Racemization in Reverse: Evidence that D-Amino Acid Toxicity on Earth Is Controlled by Bacteria with Racemases

Abstract

D-amino acids are toxic for life on Earth. Yet, they form constantly due to geochemical racemization and bacterial growth (the cell walls of which contain D-amino acids), raising the fundamental question of how they ultimately are recycled. This study provides evidence that bacteria use D-amino acids as a source of nitrogen by running enzymatic racemization in reverse. Consequently, when soils are inundated with racemic amino acids, resident bacteria consume D- as well as L-enantiomers, either simultaneously or sequentially depending on the level of their racemase activity. Bacteria thus protect life on Earth by keeping environments D-amino acid free.

Bacterial d -amino acids suppress sinonasal innate immunity through sweet taste receptors in solitary chemosensory cells

“…Life has evolved to predominately utilize L-amino acids as protein building blocks, but bacteria produce a diverse array of D-amino acids used as cell wall structural components and possibly intercellular signals. The racemase activity of bacteria and their resulting ability to interconvert and metabolize both D- and L-amino acids have been proposed to be responsible for maintaining the relatively low D-amino acid:L-amino acid ratio found on earth (34). The gram-negative bacterium Vibrio cholera and the gram-positive bacterium Bacillus subtilis produce D-amino acids, which may reduce peptidoglycan synthesis and influence cell wall remodeling (35).…”

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

“…Other described but less studied roles of d -amino acids include developmental regulation in certain groups of vertebrates (D'Aniello, 2007; Wolosker et al, 2008; Canu et al, 2014), osmoprotection and development in some invertebrates (Abe et al, 2005; Yoshikawa et al, 2011), regulation of biofilm production in several bacterial species (Cava et al, 2011), and calcium channel regulation in pollen tubes in Arabidopsis (Michard et al, 2011). d -amino acids can also accumulate in soils and aquatic sediments under the right conditions, as a result of both the spontaneous racemization of free amino acids or the accumulation of peptidoglycan and other d -amino acid rich bacterial polymers (Vranova et al, 2011; Steen et al, 2013; Zhang and Sun, 2014). Hence, d -amino acids may constitute a relevant nutrient source for soil microbes, although this aspect has not been comprehensively studied.…”

“…Catabolism of d -amino acid may be important in environments where other nitrogen sources are scarce. d -amino acids are considerably toxic for many organisms, including many bacteria, yeasts and plants (Yow et al, 2006; Chen et al, 2010; Gördes et al, 2011, 2013; Zhang and Sun, 2014; Leiman et al, 2015), and thus the ecological interactions between fungi, plants and environmental d -amino acids is worth examining. At least two pathogenic yeast species, Candida glabrata and Candida orthopsilosis harbor their own horizontally acquired amino acid racemases (Fitzpatrick et al, 2008; Marcet-Houben and Gabaldón, 2010), an aspartate-glutamate-hydantoin racemase and a proline racemase, respectively.…”

Aspartic Acid Racemization Method for Age Estimation in Human Tissues: A Review

“…Contamination factor for example connective tissues, blood vessels or bacteria may also effect to D/L ratio of amino acids (Pfeiffer et al 1995) because the bacterial wall composes of many D-amino acids. (Schleifer & Kandler 1972;Voet & Voet 2004;Zhang & Sun 2014).…”