Proteomic Analysis of Renal Biomarkers of Kidney Allograft Fibrosis-A Study in Renal Transplant Patients.

Renal transplantation is the preferred treatment of end stage renal disease, but allograft survival is limited by the development of interstitial fibrosis and tubular atrophy in response to various stimuli. Much effort has been put into identifying new protein markers of fibrosis to support the diagnosis. In the present work, we performed an in-depth quantitative proteomics analysis of allograft biopsies from 31 prevalent renal transplant patients and correlated the quantified proteins with the volume fraction of fibrosis as determined by a morphometric method. Linear regression analysis identified four proteins that were highly associated with the degree of interstitial fibrosis, namely Coagulation Factor XIII A chain (estimate 18.7, adjusted p < 0.03), Uridine Phosphorylase 1 (estimate 19.4, adjusted p < 0.001), Actin-related protein 2/3 subunit 2 (estimate 34.2, adjusted p < 0.05) and Cytochrome C Oxidase Assembly Factor 6 homolog (estimate -44.9, adjusted p < 0.002), even after multiple testing. Proteins that were negatively associated with fibrosis (p < 0.005) were primarily related to normal metabolic processes and respiration, whereas proteins that were positively associated with fibrosis (p < 0.005) were involved in catabolic processes, cytoskeleton organization and the immune response. The identified proteins may be candidates for further validation with regards to renal fibrosis. The results support the notion that cytoskeleton organization and immune responses are prevalent processes in renal allograft fibrosis.

Crystallization and preliminary X-ray diffraction analysis of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil.

Uridine phosphorylase (UPh; EC 2.4.2.3) catalyzes the phosphorolytic cleavage of the N-glycosidic bond of uridine to form ribose 1-phosphate and uracil. This enzyme also activates pyrimidine-containing drugs, including 5-fluorouracil (5-FU). In order to better understand the mechanism of the enzyme-drug interaction, the complex of Salmonella typhimurium UPh with 5-FU was cocrystallized using the hanging-drop vapour-diffusion method at 294 K. X-ray diffraction data were collected to 2.2 A resolution. Analysis of these data revealed that the crystal belonged to space group C2, with unit-cell parameters a = 158.26, b = 93.04, c = 149.87 A, alpha = gamma = 90, beta = 90.65 degrees . The solvent content was 45.85% assuming the presence of six hexameric molecules of the complex in the unit cell.

[Protein engineering of uridine phosphorylase from Escherichia coli K-12. II. Comparative study of hybrid and mutant forms of uridine phosphorylases]. / Belkovaia inzheneriia uridinfosforilazy Escherichia coli K-12 II. Sravnitel'noe izuchenie svoistv gibridnykh i mutantnykh form uridinfosforilaz.

Genes for hybrid uridine phosphorylases (UPases) consisting of fragments of amino acid sequences of UPases from Escherichia coli and Salmonella typhimurium were constructed. Producing strains of the corresponding proteins were genetically engineered. Mutant forms of the E. coli K-12 UPase were produced by site-directed mutagenesis. A comparative study of the enzyme properties of the mutant and hybrid forms of bacterial UPases was performed. It was shown that Asp27 unlike Asp5 and Asp29 residues of the E. coli UPase forms part of the active site of the protein. A scheme of the involvement of Asp27 in the binding of inorganic phosphate is proposed.

Uridine phosphorylase association with vimentin. Intracellular distribution and localization.

Uridine phosphorylase (UPase), a key enzyme in the pyrimidine salvage pathway, is associated with the intermediate filament protein vimentin, in NIH 3T3 fibroblasts and colon 26 cells. Affinity chromatography was utilized to purify UPase from colon 26 and NIH 3T3 cells using the uridine phosphorylase inhibitor 5'-amino benzylacyclouridine linked to an agarose matrix. Vimentin copurification with UPase was confirmed using both Western blot analysis and MALDI-MS methods. Separation of cytosolic proteins using gel filtration chromatography yields a high molecular weight complex containing UPase and vimentin. Purified recombinant UPase and recombinant vimentin were shown to bind in vitro with an affinity of 120 pm and a stoichiometry of 1:2. Immunofluorescence techniques confirm that UPase is associated with vimentin in both NIH 3T3 and colon 26 cells and that depolymerization of the microtubule system using nocodazole results in UPase remaining associated with the collapsed intermediate filament, vimentin. Our data demonstrate that UPase is associated with both the soluble and insoluble pools of vimentin. Approximately 60-70% of the total UPase exists in the cytosol as a soluble protein. Sequential extraction of NIH 3T3 or colon 26 cells liberates an additional 30-40% UPase activity associated with a detergent extractable fraction. All pools of UPase have been shown to possess enzymatic activity. We demonstrate for the first time that UPase is associated with vimentin and the existence of an enzymatically active cytoskeleton-associated UPase.

