Understanding and eliminating the detrimental effect of endogenous thiamine auxotrophy on metabolism of the oleaginous yeastYarrowia lipolytica

Abstract

ABSTRACTThiamine is an essential vitamin that functions as a cofactor for key enzymes in carbon and energy metabolism for all living cells. While most plants, fungi and bacteria can synthesize thiaminede novo, the oleaginous yeast,Yarrowia lipolytica, cannot. In this study, we used proteomics together with physiological characterization to understand key metabolic processes influenced and regulated by thiamine availability and identified the genetic basis of thiamine auxotrophy inY. lipolytica. Specifically, we found thiamine depletion results in decreased protein abundance of the lipid biosynthesis pathways and energy metabolism (i.e., ATP synthase), attributing to the negligible growth and poor sugar assimilation observed in our study. Using comparative genomics, we identified the missing gene scTHI13, encoding the 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase for thede novothiamine synthesis inY. lipolytica,and discovered an exceptional promoter, P3, that exhibits strong activation or tight repression by low and high thiamine concentrations, respectively. Capitalizing on the strength of our thiamine-regulated promoter (P3) to express the missing gene, we engineered the first thiamine-prototrophicY. lipolyticareported to date. By comparing this engineered strain to the wildtype, we unveiled the tight relationship linking thiamine availability to lipid biosynthesis and demonstrated enhanced lipid production with thiamine supplementation in the engineered thiamine-prototrophicY. lipolytica.IMPORTANCEThiamine plays a crucial role as an essential cofactor for enzymes in carbon and energy metabolism of all living cells. Thiamine deficiency has detrimental consequences on cellular health.Yarrowia lipolytica, a non-conventional oleaginous yeast with broad biotechnological applications, is a native thiamine auxotroph, whose effects on cellular metabolism are not well understood. Therefore,Y. lipolyticais an ideal eukaryotic host to study thiamine metabolism, especially as mammalian cells are also thiamine-auxotrophic and thiamine deficiency is implicated in several human diseases. This study elucidates the fundamentals of thiamine deficiency on cellular metabolism ofY. lipolyticaand identifies genes and novel thiamine-regulated elements that eliminate thiamine auxotrophy inY. lipolytica. Furthermore, discovery of thiamine-regulated elements enables development of thiamine biosensors with useful applications in synthetic biology and metabolic engineering.