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Background  A recently constructed cellulolytic  Yarrowia lipolytica  is able to grow efficiently on an industrial organosolv cellulose pulp, but shows limited ability to degrade crystalline cellulose. In this work, we have further engineered this strain, adding accessory proteins xylanase II (XYNII), lytic polysaccharide monooxygenase (LPMO), and swollenin (SWO) from  Trichoderma reesei  in order to enhance the degradation of recalcitrant substrate.    Results  The production of EG I was enhanced using a promoter engineering strategy. This provided a new cellulolytic  Y. lipolytica  strain, which compared to the parent strain, exhibited higher hydrolytic activity on different cellulosic substrates. Furthermore, three accessory proteins,  Tr XYNII,  Tr LPMOA and  Tr SWO, were individually expressed in cellulolytic and non-cellulolytic  Y. lipolytica . The amount of rh Tr XYNII and rh Tr LPMOA secreted by non-cellulolytic  Y. lipolytica  in YTD medium during batch cultivation in flasks was approximately 62 and 52 mg/L, respectively. The purified rh Tr XYNII showed a specific activity of 532 U/mg-protein on beechwood xylan, while rh Tr LPMOA exhibited a specific activity of 14.4 U/g-protein when using the Amplex Red/horseradish peroxidase assay. Characterization of rh Tr LPMOA revealed that this protein displays broad specificity against β-(1,4)-linked glucans, but is inactive on xylan. Further studies showed that the presence of  Tr LPMOA synergistically enhanced enzymatic hydrolysis of cellulose by cellulases, while  Tr SWO1 boosted cellulose hydrolysis only when it was applied before the action of cellulases. The presence of r Tr XYNII enhanced enzymatic hydrolysis of an industrial cellulose pulp and of wheat straw. Co-expressing  Tr XYNII and  Tr LPMOA in cellulolytic  Y. lipolytica  with enhanced EG I production procured a novel engineered  Y. lipolytica  strain that displayed enhanced ability to degrade both amorphous (CIMV-cellulose) and recalcitrant crystalline cellulose in complex biomass (wheat straw) by 16 and 90%, respectively.    Conclusions  This study has provided a potent cellulose-degrading  Y. lipolytica  strain that co-expresses a core set of cellulolytic enzymes and some accessory proteins. Results reveal that the tuning of cellulase production and the production of accessory proteins leads to optimized performance. Accordingly, the beneficial effect of accessory proteins for cellulase-mediated degradation of cellulose is underlined, especially when crystalline cellulose and complex biomass are used as substrates. Findings specifically underline the benefits and specific properties of swollenin. Although in our study swollenin clearly promoted cellulase action, its use requires process redesign to accommodate its specific mode of action.    Electronic supplementary material  The online version of this article (10.1186/s13068-017-0990-y) contains supplementary material, which is available to authorized users.

Expressing accessory proteins in cellulolytic Yarrowia lipolytica to improve the conversion yield of recalcitrant cellulose