Additional file 1 of Zymomonas diversity and potential for biofuel production
Creators: name: Felczak, Magdalena M.
name: Bowers, Robert M.
name: Woyke, Tanja
name: TerAvest, Michaela A.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Confirming the phenotypes of Drainas group strains CU1, CU1rif2 and uvs51. A. Glucose sensitivity was measured by growing strains ATCC10988 and its derivatives CU1, CU1rif2 and uvs51 statically in aerobic conditions at 30oC in ZRMG (2% glucose) or ZRMG supplemented with 10% glucose for 32 or 48 hours, respectively. B. Rifampicin resistance of strains CU1rif2 and uvs51 was confirmed by growing respective strains aerobically at 30oC on ZRMG plates without and with 10 µg/ml of rifampicin. Figure S2. 5 ml of ZRMG were inoculated from single colonies of each strain and grown overnight in anaerobic chamber to stationary phase. Cultures were diluted to OD600 0.1 in fresh anaerobic ZRMG. Isobutanol (IBA) was added to diluted cultures to final concentrations of 0.0, 0.5 and 1.0%, mixed and aliquots of 150 µl were loaded in triplicate onto 96-well plate. Incubation was performed with shaking at 30°C until growth reached saturation (18 hours). Only the first 10 hours of the growth is shown because IC50 for ZM4 and percent of inhibition for all the strains were calculated from area under the curve after 8 hours of growth. Figure S3. Repeated growth of strains ZM4 and Z6 with isobutanol. Normalized OD600 after 9 hours of growth is shown for cultures grown with 0%, 0.5%, or 1% v/v isobutanol. Figure S4. Initial OD600 of cultures used for flocculation experiment described in Figure 7. Identical volume of the same colony resuspended in ZMMG was used to inoculate 5 ml of ZMMG or ZRMG. Cultures were grown for 48 hours statically in 14 ml plastic tubes in aerobic environment or in anaerobic chamber, or with shaking at 275 rpm in Hungate tubes closed or loosely covered with aluminum foil for anaerobic and aerobic growth, respectively. Figure S5. The promoter region of the cellulose synthase (bcs) operon. A. Z. mobilis ZM4 promoter consensus sequence. Reproduced exactly as shown in: (Vera et al., 2020). B. Regulatory elements of the bcs operon: TSS -23 and -26, and -10 and -35 elements are highlighted in yellow, the ZMO1080 start codon is highlighted in green. C. Clustal Ω alignment of the region upstream of the ZMO1080 start codon of 16 Z. mobilis mobilis strains. Pomaceae and francensis are not included for clarity. ZM4 regulatory elements are colored as in B and nucleotides different from consensus are highlighted in blue. A single nucleotide deletion is highlighted in red. Table S1. Genome statistics for Zymomonas strains sequenced for this study. (see separate Excel file). Table S2. Information on Zymomonas strains and genomes. A list of all strains that were used for physiological and/or genomic comparisons. Common names and reference numbers for the American Type Culture Collection (ATCC), USDA Agricultural Research Service Culture Collection (NRRL), and the German Collection of Microorganisms and Cell Cultures (DSMZ), and the original source of isolation are provided. Strains were grouped based on genome similarity (see text). Highlights indicate the strain designation used to refer to each strain throughout the text, figures, and subsequent tables. Table S3. Names, accession numbers and topology determination of plasmids analyzed in Table 2. (see separate Excel file). Table S4. Loci and predicted functions for 41 genes present in ATCC10988 but without detectable homologs in any of the 3 derivative strains in the Drainas group. Table S5. Full list of methylated sequences found in 9 de-novo sequenced Zymomonas mobilis genomes.