Abstract
A recent report suggested that the thioredoxin-dependent metabolic regulation, which is widespread in all domains of life, existed in methanogenic archaea about 3.5 billion years ago. We now show that the respective electron delivery enzyme (thioredoxin reductase, TrxR), although structurally similar to flavin-containing NADPH-dependent TrxRs (NTR), lacked an NADPH-binding site and was dependent on reduced coenzyme F(420) (F(420)H(2)), a stronger reductant with a mid-point redox potential (E'(0)) of -360 mV; E'(0) of NAD(P)H is -320 mV. Because F(420) is a deazaflavin, this enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). It transferred electrons from F(420)H(2) to thioredoxin via protein-bound flavin; K(m) values for thioredoxin and F(420)H(2) were 6.3 and 28.6 μm, respectively. The E'(0) of DFTR-bound flavin was approximately -389 mV, making electron transfer from NAD(P)H or F(420)H(2) to flavin endergonic. However, under high partial pressures of hydrogen prevailing on early Earth and present day deep-sea volcanoes, the potential for the F(420)/F(420)H(2) pair could be as low as -425 mV, making DFTR efficient. The presence of DFTR exclusively in ancient methanogens and mostly in the early Earth environment of deep-sea volcanoes and DFTR's characteristics suggest that the enzyme developed on early Earth and gave rise to NTR. A phylogenetic analysis revealed six more novel-type TrxR groups and suggested that the broader flavin-containing disulfide oxidoreductase family is more diverse than previously considered. The unprecedented structural similarities between an F(420)-dependent enzyme (DFTR) and an NADPH-dependent enzyme (NTR) brought new thoughts to investigations on F(420) systems involved in microbial pathogenesis and antibiotic production.