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Additional file 1. Nucleotide sequence analysis of two adjacent cellulolytic enzyme genes SmBglu12A and SmLpmo10A in the genome of S. megaspores. Genomic DNA sequences encoding SmBglu12A and SmLpmo10A were highlighted in blue and green, respectively. Additional file 2. Effects of pH and temperature on the activity of the purified recombinant SmLpmo10A using the substrate PASC. A: Optimum pH; B: Optimum temperature. Additional file 3. Primers used in this study.

Additional file 1: Table S1. Plasmids used in this study. Table S2. Strains used in this study. Table S3. Primers used in this study. Figure S1. The UV-visible spectroscopy analysis of heme standard (heme std) and fermentation products of GS115 and PpH8 from 320 to 600 nm. Figure S2. UV-visible spectroscopy analysis (at 400 nm) of fermentation product of PpH8 cultured in the medium with addition of different precursors. A 5-ALA. B Fe2+. C Glycine. The fermentation without addition of precursors was carried out as control (ck). Figure S3. UV-visible spectroscopy analysis (at 400 nm) of fermentation product of PpH8 cultured in the medium with addition of different carbon sources. A Glucose. B Glycerol. C Methanol. The fermentation carried out in BMMY medium was used as control (ck). Figure S4. HPLC analysis of fermentation extracts of E. coli recombinants overexpressing different heme synthesis pathway genes. X, gltX; A, hemA; L, hemL; B, hemB; C, hemC; D, hemD; E, hemE; F, hemF; G, hemG; H, hemH. The heme and intermediates were marked with red and blue arrows, respectively. Three independent HPLC profiles were provided for each recombinant. Figure S5. HPLC analysis of fermentation extracts of E. coli recombinants co-expressing M1 and different genes in M2. M1 contains gltX, hemA and hemL genes; B, hemB; C, hemC; D, hemD; The heme and intermediates were marked with red and blue arrows, respectively. Five independent HPLC profiles were provided for each recombinant. Figure S6. Heme and intermediates productions and growth curves of strain Ec-M123 harboring plasmids pCDF-XAL, pET-BCD and pRSF-EFGH cultured in the LBFG medium supplemented with different concentrations of streptomycin (Str), kanamycin (Kan) and ampicillin (Amp). A HPLC profiles. B Growth curves. C heme productions. The concentrations of three antibiotics are indicated in μg/mL. Figure S7. The maps of recombinant plasmids pPICZH1-4 and pPICZH12-15 harboring heme synthesis pathway genes of K. phaffii. A Plasmid pPICZH1-4 containing hem1, hem2, hem3 and hem4 genes from K. phaffii. B Plasmid pPICZH12-15 containing hem12, hem13, hem14 and hem15 genes from K. phaffii.

Additional file 1: Fig. S1. The quantification of immunoblotting images was analyzed by image J. Fig. S2. Immunoblotting analysis of AKT and nuclear CREB5 expression after down regulated AKT expression. Fig. S3. The positive percentage of Ki67 increased in CREB5 overexpression tissues. Fig. S4. The quantification of immunoblotting images was analyzed by image J. Fig. S5. RT-PCR was used to detect the effect of CREB5 on the expression of mitochondrial-related gene in HN4 and HN30 cells. Fig. S6. Immunoblotting analysis of TOP1MT expression in untreated or KG-501 treated or KG-501/MK2206 treated cisplatin-resistant cells. Fig. S7. The quantification of immunoblotting images was analyzed by image J. Fig. S8. Cisplatin resistance enhances mitochondrial activity of HNSCC cells. Fig. S9. CREB5 regulates mitochondrial activity through TOP1MT. Fig. S10. The quantification of immunoblotting images was analyzed by image J. Table S1. Primary antibodies used in this study. Table S2. The primers used for real-time PCR analysis. Table S3. The small interfering RNA (siRNA) sequences used in this study. Table S4. Sequences of ChIP-PCR primers among TOP1MT promoter region.

Additional file 1: Table S1. Primers used in this study. Fig. S1. Comparation of genomeediting tool developed by Yang et al. [1] or used in ourstudy. A CYC1TT scar would leave in the genome after each round of gene editing in theprevious method. However, markerless genome editing could be achieved using ourmethod. Fig. S2. Maps of plasmids usedfor markerless genome editing in P. pastoris. A Plasmid pJQ was usedas the mother vector for the construction of markerless gene deletion orknock-in plasmids. B Map of plasmid used for markerless gene deletion. CMap of plasmid used for markerless gene knock-in. Fig.S3. qPCR results showing the mRNA expressions of IPSgene of JQ08 under aerobic (DO: 30%) and hypoxic (DO: 15%) conditions.

