Abstract
Guanidine is sensed by at least four different classes of riboswitches that are widespread in bacteria. However, only very few insights into physiological roles of guanidine exist. Genes predominantly regulated by guanidine riboswitches are Gdx transporters exporting the compound from the bacterial cell. In addition, urea/guanidine carboxylases and associated hydrolases and ABC transporters are often found combined in guanidine-inducible operons. We noted that the associated ABC transporters are configured to function as importers, challenging the current view that riboswitches solely control the detoxification of guanidine in bacteria. We demonstrate that the carboxylase pathway enables utilization of guanidine as sole nitrogen source. We isolated three enterobacteria (Raoultella terrigena, Klebsiella michiganensis, and Erwinia rhapontici) that utilize guanidine efficiently as N-source. Proteome analyses show that the expression of a carboxylase, associated hydrolases and transport genes is strongly induced by guanidine. Finding two urea/guanidine carboxylase enzymes in E. rhapontici, we demonstrate that the riboswitch-controlled carboxylase displays specificity toward guanidine, whereas the other enzyme prefers urea. We characterize the distribution of riboswitch-associated carboxylases and Gdx exporters in bacterial habitats by analyzing available metagenome data. The findings represent a paradigm shift from riboswitch-controlled detoxification of guanidine to the uptake and assimilation of this enigmatic nitrogen-rich compound.
Highlights
Guanidine is widely used in the manufacturing of plastics, as reactant in certain explosives and propellants and as a chaotropic reagent in biochemistry, a prominent role in nature has not been identified to date
We noted that the associated ATP-binding cassette-type (ABC) transporters are configured to function as importers, challenging the current view that riboswitches solely control the detoxification of guanidine in bacteria
We show that guanidine is utilized by bacteria using riboswitch-controlled carboxylases and hydrolases
Summary
Guanidine is widely used in the manufacturing of plastics, as reactant in certain explosives and propellants and as a chaotropic reagent in biochemistry, a prominent role in nature has not been identified to date. AtzF is found at a different locus in conjunction with a second urea/guanidine carboxylase gene cluster Both R. terrigena and K. michiganensis genomes contain a Gdx-type exporter under guanidine riboswitch control, whereas this activity is lacking in E. rhapontici. In order to extract information about the habitat where guanidine might play a pronounced role, we envisioned that metagenome data could be very helpful in order to connect the occurrence of a riboswitch-controlled activity to a given environment Since for these data sets there is always a more or less specific sampling, and the isolated sequences are likely to be typical of the given habitat, we analyzed riboswitches that occur in metagenome data and correlated the frequency of occurrence of Gdx-type exporters and guanidine carboxylase-type utilization pathways (GcaP) to the annotated habitat, see Figure 5 and Supporting Information File 3. We identified riboswitch-controlled GcaP activity to be more prevalent in N-scarce environments such as fresh water, marine, and soil samples, whereas in N-rich habitats such as the human gut guanidine carboxylase pathway genes are found less frequently in comparison to Gdx exporters
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