Trichinella spiralis and Trichinella pseudospiralis: developmental patterns of enzymes involved in thymidylate biosynthesis and pyrimidine salvage.

Thymidylate synthase, dihydrofolate reductase and dUTPase specific activities were found to remain at a high and constant level in crude extracts from adult worms of Trichinella spiralis, as well as from muscle larvae of both Trichinella spiralis (isolated 1-24 months after infection) and Trichinella pseudospiralis (isolated 5.5-13 months after infection). The results obtained with Trichinella pseudospiralis muscle larvae isolated with the use of pepsin did not differ from those obtained when pepsin was not used. No thymidine kinase activity could be detected in muscle larvae of either species and thymidine phosphorylase could be found only in T. pseudospiralis larvae isolated without the use of pepsin. Muscle larvae of both species contained orotidylate phosphoribosyl transferase activity, pointing to a possibility of 5-fluorouracil activation. Uridine phosphorylase, another enzyme involved in 5-fluorouracil anabolism, was also present in T. pseudospiralis muscle larvae. Results of comparative studies on inhibition of purified T. spiralis and rat thymidylate synthases by substrate (4-thio-5-fluoro-dUMP, 2-thio-5-fluoro-dCMP and N4-hydroxy-dCMP) and cofactor (ZD 9331) analogues indicated only dUMP analogues to show feeble selectivity towards the parasite enzyme. A hypothesis is discussed, assuming high expression of thymidylate synthase in muscle larvae to be connected with their cells being arrested in the cell cycle.

Enzymes of pyrimidine metabolism in the musculus complexus of the chick during development.

The pattern of cytidylate and uridylate phosphatase, uridine phosphorylase, cytidine and cytosine deaminase activities has been studied in M. complexus during chick development. The comparison of these enzyme activities with thigh muscles ones has shown that quantitative and temporal changes occur, in parallel with the unusual pre-natal and early post-natal development of M. complexus. The results suggest that during the first period of incubation, UMP might follow the anabolic pathway UMP-UTP, which leads to cytidine nucleotides, while approaching the hatching, the catabolic pathway should prevail. In addition, immediately after hatching, pyrimidine metabolism is especially supported by cytidine nucleotides.

Circadian rhythm of hepatic uridine phosphorylase activity and plasma concentration of uridine in mice.

The activity of hepatic uridine phosphorylase (EC 2.4.2.3.) in male mice (24-29 g) maintained in standardized conditions of 12 hr light (0600-1800 hr) alternating with 12 hr darkness (1800-0600 hr), food and water ad lib., exhibited a circadian rhythm (P less than 0.0001, Cosinor analysis). The peak of enzyme activity (559 +/- 25 pmol/min/mg protein) occurred at 15 hr after light onset (HALO) with the nadir (139 +/- 25 pmol/min/mg protein) at 3 HALO when samples were taken every 4 hr. Female mice showed essentially the same pattern. A circadian rhythm (P less than 0.0001, Cosinor analysis) was also observed when the light-dark cycle was shifted (reverse cycle) so that the lights went on at 2200 hr and off at 1000 hr. Under the reverse cycle condition, there was a corresponding shift in the enzyme activity with a lag period of 3.5 hr in the time of maximum and minimum enzyme activities (i.e. the peak at 11 HALO and the nadir at 23 HALO) after a 2-week adaptation period. The lag period was reduced to 1 hr after 4 weeks of adaptation, and no further change was observed after 6 weeks of adaptation. The plasma concentration of uridine also exhibited a circadian rhythm (P less than 0.0001, Cosinor analysis) with peak concentration (10 microM) occurring at 2 HALO and a nadir (5 microM) at 14 HALO. The circadian rhythm observed in the plasma concentration of uridine is the inverse of that for uridine phosphorylase activity. These results demonstrate that hepatic uridine phosphorylase plays an important role in the regulation of the uridine level in the blood which, in turn, may be involved in the humoral control of sleep by uridine. This may also be of clinical significance in enhancing the antitumor efficacy of the 5-fluorinated pyrimidines by modulating the time of their administration.

Enhanced antitumor activity of 5'-deoxy-5-fluorouridine against Lewis lung carcinoma in aged hybrid (C57BL/6 x DBA/2) F1 mice.

