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

Herring, Christopher D.; Kenealy, William R.; Joe Shaw, A.; Covalla, Sean F.; Olson, Daniel G.; Zhang, Jiayi; Ryan Sillers, W.; Tsakraklides, Vasiliki; Bardsley, John S.; Rogers, Stephen R.; Thorne, Philip G.; Johnson, Jessica P.; Foster, Abigail; Shikhare, Indraneel D.; Klingeman, Dawn M.; Brown, Steven D.; Davison, Brian H.; Lynd, Lee R.; Hogsett, David A.

doi:10.1186/s13068-016-0536-8

Biotechnology for Biofuels and Bioproducts

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
Row	Gene	Nucleotide	Type	Reference	Change	Non-synonymous	Amino acid change	YS485 (WT)	M863	M1442	M2886	Description
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_1744^a,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_0795^a	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_1296^a	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_2491^a	2541836	Deletion	C	–	Yes	Ser 113 FS	PWT	PWT	PWT	100	Ferric uptake regulator, Fur family
40	perR Tsac_2491^a	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

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
SNV single nucleotide variation, FS frame shift, PWT presumptively wild type, MNV multiple nucleotide variation
^aThese variations occurred in the small residual sequences that were not removed when the genes were knocked out
^bThe pta/ack genes were re-introduced into strain M2886

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