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Background  The oleaginous yeast,  Yarrowia lipolytica , has been utilized as an industrial host for about 60 years for various applications. Recently, the metabolic engineering of this host has become increasingly popular due to its ability to accumulate lipids as well as improvements made toward developing new genetic tools.  Y. lipolytica  can robustly metabolize glucose, glycerol, and even different lipid classes. However, little is known about its xylose metabolizing capability. Given the desirability of having a robust xylose utilizing strain of  Y. lipolytica , we performed a comprehensive investigation and elucidation of the existing components of its xylose metabolic pathway.    Results  A quick and efficient means of determining functionality of the candidate xylose pathway genes (XYR, XDH, and XKS) from  Y. lipolytica  was desirable. We challenged  Escherichia coli  mutants lacking either the xylose isomerase ( xylA ) gene or the xylulose kinase ( xylB ) gene to grow on xylose minimal media by expressing the candidate genes from  Y. lipolytica . We showed that the XKS of  Y. lipolytica  is able to rescue xylose growth of  E. coli  Δ xylB,  and the XDH enabled growth on xylitol, but not on xylose, of  E. coli  Δ xylA . Overexpression of XKS and XDH in  Y. lipolytica  improved growth on xylitol, indicating that expression of the native enzymes was limiting. Overexpression of XKS and XDH in  Y. lipolytica  also enables robust growth on xylose under high nitrogen conditions without the need for adaptation. These results prove that a complete xylose pathway exists in  Y. lipolytica , but the pathway is poorly expressed. To elucidate the XYR gene, we applied the  E. coli  Δ xylA  xylose growth challenge with 14 candidate XYR genes and XDH. The XYR2 candidate was able to rescue growth of  E. coli  Δ xylA  xylose on minimal media.    Conclusions  While a native xylose pathway exists in  Y. lipolytica , the microorganism’s inability to grow robustly on xylose is an effect of cryptic genetic circuits that control expression of key enzymes in the metabolic pathway. We have characterized the key enzymes associated with xylose metabolism and demonstrated that gene regulatory issues can be overcome using strong hybrid promoters to attain robust growth on xylose without adaptation.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-016-0562-6) contains supplementary material, which is available to authorized users.

Engineering xylose utilization in Yarrowia lipolytica by understanding its cryptic xylose pathway