phosphate. The equilibrium constant of the mutase reaction is towards ribose-5-phosphate formation. The coordinate induction of the two enzymes completes the picture of the molecular events leading to the utilization of the sugar moiety of purine nucleosides and nucleosides as an energy source (Mura, U., Sgarrella, F. and Ipata, P.L. (1978) J. Biol. Chem. 253, 7905–7909).