Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications

Abstract

Cyanobacteria are widely-diverse prokaryotes that colonize our planet. They use solar energy to assimilate huge amounts of atmospheric CO2 and produce a large part of the biomass and oxygen that sustain most life forms. Cyanobacteria are therefore increasingly studied for basic research objectives, as well as for the photosynthetic production of chemicals with industrial interests. One potential approach to reduce the cost of future bioproduction processes is to couple them with wastewater treatment, often polluted with urea, which in any case is cheaper than nitrate. As of yet, however, research has mostly focused on a very small number of model cyanobacteria growing on nitrate. Thus, the genetic inventory of the cyanobacterial phylum is still insufficiently employed to meaningfully select the right host for the right purpose. This review reports what is known about urea transport and catabolism in cyanobacteria, and what can be inferred from the comparative analysis of the publicly available genome sequence of the 308 cyanobacteria. We found that most cyanobacteria mostly harbor the genes encoding the urea catabolytic enzymes urease (ureABCDEFG), but not systematically, together with the urea transport (urtABCDE). These findings are consistent with the capacity of the few tested cyanobacteria that grow on urea as the sole nitrogen source. They also indicate that urease is important for the detoxification of internally generated urea (re-cycling its carbon and nitrogen). In contrast, several cyanobacteria have urtABCDE but not ureABCDEFG, suggesting that urtABCDE could operate in the transport of not only urea but also of other nutrients. Only four cyanobacteria appeared to have the genes encoding the urea carboxylase (uc) and allophanate hydrolase (ah) enzymes that sequentially catabolize urea. Three of these cyanobacteria belongs to the genera Gloeobacter and Gloeomargarita that have likely diverged early from other cyanobacteria, suggesting that the urea carboxylase and allophanate hydrolase enzymes appeared in cyanobacteria before urease.

A Genetic Toolbox for the New Model Cyanobacterium Cyanothece PCC 7425: A Case Study for the Photosynthetic Production of Limonene

“…The results showed that cells grew well on urea up to 2 mM, whereas higher urea concentrations reduced the duration of healthy growth and production of biomass ( Supplementary Figure S1). After 7-10 days of cultivation on urea, Cyanothece PCC 7425 can turn yellowish, as previously observed in the phylogenetically distant cyanobacteria Anabaena cylindrica, Synechococcus PCC 7002 (Sakamoto et al, 1998) and Synechocystis PCC 6803 growing on urea as the sole nitrogen source (Veaudor et al, 2019). Again as observed in Synechocystis PCC 6803 (Veaudor et al, 2018), once installed the chlorosis process decreased the cell viability measured by plating assays on standard growth medium (it contains nitrate, not urea).…”

“…Cyanobacteria, the oldest and largest phylum of prokaryotes that perform the plant-like photosynthesis (Schirrmeister et al, 2015), are regarded as the ancestors of the plant chloroplast (Ponce-Toledo et al, 2017) and the purveyors of the oxygen that shaped our biosphere (Hamilton et al, 2016). Contemporary cyanobacteria still capture a vast quantity of solar energy to assimilate huge amounts of CO 2 (Dai et al, 2018) and nitrogen (nitrate, ammonium or urea) (Singh et al, 2016;Veaudor et al, 2019) to produce an enormous biomass that sustain most life forms on our planet. In colonizing most waters (fresh, brackish and marine) and soils (even deserts) biotopes, cyanobacteria have developed as widely diverse organisms.…”

“…Cyanothece PCC 7425 has two radA DNA-repair genes whereas all three model cyanobacteria have a single-copy radA gene (Cassier-Chauvat et al, 2016). Also interestingly, Cyanothece PCC 7425 possesses the full panoply of genes coding for urea uptake and catabolism, whereas Synechococcus PCC 7942 has no such genes, and Synechocystis PCC 6803 and Synechococcus PCC 7002 have no genes for the ureolytic enzymes urea carboxylase and allophanate hydrolase (Veaudor et al, 2019).…”

“…This is the first report of the engineering of a Cyanothece strain for the photosynthetic production of a chemical, and the first demonstration that a terpene can be produced by an engineered cyanobacterium growing on urea as the sole nitrogen source. This suggests that it could be important in the future to couple chemicals productions with water treatment to reduce the costs (Veaudor et al, 2019).…”

Current knowledge and recent advances in understanding metabolism of the model cyanobacteriumSynechocystissp. PCC 6803

“…Synechocystis can also utilize urea, which is imported into the cell via a transporter complex composed of five subunits, UrtA-E [208]. Urea is converted into two molecules of ammonia via the urease complex comprising three subunits, UreA-C, which is assembled by four accessory proteins, UreD-G [209].…”