Abstract
Auxotrophy to amino acids and vitamins is a common feature in the bacterial world shaping microbial communities through cross-feeding relations. The amino acid auxotrophy of pollutant-degrading bacteria could hamper their bioremediation potential, however, the underlying mechanisms of auxotrophy remain unexplored. We employed genome sequence-based metabolic reconstruction to identify potential mechanisms driving the amino acid auxotrophy of a Sphingomonas haloaromaticamans strain degrading the fungicide ortho-phenylphenol (OPP) and provided further verification for the identified mechanisms via in vitro bacterial assays. The analysis identified potential gaps in the biosynthesis of isoleucine, phenylalanine and tyrosine, while methionine biosynthesis was potentially effective, relying though in the presence of B12. Supplementation of the bacterium with the four amino acids in all possible combinations rescued its degrading capacity only with methionine. Genome sequence-based metabolic reconstruction and analysis suggested that the bacterium was incapable of de novo biosynthesis of B12 (missing genes for the construction of the corrin ring) but carried a complete salvage pathway for corrinoids uptake from the environment, transmembrane transportation and biosynthesis of B12. In line with this the bacterium maintained its degrading capacity and growth when supplied with environmentally relevant B12 concentrations (i.e., 0.1 ng ml–1). Using genome-based metabolic reconstruction and in vitro testing we unraveled the mechanism driving the auxotrophy of a pesticide-degrading S. haloaromaticamans. Further studies will investigate the corrinoids preferences of S. haloaromaticamans for optimum growth and OPP degradation.
Highlights
Auxotrophy is the inability of an organism to synthesize a particular biomolecule which is necessary for its growth
The biosynthetic pathway of phenylalanine and tyrosine was lacking the enzyme prephenate transaminase (EC 2.6.1.79) (Figure 1). This is commonly found in arogenate-competent bacteria, like α-proteobacteria, and is responsible for the transamination of prephenate to arogenate which is used for the biosynthesis of tyrosine or phenylalanine (Graindorge et al, 2014)
A combination of genome-based metabolic reconstruction and in vitro tests demonstrated that the auxotrophy of a fungicidedegrading S. haloaromaticamans strain was driven by the lack of a methionine synthase; a cobalamin-independent (MetE) B12-independent cobalamine synthase and the absence of a de novo B12 biosynthetic pathway
Summary
Auxotrophy is the inability of an organism to synthesize a particular biomolecule which is necessary for its growth. Amino acid auxotrophy is a common feature of bacterial genomes which have been evolutionary optimized to reduce the metabolic burden stemming from the production of energetically costly amino acids (i.e., phenylalanine, tyrosine, and methionine) (Mee et al, 2014). Instead their biosynthesis is assigned to a few bacteria leading to the establishment of a mutualistic trade among bacteria to ensure access to essential biomolecules (D’Souza et al, 2014; Pande et al, 2015). Rhodobacterales dominated the expression of vitamin-B12 synthesis, but relied on Flavobacteria for the production and supply of vitamin B7. Price et al (2018) challenged experimentally the value of comparative genomic studies (i.e., their data showed that auxotrophy in bacteria is not as common as claimed by comparative genomic studies) and suggested that their findings should be always verified experimentally
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