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Table 3 Genomic resequencing results from strains in the present study: small-scale sequence variations and their occurrence in each strain

From: Strain and bioprocess improvement of a thermophilic anaerobe for the production of ethanol from wood

Row Gene Nucleotide Type Reference Change Non-synonymous Amino acid change Percent of sequencing reads Description
YS485 (WT) M863 M1442 M2886
1 Tsac_0902 944418 Deletion G Intergenic   99 95 98 99 Hypothetical protein
2 Tsac_1176 1217778 Insertion A Intergenic   100 100 99 100 Histidinol dehydrogenase, prokaryotic-type
3 Tsac_1332 1388136 Insertion A Intergenic   100 100 99 100 Hypothetical protein
4 Tsac_1641 1717467 Insertion T Yes Tyr 18 FS 100 100 100 100 MerR family transcriptional regulator
5 Tsac_2098 2143046 Insertion A Intergenic   100 100 100 100 Peptidase S11, d-alanyl-d-alanine carboxypeptidase A
6 Tsac_2308 2368691 Deletion A Intergenic   100 100 100 100 HEPN domain protein
7 Tsac_2828 21 (megaplasmid) MNV GA AG Yes Lys 104 Glu 96 88 97 95 Hypothetical protein, on megaplasmid CP003185
8 Tsac_0096 92464 Insertion T Intergenic   100 PWT 99 100 LuxR family transcriptional regulator
9 Tsac_0303 322547 Insertion A Intergenic   99 40 99 92 Fibronectin type III domain protein
10 Tsac_0902 944612 SNV A T No   PWT 49 PWT PWT Putative transposase YhgA family protein
11 Tsac_0032 30909 Insertion A Yes Gly 177 FS PWT 100 99 100 PTS system, N-acetylglucosamine-specific IIBC subunit
12 Tsac_0079 79429 Deletion A Yes Asn 86 FS PWT 74 99 100 Uncharacterised conserved protein UCP018688
13 Tsac_0144 150053 SNV C T Intergenic   PWT 98 99 100 4-Deoxy-l-threo-5-hexosulose-uronate ketol-isomerase
14 Tsac_0163 177035 SNV A C Yes Phe 104 Val PWT 100 100 100 Altronate oxidoreductase
15 adhE Tsac_0416 448858 SNV G A Yes Gly 544 Asp PWT 98 100 100 Bifunctional alcohol/aldehyde dehydrogenase
16 Tsac_0838 884294 Deletion T Yes Ser 102 FS PWT 85 99 100 Protein of unknown function DUF324
17 Tsac_0948 993551 SNV A T Yes Phe 361 Tyr PWT 100 100 100 Spore germination protein
18 hfsB Tsac_1551 1627813 Deletion A Yes Lys 146 FS PWT 100 99 100 Hydrogenase large subunit domain protein
19 hfsD Tsac_1553 1630591 SNV A T Yes Arg 107 Ser PWT 98 100 100 Iron hydrogenase, large subunit, C-terminal
20 Tsac_1726 1800969 Insertion A Yes Tyr 454 FS PWT 100 100 100 Serine/threonine protein kinase with PASTA sensor(s)
21 pta Tsac_1744a,b 1814403 Insertion G Yes Ile 3 FS PWT 100 97 PWT Phosphate acetyltransferase
22 Tsac_1782 1848944 Deletion G Yes Glu 180 FS PWT 100 99 100 Flagellar motor switch protein FliG
23 Tsac_2119 2160615 SNV C T Yes Gly 488 Glu PWT 97 100 100 Penicillin-binding protein 2
24 Tsac_2196 2239931 SNV G A No   PWT 100 99 100 Phenylalanyl-tRNA synthetase, class IIc, alpha subunit
25 Tsac_2229 2273080 SNV A G Yes Ser 283 Pro PWT 82 99 100 Bacterial inner-membrane translocator
26 Tsac_2476 2526425 SNV A G No   PWT 94 100 100 RNA polymerase, sigma 70 subunit, RpoD subfamily
27 Tsac_0535 559915 SNV C T Yes Gly 257 Asp PWT PWT 100 100 Cyanophycin synthetase
28 Tsac_0795a 835013 Deletion A Yes Ile 1000 FS PWT PWT 100 100 SNF2-related protein
29 Tsac_1054 1089642 SNV T C Intergenic   PWT PWT 100 100 Thioredoxin reductase
30 Tsac_1296a 1356848 SNV A G Yes Glu 105 Gly PWT PWT 100 100 UDP-glucose 4-epimerase
31 Tsac_1419 1491395 SNV C A Yes Ala 187 Asp PWT PWT 99 100 ATPase, F0 complex, subunit A
32 Tsac_1477 1557984 Insertion G Yes Ile 267 FS PWT PWT 100 100 Lipopolysaccharide biosynthesis
33 Tsac_1712 1787698 SNV C A Yes Pro 161 Thr PWT PWT 100 100 Diaminopimelate epimerase
34 Tsac_2390 2460517 SNV C T Yes Leu 311 Phe PWT PWT 99 100 Hypothetical protein
35 Tsac_2507 2555785 SNV G A Yes Gln 840 stop PWT PWT 100 100 PTS system transcriptional activator
36 Tsac_1486 1566717 MNV AA TT Intergenic   PWT PWT PWT 100 Flavodoxin/nitric oxide synthase
37 Tsac_1725 1799018 SNV G A Yes Ala 50 Thr PWT PWT PWT 100 Protein serine/threonine phosphatase
38 Tsac_2189 2229111 Insertion T Yes Asp 144 FS PWT PWT PWT 100 Two component transcriptional regulator, LuxR family
39 perR Tsac_2491a 2541836 Deletion C Yes Ser 113 FS PWT PWT PWT 100 Ferric uptake regulator, Fur family
40 perR Tsac_2491a 2541840 Deletion T Yes Tyr 115 FS PWT PWT PWT 100 Ferric uptake regulator, Fur family
41 Tsac_0622 659800 SNV T G Intergenic   PWT PWT PWT 45 Hypothetical protein
42 Tsac_0634 677092 SNV T G Intergenic   PWT PWT PWT 41 Glucokinase, ROK family
  1. Where the sequence analysis software detected the mutation in greater than 20 % of reads, the percent of reads with the mutation is given. Otherwise, the percent of sequencing reads is not calculated
  2. SNV single nucleotide variation, FS frame shift, PWT presumptively wild type, MNV multiple nucleotide variation
  3. aThese variations occurred in the small residual sequences that were not removed when the genes were knocked out
  4. bThe pta/ack genes were re-introduced into strain M2886