Purine and pyrimidine metabolism by estuarine bacteria

Abstract

Nucleotide bases are ubiquitous in living organisms, but the fate of these compounds in natural environments is poorly understood. Here we studied the metabolism of selected purines and pyrimidines in estuarine bacterial assemblages from the Øresund, Denmark. Depletion of nucleotide bases in the incubations was followed by the appearance of urea. The purine guanine and the catabolic intermediates hypoxanthine and xanthine were depleted 2 times faster from seawater incubations than the purine adenine, and 8 to 35 times faster than the pyrimidines thymine, cytosine, and uracil over the course of 141 h. After 48 h, 45 to 60% of guanine-N, hypoxanthine-N and xanthine-N was converted to urea-N while the conversion of adenine and pyrimidines to urea was slower, corresponding to 34% and 19 to 23%, respectively. After 96 h, urea concentrations declined in most of the incubations, indicating hydrolysis of urea by the bacterial populations. Bacterial metabolism of adenine in Øresund water was estimated to contribute up to 10% of the urea pool, but due to the efficient conversion of adenine, the ecosystem importance of adenine degradation to urea production was most likely greater. Growth of bacterial microcolonies on 0.2 µm pore-sized polycarbonate filters floating on natural seawater enriched with individual nucleotide bases varied significantly with substrate enrichment. Despite growth of only a small fraction of bacteria present in the natural assemblage on the filters, variation in bacterial microcolony biomass explained most of the variation in substrate utilization and urea production among the treatments. Our results suggest that bacterial catabolism of particularly purines and their intermediates, and to lesser extent pyrimidines, is a major process by which the N moiety of natural, heterocyclic bases are converted into urea which is easily assimilated.KEY WORDS: Purines · Pyrimidines · Urea production · Estuarine bacteria · Microcolony approach Resale or republication not permitted without written consent of the publisher

Role of urea in microbial metabolism in aquatic systems: a biochemical and molecular review

“…Uric acid is further broken down into ureides such as allantoin and allantoic acid by the enzymes uricase, allantoinase, and allantoicase (allantoate amidinohydrolase), producing urea (Vogels & Van der Drift 1976, Garrett & Grisham 1995, Wang et al 2008). Interestingly, guanine appears to be more widely produced, leading to a higher availability, and therefore higher rates of uptake and catabolism, compared with adenine in the marine environment (Antia et al 1975, Shah & Syrett 1982, 1984, Berg & Jørgensen 2006. On the basis of sequence similarity, a putative purine transporter gene, AaURA, was discovered in Aureococcus anophagefferens and shown to be highly expressed during growth on a number of different N sources and under N-limited conditions (Berg et al 2008).…”

“…Among the natural sources of urea in the water column are regeneration by heterotrophic bacteria (Mitamura & Saijo 1981, Cho & Azam 1995, Cho et al 1996, Berg & Jørgensen 2006, excretion by macro-and microzooplankton (Corner & Newell 1967, Mayzaud 1973, Bidigare 1983, Miller & Glibert 1998, L'Helguen et al 2005, Miller & Roman 2008, Painter et al 2008, and release by phytoplankton (Hansell & Goering 1989, Bronk et al 1998, Bronk 2002. Urea is also produced by benthic heterotrophic bacteria and macrofauna and released from sediments into the water column (Lomstein et al 1989, Lund & Blackburn 1989, Pedersen et al 1993, Therkildsen et al 1997.…”

“…In addition to uptake of external urea into the cell, urea is produced intracellularly in most organisms by the urea cycle and/or by purine catabolism (Vogels & Van der Drift 1976, Antia et al 1991, Allen et al 2006, Berg & Jørgensen 2006, Wang et al 2008). The first step in the utilization of purines as a N source involves the deamination of guanine to xanthine, or the deamination of adenine to hypoxanthinine, followed by the conversion of hypoxanthine to xanthine (Vogels & Van der Drift 1976).…”

A simple high performance liquid chromatography method for the measurement of nucleobases and the RNA and DNA content of cellular material

“…Other nucleobases were detected at 4.58 min (5mC), 5.63 min (HX), and 5.89 min (X), respectively. The LOD concentrations for primary nucleobases ranged from 20-32 nmol L -1 (Table 1), and were comparable to or lower than those reported previously for HPLC and UPLC analyses (Berg and Jørgensen 2006;Fan et al 2007;Sotgia et al 2010;Tavazzi et al 2005). The LOQ concentrations ranged from 65 to 110 nmol L -1 .…”

Dual processes for cross-boundary subsidies: incorporation of nutrients from reef-derived kelp into a seagrass ecosystem

“…We did not examine the suite of amino acids in the kelp-derived DON but did detect urea. While kelp itself is unlikely to release urea, microbial communities are likely to catabolise larger N compounds to urea (Berg & Jørgensen 2006). The ability of leaves to uptake DON derived directly or indirectly from kelp provides seagrass with a shortcut to bioavailable N directly from the N between seagrass leaves only and those with rhizome and roots in our experiment suggests that N can be taken up through both leaves and roots, which is supported by Vonk et al (2008) who demonstrated that both DIN and DON are taken up by seagrass leaves and roots.…”