Additional file 1: Table S1. Primers used in this study. Table S2. qRT-PCR primers used in this study. Table S3. Comparison of enzymatic properties of TlGa15B-GA2 and ReGa15A. Fig. S1. SDS-PAGE analysis of the recombinant ReGa15A. Fig. S2. The thermostability of the purified recombinant ReGa15A. Fig. S3. Multiple sequence alignment of ReGa15A (GenBank: CAC28076.1) and TlGa15B. Fig. S4. SDS-PAGE analysis of the recombinant ReGa15A, TlGa15B-GA2 and mutants. Fig. S5. MD simulation analysis of TlGa15B-GA2 and mutants.

Additional file 1: Table S1. The primers used for real-time PCR analysis. Figure S1. FTIR spectra of folic acid (FA) and folic acid derived carbon dots (FA-CDs) prepared in this research. Figure S2. H1 NMR spectra of FA. Figure S3. H1 NMR spectra of FA-CDs. Figure S4. Biocompatibility and cellular uptake CDs in RAW264.7 cells. (A) CCK8 assay of RAW264.7 cells after incubation with different concentration of CDs for 24 h, 48 h, and 72 h. (B) Live & dead staining of RAW264.7 cells incubated with different concentration of CDs for 24 h. Scar bar: 40 μm (C) Cellular uptake of CDs in RAW264.7 cells with or without LPS stimulation, or LPS-induced RAW264.7 cells with FRs pre-blocked. Scar bar: 50 μm.

Additional file 1: The Ramachandran plot of homology modeling for TlGa15B.

Additional file 2: SDS-PAGE analysis of the recombinant TlGa15B and mutants. Lane 1, 3, 5, the culture supernatant of transformants TlGa15B, TlGa15-GA1, and TlGa15-GA2; lane 2, 4, 6, the purified TlGa15B, TlGa15-GA1, and TlGa15-GA2.

Additional file 6: The specific activity of TlGa15B and its mutants in the temperature range from 20 to 90 ℃.

Additional file 4 LC-MS/MS analysis of the formation of disulfide bonds in the TlGa15B mutants. a: the disulfide-linked peptide SNPSGGLCT/SASGPCA (132C/492C); b: the disulfide-linked peptide PLWYCIV/SAIPCSA (548C/562C).

Additional file 1: Figure S1. A summary of the micro plasma processing system.

Additional file 3: The thermostability of the purified recombinant TlGa15B.

Additional file 5: The modeled structure of TlGa15B-GA2. Six candidate mutated sites away from the catalytic center were indicated in blue balls. Two disulfide bonds were indicated as yellow sticks.

Additional file 7: Primers used in this study.

Additional file 2. Supplementary Table legends and supplementary Figures.

Table S2. Gene ontology analysis revealed 12 candidate genes for miR-196a whose altered expression could contribute to the chemoresistant phenotype. (DOC 40 kb)

Table S4. Sequences of the RIP primers for LINC00460. (DOCX 16 kb)

Table S5. Relationship between plasma exosomal miR-196a level and clinicopathologic features in HNC; Table S6. Cox proportional hazards regression models for estimating overall survival related to Table S5. (DOC 86 kb)

Table S2. Sequences of the qRT-PCR primers. (DOCX 17 kb)

Table S2. The primers used in this study. (DOC 14 kb)

Figures S1â S24. with figure legends. (PDF 14700 kb)

Table S4. The differentially expressed miRNA in 3 pairs of NFs and CAFs. (DOC 234 kb)

Table S1. The RRIDs of the cell lines used in this study. (DOCX 15 kb)

Table S7. Primary antibodies used in this study. (DOC 58 kb)

Figure S1. Co-culture with CAFs prompts the malignant phenotypes of HNC cells. Figure S2. Identification of exosomes purified from CAFs and NFs. Figure S3. Treatment with fibroblast-exosomes prompts the malignant phenotypes of HNC cells. Figure S4. MiR-3188 expression in HNC cells after transfected with miR-3188 mimics or inhibitor. Figure S5. miR-3188 inhibits the growth of HN30 cells and facilitates the apoptosis of HN30 cells in vitro. Figure S6. Functional analyses of the effects of miR-3188 on HNC cell migration and invasion. Figure S7. BCL2 facilitates the growth of HN30 cells and inhibits the apoptosis of HN30 cells in vitro. Figure S8. The expression of Cyclin D1 in HNC cells after BCL2 knockdown or overexpression. Figure S9. BCL2 expression was recovered by the transfection of BCL2 expression vector in miR-3188-expressing HNC cells. Figure S10. MiR-3188 expression in CAL27, NFs and exosomes after transfection of miR-3188 mimics or inhibitor. Figure S11. MiR-3188 and BCL2 mRNA expression in xenografts. Figure S12. MiR-3188 expression in HNC tissues and plasma of HNC patients. Figure S13. The correlation of plasma miR-3188 expression and clinicopathological characteristics of HNC patients. (PPTX 22445 kb)

