Supplementary Figures and Tables

FOR

Genomic analysis of thermophilicBacillus coagulans strains: efficient producers for platform bio-chemicals

Fei Su and Ping Xu*

State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China

*Correspondence:

(Ping Xu)

Authors emails:

FS:

PX:

Supplementary Table

Table S1 Selected genomes used in genome-wide positive selection analysis.

Strain / Taxonomic ID / Accession Number
Bacillusamyloliquefaciens DSM 7 / 692420 / NC_014551
Bacillusanthracis str. Ames / 198094 / NC_003997
Bacillus anthracis str. ‘Ames Ancestor’ / 261594 / NC_007530
Bacillus anthracis str. Sterne / 260799 / NC_005945
Bacillus cellulosilyticus DSM 2522 / 649639 / NC_014829
Bacillus cereus ATCC 10987 / 222523 / NC_003909
Bacillus cereus ATCC 14579 / 226900 / NC_004721
Bacillus clausii KSM-K16 / 66692 / NC_006582
Bacillus coagulans 2-6 / 941639 / NC_015634
Bacillus coagulans 36D1 / 345219 / NC_016023
Bacillus coagulans XZL4 / 1071395 / AFWM00000000
Bacillus coagulans XZL9 / 1245026 / ANAP00000000
Bacillus coagulans H-1 / 1236905 / ANAQ00000000
Bacillus coagulans DSM1 = ATCC 7050 / 1121088 / ALAS01000000
Bacillus cytotoxicus NVH 391-98 / 315749 / NC_009674
Bacillus halodurans C-125 / 272558 / NC_002570
Bacillus licheniformis DSM 13 = ATCC 14580 / 279010 / NC_006322
Bacillus megaterium DSM 319 / 592022 / NC_014103
Bacillus pumilus SAFR-032 / 315750 / NC_009848
Bacillus selenitireducens MLS10 / 439292 / NC_014219
Bacillus subtilis subsp. spizizenii str. W23 / 655816 / NC_014479
Bacillus subtilis subsp. subtilis str. 168 / 224308 / NC_000964
Bacillus thuringiensis BMB171 / 714359 / NC_014171
Bacillus thuringiensis serovar chinensis CT-43 / 541229 / NC_017208
Bacillus thuringiensis str. Al Hakam / 412694 / NC_008600
Bacillus weihenstephanensis KBAB4 / 315730 / NC_010184

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Table S2 Homologous genes involved in protein secretion systems across all sequenced Bacillus coagulans genomes.

Gene / 36D1 / XZL9 / XZL4 / 2-6 / H-1 / DSM1
secY / YP_004859138.1 / 1245026.3.peg.2057 / 1398.8.peg.3220 / YP_004567583.1 / 1398.9.peg.1626 / 6666666.17355.peg.1970
secE / YP_004859175.1 / 1245026.3.peg.2094 / 1398.8.peg.3256 / - / 1398.9.peg.2240 / 6666666.17355.peg.1934
secG / YP_004860185.1 / 1245026.3.peg.2221 / 1398.8.peg.1729 / YP_004569678.1 / 1398.9.peg.1359 / 6666666.17355.peg.841
secD/F / YP_004860627.1 / 1245026.3.peg.1756 / 1398.8.peg.3094 / YP_004569275.1 / 1398.9.peg.3134 / 6666666.17355.peg.2687
secA / YP_004858500.1 / 1245026.3.peg.2781 / 1398.8.peg.1489 / YP_004568116.1 / 1398.9.peg.905 / 6666666.17355.peg.796
yajC / YP_004860621.1 / 1245026.3.peg.1762 / 1398.8.peg.3099 / YP_004569280.1 / 1398.9.peg.3139 / 6666666.17355.peg.2692
yidC / YP_004859272.1
YP_004861200.1 / 1245026.3.peg.1127
1245026.3.peg.1353 / 1398.8.peg.1007
1398.8.peg.320 / YP_004570415.1
YP_004568724.1 / 1398.9.peg.194
1398.9.peg.2359 / 6666666.17355.peg.37
6666666.17355.peg.1330
ffh / YP_004858089.1 / 1245026.3.peg.2515 / 1398.8.peg.1425 / YP_004568550.1 / 1398.9.peg.1367 / 6666666.17355.peg.1148
ftsY / YP_004858091.1 / 1245026.3.peg.2513 / 1398.8.peg.1422 / YP_004568548.1 / 1398.9.peg.1369 / 6666666.17355.peg.1146
tatA / YP_004858903.1 / 1245026.3.peg.2882 / 1398.8.peg.112 / YP_004567758.1 / 1398.9.peg.2988 / 6666666.17355.peg.505
tatC / YP_004859509.1 / 1245026.3.peg.1150 / 1398.8.peg.2468 / YP_004570171.1 / 1398.9.peg.3206 / 6666666.17355.peg.1375
SPaseI / YP_004858082.1 / 1245026.3.peg.2523 / 1398.8.peg.1432 / YP_004568557.1 / 1398.9.peg.2382 / 6666666.17355.peg.1156
SPaseII / YP_004858154.1 / 1245026.3.peg.3651 / 1398.8.peg.1357 / YP_004568485.1 / 1398.9.peg.1737 / 6666666.17355.peg.2471