The antitumor activity of 5'-deoxy-5-fluorouridine (5'-DFUR) against Lewis lung carcinoma was examined by implanting the tumor subcutaneously into young (8-11 weeks) and old (24-41 weeks) hybrid (C57BL/6 x DBA/2)F1 (BDF1) male mice. Oral administration of 5'-DFUR induced a small (7 of 100) but significant (p less than 0.05) number of 70-d survivors in young mice. However, the antitumor activity was further enhanced in the old mice, and 15 of 46 (32.6%) and 11 of 62 (17.7%) mice survived for 70-d by treatment with 2000 and 1000 mg 5'-DFUR/kg/d, respectively, given on days 1, 5, and 9. The reason for the higher cure rate in old mice was partly analyzed. Toxicity of 5'-DFUR in young and old mice did not differ significantly, regardless of the presence (except 2000 mg/kg) or absence of Lewis lung carcinoma. No survivors were observed after treatment with 5'-DFUR when the tumors were implanted into the aged (15-38 weeks) syngeneic hosts, C57BL/6 mice. On the other hand, the survival time of BDF1 mice implanted with a constant number of the tumor cells increased significantly with the increase in host age and reached a maximum at the age of 24 weeks. These findings suggest that an optimal activation of 5'-DFUR (to 5-FU) was carried out in the old BDF1 mice bearing Lewis lung carcinoma and/or that a host-mediated antitumor mechanism of BDF1 mice, which is reinforced with aging, might participate in the enhancement of the antitumor activity of 5'-DFUR against this tumor.

Effects of N,N-dimethylformamide and sodium butyrate on enzymes of pyrimidine metabolism in cultured human tumor cells.

Effects of a 7-day treatment with the maturational agents DMF and sodium butyrate on enzymes of pyrimidine metabolism, growth rate and cell maturation were assessed in 5 human tumor cell lines, ARH-77 (myeloma), K-562 (chronic myeloid leukemia), KG-1 (myeloid leukemia), HL-60 (promyelocytic leukemia) and RWLy-1 (non-Hodgkin's lymphoma). DMF lengthened the doubling times of all five cell lines while sodium butyrate lengthened only those of K-562, HL-60 and RWLy-1. Full maturation was induced only in HL-60 by either agent and in K-562 by butyrate. Exposure resulted in a decreased activity of the anabolic enzyme orotate phosphoribosyltransferase (EC 2.4.2.10) and increased activities of the catabolic enzymes thymidine phosphorylase (EC 2.4.2.4) and dihydrouracil dehydrogenase (EC 1.3.1.2). Changes in the amphibolic enzyme, uridine phosphorylase (EC 2.4.2.3) did not follow any apparent pattern. This study indicates that the pattern of pyrimidine metabolism differs between the differentiated and slowly growing, and undifferentiated rapidly growing counterpart of several human tumors, suggesting that enzymes of pyrimidine metabolism can be used as markers for cellular growth and/or maturity.

Mechanisms of potentiation of antitumor activity of 5-fluorouracil by ribothymidine in a mouse tumor system.

In the presence of ribothymidine, the uptake of 5-fluorouracil (5-FU) was enhanced in Ehrlich ascites carcinoma cells in vitro, and was efficiently converted to FU-nucleotides. In these cells, almost all ribothymidine was found to be converted to thymine by, presumably, uridine phosphorylase. The enhanced uptake of 5-FU and its efficient conversion to FU-nucleotides were also observed in Ehrlich ascites carcinoma of ribothymidine-coadministered mice. The radioactivity of 5-FU-14C in the carcinoma cells, which was detected mainly in the acid-soluble fraction immediately after the administration and then shifted to the ribonucleic acid fraction, was approximately 2-fold higher in the ribothymidine-coadministered group than in the control group. On the other hand, ribothymidine-14C was also taken up by the carcinoma cells and an appreciable portion of its radioactivity appeared in the thymine fraction. Thymine produced from ribothymidine-14C was also detected in the extracellular ascitic fluid. The conversion of ribothymidine to thymine was assumed to be catalyzed by uridine phosphorylase, suggesting that ribose 1-phosphate was coproduced and served as a ribose donor for 5-FU. These results suggest that ribothymidine may act as a ribose donor for 5-FU to form FU-nucleotides via 5-fluorouridine in carcinoma cells, resulting in the potentiation of 5-FU activity.

Enzymes of pyrimidine biosynthesis in Crithidia luciliae.