Table S3. Smart Silencer and siRNA sequences. (DOCX 16 kb)

Table S1. Dysregulated miRNAs in CAF-derived exosomes compared with NFs. (DOC 53 kb)

Table S5. Sequences of the ChIP promoter primers. (DOCX 16 kb)

Supplementary methods. (DOC 54 kb)

Table S1. Primary antibodies used for Western blotting, Immunohistochemistry, and Immunofluorescence. (DOC 42 kb)

Tables S8â S10. Sequences of primers and siRNAs used in this study. (DOC 152 kb)

Table S3. The Sequences used in this study. (DOC 61 kb)

Table S3. Relationship between tissue miR-196a level and clinicopathologic features in HNC; Table S4. Cox proportional hazards regression models for estimating overall survival related to Table S3. (DOC 86 kb)

Additional file 2. Top 50 PFAM domains in I. lacteus CD2 genome.

Additional file 11. Primers used for RT-qPCR.

Additional file 8. GO enrichment analysis of differently expressed genes in comparisons of LC3d versus Glu3d (a), LC6d versus LC3d (b).

Additional file 10. Verifying the differential expression as revealed by RNA-seq for selected lignocellulose-degrading genes by RT-qPCR.

Additional file 3. Oxidoreductive enzymes involved in lignocellulose degradation in I. lacteus CD2 and selected Polyporales genomes.

Additional file 5. TCA cycle, GLOX cycle, and predicted oxalate metabolism in I. lacteus CD2.

Additional file 1. Summary of I. lacteus CD2 annotations.

Additional file 6. Distribution of the genes encoding glycoside hydrolases and enzymes with auxiliary activities on the 10 largest contigs of I. lacteus CD2 genome.

Additional file 9. KEGG enrichment analysis of differently expressed genes in comparisons of LC3d versus Glu3d (a), LC6d versus LC3d (b).

Additional file 4. Predicted heme biosynthesis pathway and its regulation in I. lacteus CD2.

Additional file 3. Effect of pH and temperature on the activity and stability of IlMnP1 and IlMnP2. (a) The pH-activity profiles. The activities at the pH optima were set as 100%. (b) The pH-stability profiles. The initial MnP activities before treatment were set as 100%. (c) The temperature-activity profiles. The activities at the temperature optima were set as 100%. (d) The temperature-activity profiles. The initial MnP activities before heat treatment were set as 100%.

Additional file 7. Primers used in this study.

Additional file 2. Purified recombinant IlMnP1 and IlMnP2 as analyzed by SDS-PAGE. Lanes: M, the protein molecular mass marker; 1, the purified IlMnP1; 2, the purified IlMnP2.

Additional file 6. The product veratraldehyde steadily increased with a linear relationship to the concentrations of VA when oxidized by 0.5 U/mL IlMnP1 (a) or IlMnP2 (b). The reaction systems contained the malonate buffer (pH 5.0) and were incubated for 48 h in presence of 1 mM Mn2+.

Additional file 5. The non-phenolic lignin model compound veratryl alcohol was not oxidized by either IlMnP1 or IlMnP2 as analyzed by HPLC. The enzymes (0.5 U/mL IlMnP1 and IlMnP2, respectively) were incubated with VA in the acetate, citrate, lactate, or succinate buffer (50 mM, pH 5.0) with 1 mM Mn2+ at 30 °C for 48 h.

Additional file 1. The nucleotide and deduced amino acid sequences of the manganese peroxidase isoenzymes IlMnP1 (a) and IlMnP2 (b) of I. lacteus CD2. The signal peptide of the two manganese peroxidases was shown in red. The putative Cis-acting elements in the regulatory region are underlined. CreA: CreA-binding sites; XRE: xenobiotic-responsive elements; NIT2: NIT2 transcription factor consensus binding sequences; HSE: heat shock element.

Additional file 4. Amino acid sequence alignment of IlMnP1 and IlMnP2 with selected MnPs, VPs, and LiPs. Inverted triangle: the cysteines that might form disulfide bridges; diamond: the structural Ca2+-binding residues; triangle: the active site histidine residues; hexagon: the acid residues forming the Mn2+ oxidation site; square: the tryptophan responsible for aromatic substrate oxidation. The GenBank accession numbers for these enzymes were: IlMnP1, KX620478; IlMnP2, KX620479; PoMnP2, KDQ32034.1; PoMnP4, 4BM1; PoMnP5, KDQ27903.1; PoMnP6, KDQ28248.1; PcMnP-H4, P19136.1; PeVP2, 2BOQ; PcLiP-H2, P11542.2; PcLiP-H8, AAB00798.1.