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Table S3 Homology involved in natural competence across all sequenced Bacillus coagulans genomes.

Gene / 36D1 / XZL9 / XZL4 / 2-6 / H-1 / DSM1
comC / YP_004860595.1 / 1245026.3.peg.1792 / 1398.8.peg.3130 / YP_004569308.1 / 1398.9.peg.3168 / 6666666.17355.peg.2979
comEA / YP_004860706.1 / 1245026.3.peg.939 / 1398.8.peg.2556 / YP_004569202.1 / 1398.9.peg.697 / 6666666.17355.peg.410
comEB / YP_004860707.1 / 1245026.3.peg.938 / 1398.8.peg.2557 / YP_004569201.1 / 1398.9.peg.698 / 6666666.17355.peg.409
comEC / YP_004860708.1 / 1245026.3.peg.937 / 1398.8.peg.2558 / YP_004569200.1 / 1398.9.peg.699 / 6666666.17355.peg.408
comER / YP_004860705.1 / 1245026.3.peg.940 / 1398.8.peg.2555 / YP_004569203.1 / 1398.9.peg.696 / 6666666.17355.peg.411
comFA / YP_004858523.1 / 1245026.3.peg.2742 / 1398.8.peg.1464 / YP_004568096.1 / 1398.9.peg.1927 / 6666666.17355.peg.2210
comFC / YP_004858522.1 / 1245026.3.peg.2743 / 1398.8.peg.1465 / YP_004568097.1 / 1398.9.peg.1926 / 6666666.17355.peg.2211
comGA / YP_004860770.1 / 1245026.3.peg.864 / 1398.8.peg.2628 / YP_004569140.1 / 1398.9.peg.1140 / 6666666.17355.peg.1769
comGB / YP_004860771.1 / 1245026.3.peg.863 / 1398.8.peg.2629 / YP_004569139.1 / 1398.9.peg.1139 / 6666666.17355.peg.1768
comGC / YP_004860772.1 / 1245026.3.peg.862 / 1398.8.peg.2630 / YP_004569138.1 / 1398.9.peg.1138 / 6666666.17355.peg.1767
comGD / YP_004860773.1 / 1245026.3.peg.861 / 1398.8.peg.2631 / YP_004569137.1 / 1398.9.peg.1137 / 6666666.17355.peg.1766
comGE / YP_004860774.1 / 1245026.3.peg.860 / 1398.8.peg.2632 / YP_004569135.1 / 1398.9.peg.1136 / 6666666.17355.peg.1765
comGF / YP_004860775.1 / 1245026.3.peg.859 / 1398.8.peg.2633 / YP_004569134.1 / 1398.9.peg.1135 / 6666666.17355.peg.1764
comGG / YP_004860776.1 / 1245026.3.peg.858 / 1398.8.peg.2634 / YP_004569133.1 / 1398.9.peg.1134 / 6666666.17355.peg.1763
comK / YP_004858885.1
YP_004858388.1 / 1245026.3.peg.1582
1245026.3.peg.167 / 1398.8.peg.2540
1398.8.peg.1075 / YP_004567779.1 / 1398.9.peg.2828
1398.9.peg.2105 / 6666666.17355.peg.476
6666666.17355.peg.1031
comQ / YP_004860037.1 / 1245026.3.peg.1596 / - / - / - / -

Table S4 CRISPRs associated genes found in the Bacillus coagulans genomes.

