Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Abstract

Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. Graphical abstract.

Keywords: Bioconversion; Biorefinery; Circular bioeconomy; Metabolic engineering; Non-conventional yeasts; Pectin-rich agro-industrial residues.

Graphical abstract

Fig. 1

Schematic representation of the chemical structure of four pectic polysaccharides: homogalacturonan (HG), substituted HG xylogalacturonan (XGA) and rhamnogalacturonan I and II (RG-I and RG-II), based on (Mohnen 2008)

Fig. 2

Dry-weight composition of pectin-rich residues, in particular sugar beet pulp 1 (Berlowska et al. 2018) and 2 (Edwards and Doran-Peterson 2012), apple pomace 1 (Grohmann and Bothast 1994) and 2 (Bhushan et al. 2008) and citrus peel 1 (Zhou et al. 2008) and 2 (John et al. 2017)

Fig. 3

Schematic representation of S. cerevisiae strains (wild type and genetically engineered with heterologous d-galacturonic acid degradation pathways. aS. cerevisiae wild-type strain showing the basal natural uptake of d-galacturonic acid by Gal2p transporter and passive diffusion of the undissociated form through plasma membrane (PM). b Engineered S. cerevisiae strains expressing d-GalA membrane transporter Gat1 from Neurospora crassa and the uronate dehydrogenase (UDH) from Agrobacterium tumefaciens and d-galacturonic acid reductase (GAAA) from Aspergillus niger to convert d-GalA into the metabolites meso-galactaric acid and l-galactonate, (Benz et al. 2014). c Engineered S. cerevisiae strain with d-galacturonic acid plasma membrane transporters from N. crassa (GAT1) and enzymes of the d-GalA catabolic pathway GaaA, GaaB, GaaC and GaaD from A. niger (in green) and LGD1 from Trichoderma reesei (in purple); d-Fructose was used as co-substrate (Biz et al. 2016). d Engineered S. cerevisiae strains with the non-glucose repressible plasma membrane d-galacturonic acid transporter GatA from A. niger (GATA) and d-GalA catabolic pathway as in c); d-glucose was used as co-substrate (Protzko et al. 2018)

Fig. 4

Schematic representation of the d-galacturonic acid catabolic pathway proposed for Rhodosporidium toruloides IFO0880. The genes GUT1, GUT2, FBP and PGI belong to central metabolism. TAG, triacylglycerol; PPP, pentose phosphate pathway (based on (Protzko et al. 2019)

Fig. 5

Schematic representation of the initial steps of arabinose metabolism in fungi (the oxidoreductase pathway) or in bacteria (the isomerase pathway). XK, d-xylulose kinase; AI, l-arabinose isomerase; RK, l-ribulokinase; RPE, l-ribulose-5-phosphate 4-epimerase; XDH, xylitol dehydrogenase; AR, l-arabinose reductase; LAD, l-arabitol 4-dehydrogenase; LXR, l-xylulose reductase (adapted from Fonseca et al., 2007)

Fig. 6

Schematic representation of the oxidative pentose phosphate pathway (Wamelink et al. 2008)

Fig. 7

Acetic acid metabolism in yeast. The PDH pathway is indicated by blue arrows, while the PDH bypass is indicated by orange arrows. PDH: pyruvate dehydrogenase; PDC: pyruvate decarboxylase; ALD: aldehyde dehydrogenase; ACS: acetyl-CoA synthetase; ADH: alcohol dehydrogenase (Huang et al. 2016)

Fig. 8

Phylogenetic tree of relevant yeasts and related filamentous fungi discussed in this work. The tree was constructed using the neighbour-joining method based on the alignment of the large subunit (26S) ribosomal DNA sequence. The sequences used were obtained from “EnsemblFungi” database. The yeasts coloured with blue (the Ascomycetous yeasts Kluyveromyces marxianus, Kluyveromyces lactis, Meyerozyma guilliermondii, Pichia stipitis, Ogataea polymorpha and Pichia kudriavzevii) are capable of utilizing d-xylose and l-arabinose as carbon sources (C-sources). Red colour represented basidiomycetous yeasts (underlined), such as Rhodosporidium toruloides, Rhodotorula graminis and Pseudozyma hubeiensis and filamentous fungi (Trichoderma reesei, Aspergillus niger and Neurospora crassa) which are able to grow in d-galacturonic acid and also in d-xylose and l-arabinose. The yeast species Torulaspora delbrueckii represented in yellow is capable to grow in d-galacturonic acid and d-xylose. The phylogenetic tree also includes (black colour) Saccharomyces cerevisiae S288C, Zygosaccharomyces bailii, Yarrowia lipolytica and Komagataella phaffii. The yeast species S. cerevisiae K. marxianus, M. guilliermondii, P. stipitis, P. kudriavzevii and T. delbrueckii are interesting bioethanol producers, while H. uvarum is also responsible for the fruity-like aromatic compounds in fermented beverages. Y. lipolytica, P. hubeiensis, R. graminis and R. toruloides are oleaginous yeasts which can convert C-sources into high concentrations and a wide range of lipids. The species K. phaffii is mainly used as cell factory for heterologous protein expression while Z. bailii exhibits a remarkable tolerance to weak acids