Hydrolytic secretome engineering in Yarrowia lipolytica for consolidated bioprocessing on polysaccharide resources: review on starch, cellulose, xylan, and inulin

Abstract

Consolidated bioprocessing (CBP) featuring concomitant hydrolysis of renewable substrates and microbial conversion into value-added biomolecules is considered to bring substantial benefits to the overall process efficiency. The biggest challenge in developing an economically feasible CBP process is identification of bifunctional biocatalyst merging the ability to utilize the substrate and convert it to value-added product with high efficiency. Yarrowia lipolytica is known for its exceptional performance in hydrophobic substrates assimilation and storage. On the other hand, its capacity to grow on plant-derived biomass is strongly limited. Still, its high potential to simultaneously overproduce several secretory proteins makes Y. lipolytica a platform of choice for expanding its substrate range to complex polysaccharides by engineering its hydrolytic secretome. This review provides an overview of different genetic engineering strategies advancing development of Y. lipolytica strains able to grow on the following four complex polysaccharides: starch, cellulose, xylan, and inulin. Much attention has been paid to genome mining studies uncovering native potential of this species to assimilate untypical sugars, as in many cases it turns out that dormant pathways are present in Y. lipolytica’s genome. In addition, the magnitude of the economic gain by CBP processing is here discussed and supported with adequate calculations based on simulated process models. Key points • The mini-review updates the knowledge on polysaccharide-utilizing Yarrowia lipolytica. • Insight into molecular bases founding new biochemical qualities is provided. • Model industrial processes were simulated and the associated costs were calculated.

Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement

“…Consolidated bioprocessing (CBP) requires the simultaneous production of hydrolases able to degrade plant-derived polymeric substrates and of enzymes allowing the microbial conversion of the released sugars into value-added compounds, in a single step. The progresses that have been made in this competitive research area have been reviewed in a very recent publication, in which the authors discuss the economic advantages of CBP, simulate different industrial CBP models based on GM Y. lipolytica and calculate the associated costs [ 319 ]. All these tools and strategies will contribute to establish Y. lipolytica as a workhorse for a wide range of applications in the very competitive world of white biotechnology.…”

Yarrowia lipolytica strains and their biotechnological applications: how natural biodiversity and metabolic engineering could contribute to cell factories improvement

“…Beside their interest for the design of metabolic engineering strategies, GEMs can also be applied to predicting the metabolic responses of yeast cells to environmental conditions such as industrial-scale production, as demonstrated at the University of Graz (Austria) during the optimization of a Y. lipolytica bioprocess for lipid production [276]. Some statistical modeling tools, such as response surface methodology, are also now currently applied to bioprocess optimization, from wild-type as well as for GM strains [277][278][279][280]. As seen above in Section 2.3.3, a lot of research is performed on remodelling the hydrolytic secretome of Y. lipolytica in order to allow the use of plant biomass as a renewable and cheap carbon source, an approach aiming towards sustainable development and circular bio-economy.…”

Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals

“…Yarrowia lipolytica is a non-conventional yeast with significant biotechnological potential due to its native ability to produce bio-surfactants, γ -decalactone, citric acid, intracellular lipids and lipase [ 94 ]. It has undergone multiple engineering studies to increase its hydrolytic secretome to include growth on complex polysaccharides such as starch, cellulose, xylan and inulin.…”

“…Genome analysis of Y. lipolytica revealed the presence of multiple intracellular and extracellular β-glucosidase genes and putative cellobiose transporters, which explained why cellobiose could be assimilated intracellularly, but growth on cellulose was not possible [ 95 ]. Growth on pre-treated corn stover was achieved (50%) after engineering in the T. reesei cellulase genes EGII and CBHII [ 94 ]. A dormant pathway for xylose utilisation was found in the Y. lipolytica genome, but not xylan degradation.…”

“…Multiple studies engineered xylanase genes into Y. lipolytica , including the cell-surface expression of the XYN gene from Thermobacillus xylanilyticus [ 96 ]. Interestingly, the sole expression of XynII from Trichoderma harzianum into Y. lipolytica enabled growth on birchwood xylan as the sole carbon source [ 94 ].…”