Abstract
Ammonia serves as the source of energy and reductant and as a signaling molecule that regulates gene expression in obligate ammonia-oxidizing chemolithotrophic microorganisms. The gammaproteobacterium, Nitrosococcus oceani, was the first obligate ammonia-oxidizer isolated from seawater and is one of the model systems for ammonia chemolithotrophy. We compared global transcriptional responses to ammonium and the catabolic intermediate, hydroxylamine, in ammonium-starved and non-starved cultures of N. oceani to discriminate transcriptional effects of ammonium from a change in overall energy and redox status upon catabolite availability. The most highly expressed genes from ammonium- or hydroxylamine-treated relative to starved cells are implicated in catabolic electron flow, carbon fixation, nitrogen assimilation, ribosome structure and stress tolerance. Catabolic inventory-encoding genes, including electron flow-terminating Complexes IV, FoF1 ATPase, transporters, and transcriptional regulators were among the most highly expressed genes in cells exposed only to ammonium relative to starved cells, although the differences compared to steady-state transcript levels were less pronounced. Reduction in steady-state mRNA levels from hydroxylamine-treated relative to starved-cells were less than five-fold. In contrast, several transcripts from ammonium-treated relative to starved cells were significantly less abundant including those for forward Complex I and a gene cluster of cytochrome c encoding proteins. Identified uneven steady-state transcript levels of co-expressed clustered genes support previously reported differential regulation at the levels of transcription and transcript stability. Our results differentiated between rapid regulation of core genes upon a change in cellular redox status vs. those responsive to ammonium as a signaling molecule in N. oceani, both confirming and extending our knowledge of metabolic modules involved in ammonia chemolithotrophy.
Highlights
Obligate ammonia-oxidizing chemolithotrophic bacteria (AOB) facilitate key transformations in the global nitrogen cycle that interconnect nitrification, denitrification and ammonification (Klotz and Stein, 2011; Stein and Klotz, 2011; Simon and Klotz, 2013)
Steady-state mRNA levels varied from +30 to −16-fold when provided with ammonium or hydroxylamine relative to cells deprived of energy (Figure 2)
Responses to ammonium resulted in greater variation across the genome when compared to responses to hydroxylamine in genes that were under-expressed relative to starved control cells, variation in upregulated genes was similar between the two treatments (Figure 2)
Summary
Obligate ammonia-oxidizing chemolithotrophic bacteria (AOB) facilitate key transformations in the global nitrogen cycle that interconnect nitrification, denitrification and ammonification (Klotz and Stein, 2011; Stein and Klotz, 2011; Simon and Klotz, 2013). Ammonia oxidation is facilitated by two dedicated enzyme complexes that were once considered unique to AOB (Arp et al, 2002): ammonia monooxygenase (AMO, amoCAB, EC:1.14.99.39) and hydroxylamine dehydrogenase (HAO, haoA, EC:1.7.2.6). When expressed together in non-chemolithotrophs, such as methane-oxidizing bacteria (MOB; including Proteobacteria and Verrucomicrobia), these two protein complexes facilitate nitritation; the electrons extractable from hydroxylamine cannot be used to support growth via chemolithotrophic catabolism (Klotz and Stein, 2011; Stein and Klotz, 2011). In order to utilize the electrons extracted from www.frontiersin.org
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