Evidence has been obtained for the presence of enzymes of both the de novo and salvage pyrimidine pathways in the protozoan parasite, Crithidia luciliae. Carbamyl phosphate synthetase-II activity could not be unequivocally demonstrated in crude extracts. However, a distinct peak of activity with a molecular weight of approximately 500 000 was observed following chromatography on Sepharose CL-6B. The enzyme preferentially utilised glutamine with respect to ammonia. It was inhibited by UTP and 5-phosphoribosyl-1-diphosphate had a small activating effect. Carbamyl phosphate synthesis by a 'phosphorolytic' citrullinase could not be demonstrated. The ensuing three de novo enzymes could also be separated on Sepharose CL-6B. Approximate molecular weights were estimated: aspartate transcarbamylase (150,000); dihydroorotase (90,000) and dihydroorotate dehydrogenase (70,000). As reported previously, orotate phosphoribosyltransferase and orotidylate decarboxylase were particulate, being associated with the glucosome. Activities of the salvage enzymes, uracil phosphoribosyltransferase, uridine phosphorylase and uridine nucleosidase were observed. All enzymes were cytoplasmic. No uridine kinase activity was detected.

Pyrimidine nucleoside phosphorylase assay by automated high-performance liquid chromatography.

A new assay for pyrimidine nucleoside phosphorylase is reported. This method utilizes an isocratic reversed-phase high-performance liquid chromatographic system for separation of nucleosides and bases. Product detection is accompanied by ultraviolet monitoring and radioactive flow detection. Use of an automated sample injector allows for the analysis of a series of samples, with data recorded onto a microprocessor-based cassette recorder. Data can then be downloaded into computer memory. The velocity of uridine phosphorylase (E.C. 2.4.2.3) was a linear function of enzyme concentration. The Michaelis constant for uridine at pH 8.0 was found to be in close agreement with the value obtained by a thin-layer chromatographic assay method.

High uridine phosphorylase activity in human melanoma tumor.

Uridine (Urd) phosphorylase and Urd kinase activities were examined in 4 human tumor types including melanoma and human and mouse melanoma cell lines. Urd phosphorylase activity in melanoma tumor specimens was higher than in specimens of colon, ovarian, and breast tumors. Urd kinase activity levels were similar in the 4 tumor types. In 3 human melanoma cell lines examined, Urd phosphorylase activity was markedly greater than in mouse B16 melanoma cells, while Urd kinase activity did not differ appreciably in the human and mouse cell lines. Urd phosphorylase activity in crude extract preparations from different melanoma cell lines showed similar substrate affinity and sensitivity to 1-(2'-deoxy-beta-D-glucopyranosyl)-thymine, a specific inhibitor. The high Urd phosphorylase activity found in melanoma tumor tissue may be exploited in the treatment of malignant melanoma with antipyrimidine agents. Cultured human melanoma cells retain this biochemical characteristic and may serve as appropriate in vitro models for the human tumor in studies concerning pyrimidine metabolism.

Effect of coadministration of thymine or thymidine on the antitumor activity of 1-(2-tetrahydrofuryl)-5-fluorouracil and 5-fluorouracil.

The antitumor activity of 1-(2-tetrahydrofuryl)-5-fluorouracil (FT-207) on sarcoma was enhanced by oral coadministration of uracil, thymine, or thymidine. The activity was enhanced equally by thymine and by uracil than by thymidine, but thymine caused loss in body weight. The antitumor activity of 5-fluorouracil (5-FU) was also enhanced by thymine or uracil, but both caused loss in body weight. Degradation of 5-FU in vitro was inhibited more by thymine than by uracil. Phosphorylation of 5-FU, however, was not inhibited by uracil, thymine, or thymidine, even at 100 times the concentration of 5-FU. These results suggest that the mechanism of enhancement of the antitumor activity of FT-207 by thymine or thymidine was similar to that by uracil, and that uracil had more effect than thymine or thymidine in enhancing antitumor effect of these drugs to FT-207 without toxicity.

Incorporation characteristics of uracil, uridine, and orotic acid into ribonucleic acid of neoplastic cells.

Incorporation of uracil and uridine into ribonucleic acid (RNA) was compared among the ascitic and solid forms of Ehrlich mouse tumor, Morris hepatoma, Rhodamine sarcoma, gastric cancer and ulcer from human patients, and several normal rat tissues. Of these cells tested, the cells of Ehrlich ascites and solid tumors, human gastric cancer and ulcer, and certain tissues of a normal rat showed a considerably high activity. Furthermore, Ehrlich ascites tumor cells indicating a high incorporation activity was also high in activities of both phosphorylase and kinase for uridine, while Rhodamine sarcoma as a representative having a low incorporation activity was considerably low in these two enzymic activities. RNA synthesis from uridine phosphates by Rhodamine sarcoma was maintained to a fairly high extent contrary to its low activities of the phosphorylase and the kinase. Consequently, the low utilization of uracil and uridine by certain tumors was suggested to be due to the extremely low activities of both enzymes.