Gene / 36D1 / XZL9 / XZL4 / 2-6 / H-1 / DSM1
cas1 / YP_004859904.1
YP_004858802.1 / 1245026.3.peg.3448
1245026.3.peg.2324 / - / YP_004569895.1
YP_004567837.1 / 1398.9.peg.1189
1398.9.peg.896 / 6666666.17355.peg.3003
6666666.17355.peg.956
cas2 / YP_004859905.1
YP_004859898.1 / 1245026.3.peg.3447
1245026.3.peg.3452 / - / - / 1398.9.peg.1190 / 6666666.17355.peg.3004
6666666.17355.peg.3001
cas3 / - / - / - / YP_004569897.1 / 1398.9.peg.1186 / -
cas4 / YP_004859901.1 / 1245026.3.peg.3449 / - / YP_004569896.1 / 1398.9.peg.1188 / -
cas5 / YP_004859899.1 / 1245026.3.peg.3451 / - / YP_004569898.1 / 1398.9.peg.1185 / -
cas6 / YP_004859896.1 / 1245026.3.peg.3454 / - / YP_004569901.1 / 1398.9.peg.1182 / -
Cas7 / YP_004858801.1 / 1245026.3.peg.2323 / - / YP_004569899.1
YP_004567838.1 / 1398.9.peg.1184, 1398.9.peg.897 / -

Table S5 Positions of genome island identified by the IslandViewer.

Start / End / Size (bp) / Strain / CRISPRs
87986 / 97159 / 9173 / 2-6
363517 / 443775 / 80258 / 2-6
655959 / 674254 / 18295 / 2-6
756190 / 769710 / 13520 / 2-6
966470 / 982915 / 16445 / 2-6
1435266 / 1447848 / 12582 / 2-6
2319571 / 2326656 / 7085 / 2-6
2494653 / 2511754 / 17101 / 2-6 / CRISPR_2-6_1
CRISPR_2-6_2
2549493 / 2566765 / 17272 / 2-6
2599351 / 2627495 / 28144 / 2-6
2698240 / 2710711 / 12471 / 2-6
2934689 / 2949009 / 14320 / 2-6
2993680 / 3006572 / 12892 / 2-6
3021687 / 3040967 / 19280 / 2-6
584104 / 595133 / 11029 / 36D1
878999 / 895649 / 16650 / 36D1
921934 / 949810 / 27876 / 36D1
1152116 / 1171064 / 18948 / 36D1
1190572 / 1195249 / 4677 / 36D1
1288692 / 1295225 / 6533 / 36D1
1508431 / 1512478 / 4047 / 36D1
1545948 / 1550682 / 4734 / 36D1
1679751 / 1686420 / 6669 / 36D1
1776768 / 1800425 / 23657 / 36D1
1882545 / 1887693 / 5148 / 36D1
1930663 / 1951425 / 20762 / 36D1
1963894 / 1986898 / 23004 / 36D1
2114200 / 2128341 / 14141 / 36D1 / CRISPR_36D1_2
CRISPR_36D1_3
2164891 / 2184866 / 19975 / 36D1
2270837 / 2276253 / 5416 / 36D1

Supplementary Figure

Figure S1 Acetoin and butanediol productions in 500-ml flasks under aerobic conditions by B. coagulans 2-6 and XZL9. Glucose (80 g/liter) and xylose (60 g/liter) were used to ferment under aerobic conditions by B. coagulans strains 2-6 (glucose) and XZL9 (xylose) at 50°C. The analytical methods of the concentration of acetoin and butanediol were the same as that described in Ma et al.1.

1Ma, C. et al. Enhanced 2,3-butanediol production by Klebsiella pneumoniae SDM. Appl. Microbiol. Biotechnol.82, 49-57 (2009).

1