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The Yeast Geotrichum Candidum Encodes Functional Lytic

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The Yeast Geotrichum Candidum Encodes Functional Lytic The yeast Geotrichum candidum encodes functional lytic polysaccharide monooxygenases Simon Ladevèze, Mireille Haon, Ana Villares, Bernard Cathala, Sacha Grisel, Isabelle Herpoël-Gimbert, Bernard Henrissat, Jean-Guy Berrin To cite this version: Simon Ladevèze, Mireille Haon, Ana Villares, Bernard Cathala, Sacha Grisel, et al.. The yeast Geotrichum candidum encodes functional lytic polysaccharide monooxygenases. Biotechnology for Biofuels, BioMed Central, 2017, 10 (1), 10.1186/s13068-017-0903-0. hal-01668799 HAL Id: hal-01668799 https://hal-amu.archives-ouvertes.fr/hal-01668799 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Ladevèze et al. Biotechnol Biofuels (2017) 10:215 DOI 10.1186/s13068-017-0903-0 Biotechnology for Biofuels RESEARCH Open Access The yeast Geotrichum candidum encodes functional lytic polysaccharide monooxygenases Simon Ladevèze1, Mireille Haon1, Ana Villares2, Bernard Cathala2, Sacha Grisel1, Isabelle Herpoël‑Gimbert1, Bernard Henrissat3,4,5 and Jean‑Guy Berrin1* Abstract Background: Lytic polysaccharide monooxygenases (LPMOs) are a class of powerful oxidative enzymes that have revolutionized our understanding of lignocellulose degradation. Fungal LPMOs of the AA9 family target cellulose and hemicelluloses. AA9 LPMO-coding genes have been identifed across a wide range of fungal saprotrophs (Ascomy‑ cotina, Basidiomycotina, etc.), but so far they have not been found in more basal lineages. Recent genome analysis of the yeast Geotrichum candidum (Saccharomycotina) revealed the presence of several LPMO genes, which belong to the AA9 family. Results: In this study, three AA9 LPMOs from G. candidum were successfully produced and biochemically character‑ ized. The use of native signal peptides was well suited to ensure correct processing and high recombinant production of GcLPMO9A, GcLPMO9B, and GcLPMO9C in Pichia pastoris. We show that GcLPMO9A and GcLPMO9B were both active on cellulose and xyloglucan, releasing a mixture of soluble C1- and C4-oxidized oligosaccharides from cellulose. All three enzymes disrupted cellulose fbers and signifcantly improved the saccharifcation of pretreated lignocellu‑ losic biomass upon addition to a commercial cellulase cocktail. Conclusions: The unique enzymatic arsenal of G. candidum compared to other yeasts could be benefcial for plant cell wall decomposition in a saprophytic or pathogenic context. From a biotechnological point of view, G. candidum LPMOs are promising candidates to further enhance enzyme cocktails used in biorefneries such as consolidated bioprocessing. Background [3]. Teir signifcant contribution to the saccharifcation Lignocellulosic biomass is a central resource for biofuel of biomass led to their incorporation in last-generation and bio-based industries. Increasing the recovery yields commercial enzyme cocktails [4]. LPMOs are secreted of the monosaccharide during lignocellulose conversion enzymes [5], and signal peptide removal uncovers the is one of the main bottlenecks of the biofuel produc- N-terminal histidine. Tis histidine forms part of a histi- tion process due to the complex structure of lignocel- dine brace that holds the copper ion, which is critical for lulosic material limiting enzymatic digestibility [1, 2]. enzymatic activity. Lytic polysaccharide monooxygenases (LPMOs), a new In the CAZy database, LPMOs are placed within the class of microbial enzymes, were identifed as boosters Auxiliary Activity (AA) enzyme class [6] in families AA9, of biomass deconstruction through the oxidative cleav- AA10, AA11, and AA13 [7, 8]. In flamentous fungi, age of polysaccharides increasing the activity of cellulases AA11 LPMOs cleave chitin [9] and AA13 target starch [10], while AA9 members target cellulose and hemicel- *Correspondence: jean‑[email protected] luloses [11]. In May 2017, out of 3400 members belong- 1 INRA, Aix Marseille University BBF, Biodiversité et Biotechnologie ing to the AA9 LPMO family [12], the 26 characterized Fongiques, 13288 Marseille, France Full list of author information is available at the end of the article ones all originated from flamentous fungi. Te substrate © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Ladevèze et al. Biotechnol Biofuels (2017) 10:215 Page 2 of 11 specifcities of some of these AA9 LPMOs are restricted arsenal of carbohydrate-degrading enzymes of G. can- to cellulose [13], while others display a broader sub- didum compared with other yeasts could be involved in strate specifcity toward xyloglucans and/or beta-glucans plant cell wall degradation in a saprophytic or pathogenic in addition to cellulose [14–17]. A few of them are also context but experimental investigations are necessary to active on soluble cello-oligosaccharides [15, 18, 19]. Te validate the hypothesis. In this study, we investigated the LPMO9H from Podospora anserina has been shown to substrate specifcities and contribution to biomass degra- create nicking points on cellulose microfbrils trigger- dations of three G. candidum AA9 LPMOs. ing the disintegration of the cellulose fbrillar structure through modifcation of accessible and inaccessible sur- Results faces of the fbrils [20]. Production of G. candidum AA9 LPMOs AA9 LPMO-coding genes have been identifed across Te genes products encoding GcLPMO9A (GECA Ascomycota and Basidiomycota including wood-rot- 32s02892g), GcLPMO9B (GECA32s00307g), GcLPMO9C ting fungi (white rots and brown rots); litter degrad- (GECA21s01121g), and GcLPMO9D (GECA08s04487g) ers; symbiotic, endophytic fungi; and fungal pathogens are all formed by a single AA9 catalytic module starting [21]. However, so far they have not been found in more with the canonical-conserved histidine residue common basal lineages. Te yeast Geotrichum candidum (teleo- to all LPMOs. Te AA9 modules are preceded by around morph = Galactomyces candidus) belongs to the Saccha- 18–20 residues’ signal peptides and carry a C-terminal romycotina subphylum within the Ascomycota phylum in extension (Table 1). Te overall amino acid sequence the Kingdom of Fungi. It compromises most of the asco- similarity of the G. candidum AA9 LPMOs with each mycete yeasts (e.g., Saccharomyces cerevisiae). G. candi- other is relatively high, ranging from 47 to 67%, in spite dum is well known for its creamy white color it creates of wide variations in sequence length, which ranges on the rind of brie and camembert, and is able to grow from 288 residues (GcLPMO9A) to 530 residues (GcLP- on wooden cheese boxes [22]. Some strains of Geotri- MO9C). To produce the recombinant proteins in Pichia chum candidum display high cellulolytic and xylanolytic pastoris, the C-terminal sequences were removed. An activities and can degrade efciently flter paper and cot- important feature to consider upon production of recom- ton. A GH7 cellobiohydrolase, which was found to be binant LPMOs is the perfect processing of the signal pep- the predominant protein in G. candidum secretome, was tides during secretion to ensure correct binding of the characterized and shown to have interesting biochemi- catalytic copper ion by the N-terminal histidine residue. cal properties compared with canonical Trichoderma Optimal processing of signal peptides during heterolo- reesei cellobiohydrolases, such as a broader pH range gous production is protein dependent, and heterogeneity and reduced product inhibition [23]. Recently, genomic on N-terminal sequences is a recurrent problem [25]. In analysis of the strain G. candidum CLIB 918 revealed P. pastoris, the use of the α-mating factor (α-MF) as sig- the presence of four genes encoding AA9 LPMOs [24]. nal peptide is sometimes associated with incorrect cleav- Together with four GH45 endoglucanases, these AA9 age by the Ste13 protease [26]. Terefore, we designed LPMO genes have been specifcally retained by G. candi- plasmid constructs using both the α-MF and the native dum after the flamentous fungi–yeasts split concomitant signal sequences of each G. candidum LPMOs to foster with the yeasts’ genome contraction, thus contributing recombinant protein production in P. pastoris. Using this to the phenotypic specifcity of lineages [24]. Te unique strategy, GcLPMO9A, GcLPMO9B, and GcLPMO9C Table 1 Production and activity details of AA9 LPMO used in this study Protein Modularity Predicted Signal Production Specifc Total activity Competitive assay (% residual N-glycosylation peptide yield (g/L) activity (U/L) activity) sites (U/g)a
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