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Additional file 1.

Additional file 1.

Additional file 4: Figure S4. Phylogenetic analysis of lignin-induced P. anserina AA7 oxidoreductases.

Additional file 3. Structure-based amino acid “segments only” sequence alignment of AA9 LPMOs.

Additional file 2. Structure-based amino acid “full sequence” alignment of AA9 LPMOs.

Additional file 2: Proteomic analysis: Figure S2. Proteomic analysis of secreted proteins during growth of P. anserina on glucuronoarabinoxylan (GAX) and GAX + Lignin. Grouped according to functional annotations. Figure S3. Proteomic analysis of secreted individual proteins during growth of P. anserina on glucuronoarabinoxylan (GAX) and GAX + Lignin. Accession numbers according to JGI database (P. anserina mat + v1.0).

Additional file 1: Substrate characterization data: Figure S1. Py-GC-HR-MS pyrograms (TIC) of wheat straw, wheat straw lignin and glucuronoarabinoxylan (GAX). Table S1. Py-GC-HR-MS relative abundance of lignin compounds in wheat straw lignin isolate used for fermentations with P. anserina. Table S2. Semiquantitative 1H–13C HSQC NMR structural characterization of wheat straw lignin isolate used for fermentations with P. anserina.

Additional file 1. Fig. S1. MW distributions of TXG-digests from NcLPMO9C and NcLPMO9M. Fig. S2. HPAEC elution patterns of β-galactosidase treated XEG and NcLPMO9C digested TXG. Fig. S3. MALDI-TOF mass spectra of β-galactosidase treated XEG and NcLPMO9C digested TXG. Fig. S4. Negative ion mode CID-MS/MS fragmentation patterns of XXX and XLL present in the NcLPMO9C-TXG-digest. Fig. S5. Negative ion mode CID-MS/MS fragmentation patterns of XGX and LXG present in the NcLPMO9M-TXG-digest. Fig. S6. HILIC-ESI-MS base-peak chromatograms of BCXG-digests from NcLPMO9C and NcLPMO9M. Fig. S7. Phylogenetic tree in circle style of “full length” (FL) AA9 LPMOs. Fig. S8. Phylogenetic tree in circle style of “segments only” (SO) AA9 LPMOs. Fig. S9. Crystal structures and homology models of LPMOs tested on XG. Fig. S10. HPAEC elution patterns of TXG, and of TXG digested with NcLPMO9F with the addition of Asc. Fig. S11. HPAEC elution patterns of TXG, and of TXG digested with MtLPMO9I with the addition of Asc. Table S1. Selected mass (m/z) list for non-, C4- and C1-oxidized TXG oligosaccharides. Table S2. List of non-oxidized XG oligosaccharides identified based on fragmentation patterns in CID-MS/MS present in the NcLPMO9C-TXG-digest. Table S3. List of non-oxidized XG oligosaccharides identified based on fragmentation patterns in CID-MS/MS present in the NcLPMO9M-TXG-digest. Table S4. Characterized LPMOs; organism, Genbank accession number, LPMO name (if applicable), PDB entry (if applicable) and reference (if applicable).

Additional file 4: Figure S1. Residual lignin, glucuronoarabinoxylan (GAX) and glucan (cellulose) in fungal-treated wheat straw during growth (1, 3 and 7Â weeks). Cs Ceriporiopsis subvermispora, Pe Pleurotus eryngii, Le Lentinula edodes. Average and standard deviation of analytical triplicates on pooled biological triplicates.

Additional file 6: Figure S3. Structural changes of fungal-treated wheat straw lignin during fungal growth (1, 3, and 7 weeks) determined by semi-quantitative py-GC–MS. Cs Ceriporiopsis subvermispora, Pe Pleurotus eryngii, and Le Lentinula edodes. S/G ratio (a) and relative abundances of unsubstituted (b), Cα-oxidized (c), and Ph–Cγ (d) substructures are based on the structural classification shown in Additional file 2: Table S1. Square Cs1, filled square Cs12, triangle Pe3, filled triangle Pe6, circle Le8, filled circle Le10. Average and standard deviation of analytical triplicates on pooled biological triplicates.

Additional file 2: Table S1. Identity, structural classification and relative abundance of lignin-derived pyrolysis products by 13C-IS py-GC–MS. Control and fungal-treated wheat straw samples after 7 weeks of treatment. Cs Ceriporiopsis subvermispora, Pe Pleurotus eryngii, and Le Lentinula edodes. Average of analytical triplicates on pooled biological triplicates.

Additional file 5: Figure S2. EI–MS (70 eV) spectra and structures of vanilloyl acetaldehyde (VAL) and syringoyl acetaldehyde (SAL) observed by py-GC–MS. Compounds were identified on the basis of fragmentation pattern and retention time. Average mass spectrum across the chromatographic peak with noise subtraction at two sides.

Additional file 7: Table S3. Assignments of the lignin 13Câ 1H correlation peaks in the HSQC spectra of control and fungal-treated wheat straw. (t) Tentative assignment.

Additional file 8: Figure S4. HSQC NMR spectra of fungal-treated wheat straw. Cs12 (a, b), Pe3 (c, d), Pe6 (e, f) Le8 (g, h) Le10 (i, j). a, c, e, g, i: Aliphatic (δC/δH 50–90/2.5–6.0) region, b, d, f, h, j: aromatic/unsaturated (δC/δH 90–160/6.0–8.0) region. Structures of annotated correlation peaks are presented in Fig. 5. Gmod and Smod are presented in a lighter color of G and S, respectively. Carbohydrate and unassigned signals are presented in gray. u: unassigned signal overlapping Aα/A′α.

10% SDS-PAGE of purified endo-xylanase from G. thermodenitrificans T12 followed by PageBlue staining. Lane 1: Protein marker; Lane 2: Pellet fraction; Lane 3: cell-free extract; Lane 4: non-binding protein fraction from FPLC; Lane 5: Purified recombinant GtXynA1; Lane 6: Purified and desalted recombinant GtXynA1; Lane 7: Protein marker. (DOCX 614 kb)

Additional file 8: Table S3. Selected cellulase-rich Basidiomycota from the JGI database1.

Additional file 1: Table S1. Primers used in this study. Table S2. Statistical differences over time in MnP and Lcc activity and chitin content in compost as presented in Fig. 2. Time points sharing a letter are not significantly different (ANOVA with Bonferroni post hoc test, p

Additional file 7: Table S2. Selected cellulase-rich Ascomycota from the JGI database1.

FPLC purification of GtXynA1. Protein fraction not bound to the nickel column eluted with the first 65 mL eluent. Bound GtXynA1 protein was removed from the nickel column using a imidazole gradient (yellow line) which increased from 0 mM to 500 mM over a time span of 20 min (A). Fractions 22–25 were pooled and used for desalting the purified GtXynA1 (B). Fractions 8–10 of the desalting column were pooled and then used for further experiments. (DOCX 311 kb)

Additional file 1: Figure S1. pH (A) and temperature profiles (C) of the incubated ReGH67 with the aldouronic acids mixture (AAc) and the pH (B) and temperature profiles (D) of the incubated ReGH115 with beechwood xylan.