Additional file 1 of Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3
Creators: name: Zhao, Shuting
name: Deng, Dongtao
name: Wan, Tianzheng
name: Feng, Jie
name: Deng, Lei
name: Tian, Qianyi
name: Wang, Jiayu
name: Aiman, Umm E.
name: Mukhaddi, Balym
name: Hu, Xiaofeng
name: Chen, Shaolin
name: Qiu, Ling
name: Huang, Lili
name: Wei, Yahong
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 1: Figure S1. Morphological characterisation of Erwinia billingiae QL-Z3 by scanning electron microscopy (SEM). (scale bar = 3 µm). Figure S2. Effects of substrate concentration, nitrogen source, and pH on lignin degradation of Erwinia billingiae QL-Z3. a Lignin concentration; b pH; c Nitrogen source. Average values of three replicates are shown with the standard errors of the mean shown as error bars. Each experimental group was conducted in triplicate. Figure S3. Circular representation of the genome (chromosome and plasmid) of Erwinia bilingiae QL-Z3. a Chromosome; b Plasmid. Figure S4. Classification of eggNOG annotations of the Erwinia bilingiae QL-Z3 genome. Figure S5. KEGG pathway of the Erwinia bilingiae QL-Z3 genome. Figure S6. CAZy function classification of the Erwinia bilingiae QL-Z3 genome. Figure S7. Gene knockout PCR validation of the eight genes predicted to participate in lignin degradation. M1&amp;M2&amp;M3, 2 kb marker; 1,Negative control: △EDYP_48_QL-Z3; 2, △EDYP_48; 3, Positive control: △EDYP_48_S17-1; 4, Negative control: △ELAC_205_QL-Z3; 5, △ELAC_205; 6, Positive control: △ELAC_205_S17-1; 7, Negative control:△EDIO_858_QL-Z3; 8, △EDIO_858; 9, Positive control: △EDIO_858_S17-1; 10, Negative control: △EOXI_996_QL-Z3; 11, △EOXI_996; 12, Positive control:△EOXI_996_S17-1; 13, Negative control:△ESOD_1236_QL-Z3; 14, △ESOD_1236; 15, Positive control:△ESOD_1236_S17-1; 16, Negative control: △EMON_3330_QL-Z3; 17, △EMON_3330; 18, Positive control: △EMON_3330_S17-1; 19, Negative control: EMCAT_3587_QL-Z3; 20, EMCAT_3587; 21, Positive control: EMCAT_3587_S17-1; 22, Negative control: ECAT_3467_QL-Z3; 23, ECAT_3467; 24, Positive control: EMCAT_3467_S17-1. Figure S8. Complementation PCR validation of the eight genes predicted to participate in lignin degradation. Note: M, 2 kb Marker; 1, ΔEDYP_48 (EDYP_48); 2, △ELAC_205 (ELAC_205); 3, △EDIO_858 (EDIO_858); 4, △EOXI_996 (EOXI_996); 5, △ESOD_1236 (ESOD_1236); 6, △EMON_3330 (EMON_3330); 7, △ECAT_3467 (ECAT_3467); 8, △EMCAT_3587 (EMCAT_3587). Figure S9. Western Blot analysis of the six purified proteins predicted to participate in lignin degradation. M, Marker; 1, The precipitation of liquid; 2, Supernatant; 3–4, Outflow liquid; 5–11, Target protein. a EDYP_48; b ELAC_205; c EDIO_858; d ESOD_1236; e EMON_3330; f EMCAT_3587. Figure S10. Optimization results of enzyme activity conditions pH (a) Temperature (b) of EDYP_48 and ELAC_205. Blue: EDYP_48, red: ELAC_205. Average values of three replicates are shown with the standard errors of the mean shown as error bars. Each experimental group was conducted in triplicate. Table S1-1. L9 (33) Test design of Degradation rate optimization. Table S1-2. Orthogonal model analysis of variance of Degradation rate optimization. Table S2. Comparison of degradability of lignin degrading microorganisms. Table S3. General features of Erwinia bilingiae QL-Z3 genome. Table S4. Primers used for gene knockout. Table S5. Primers used for gene complementation. Table S6. Gene real-time expression levels at 6 h and 72 h under lignin and starvation were shown. Table S7. Specific activities of heterologously expressed and purified ligninolytic enzymes. Table S8. The main degradation products of Alkali lignin obtained in different enzymes combinations. Table S9-1. L9 (33) Test design of LiP. Table S9-2. Orthogonal model analysis of variance of LiP. Table S9-3. L9 (33) Test design of Lac. Table S9-4. Orthogonal model analysis of variance of Lac. Table S9-5. L9 (33) Test design of MnP. Table S9-6. Orthogonal model analysis of variance of MnP. Table S10. Comparison of three enzyme activities (LiP, MnP and Lac) of lignin-degrading microorganism.