Additional file 1 of Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress
Creators: name: Shabbir, Samina
name: Wang, Weiting
name: Nawaz, Mohsin
name: Boruah, Prerona
name: Kulyar, Muhammad Fakhar-e-Alam
name: Chen, Mao
name: Wu, Bo
name: Liu, Panting
name: Dai, Yonghua
name: Sun, Lingling
name: Gou, Qiyu
name: Liu, Renbin
name: Hu, Guoquan
name: Younis, Tahira
name: He, Mingxiong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1.  Figure S1 Schematic procedure used in the knock-out of ZM532, ZMO_RS02740 and ZMO_RS06525 in ZM4 and ZM532. Figure S2 Venn diagram depicting the unique and shared differentially expressed genes between the two Z. mobilis, ZM532 strains, (A) AF_ZM532vsRM_532 (yellow) and its wild type AF_ZM4 vsRM_ZM4 (purple); (B) AF_ZM532vsAF_ZM4 (purple) and RM_ZM532vsRM_ZM4 in response to acetic acid and furfural combine treatments. Figure S3 Overview of the quantitative mass spectrometry results (A) Number of proteins identified in each sample; (B) Distribution of peptide length range; (C) Protein molecular weight distribution; (D) Reproducibility between biological replicates. Figure S4 Represented DEPs subcellular localization analysis. Figure S5 Venn diagram showing the shared and specific (DEP) between ZM4 and ZM532 in response to acetic acid and furfural treatments. Figure 6 KEEG enrichment analysis of the DEPs p &lt; 0.05 in (A) ZM532_AF_vsZM532_RM and (B) ZM4_AF_vs_ZM4_RM; (C) AF_ZM532_vs_AF_ZM4; (D) RM_ZM532_vs_RM_ZM; (E) COG functional classification of the DE proteins. The proteins with significant homologies in the COG database were classified into 21 COG categories. Capital letters on the x-axis indicate COG categories on the right side of the histogram. Figure S7 KEGG pathway annotation for Z. Mobilis. The abscissa represents the number of proteins; the pathway categories are shown on the y-axis. Figure S8 Transcript abundance of 10 selected differentially expressed genes (DEGs) in the two samples (brown bar represents either ZM4 or ZM532 which gave similar expression; gray bar represents expression in the wild type, ZM4; ash bar represents expression in the mutant strain, ZM532. The error bar represents standard error of the three technical repeats. Table S1. List of Primer pairs used in study. Table S2. List of primers used for qPCR experiment. Table S3. List of primers, strains and plasmids. Table S4. List of primers, strains and plasmids. Table S5. INDEL in re-sequence ZM532 by comparing with previous published ten genome-shuffled mutant strain and Z. mobilis ZM4 (GenBank: AE008692.2). Table S6. Overview of the transcriptome sequencing dataset and quality check. Table S7 Differentially Expressed Genes of ZM532 strain in rich media and media with acetic + furfural treatments. Table S8 Differentially Expressed Genes of wild type ZM4 in rich media and media with acetic + furfural treatment. Table S9 Differentially Expressed proteins of ZM4 strain in rich media and media with acetic + furfural treatments. Table S10 Differentially Expressed proteins of ZM532 strain in rich media and media with acetic + furfural treatments.