Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system

Aguilar, César; Escalante, Adelfo; Flores, Noemí; de Anda, Ramón; Riveros-McKay, Fernando; Gosset, Guillermo; Morett, Enrique; Bolívar, Francisco

doi:10.1186/1471-2164-13-385

Table 1 Mutations that occurred in the evolved PB12 strain during the adaptive process

From: Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system

A)	Gene	Basic description	Mutations
		Hypothetical genes	JM101 and PB11	PB12	Nucleotide	Pos/Change
	gfcD*	Hypothetical lipoprotein.	GTA	cTA	916	306 V-L
	yafV*	Predicted C-N hydrolase family amidase, NAD(P)-binding.	CGC	CaC	452	151 R-H
	+ytfR^(WG)	Putative ATP-binding component of a galactose ABC transporter.	GTC	GcC	602	201 V-A
		Metabolism and Transport	JM101 and PB11	PB12	Nucleotide	Pos/Change
	+actP*	Acetate/glycolate permease in the solute:sodium symporter (SSS) family.	GTA	GcA	731	244 V-A
	arnT*	L-Ara4N transferase catalyzes addition of L-Ara4N to lipid A under some conditions.	TAC	TgC	1193	398 Y-C
	+chbC*	Integral membrane transport protein, member of the chitobiose PTS transporter.	GCG	GtG	347	116 A-V
	+csgF^(WG)	Curli secretion and assembly complex.	AAU	AgU	89	30 N-S
	+dgoT*	Probable galactonate transporter, member of the major facilitator superfamily (MFS) of transporters.	GAT	GgT	653	218 D-G
	dhaM*	Dihydroxyacetone kinase subunit M, homologous to certain PTS components.	TGG	TGa	1038	346 W-stop
	+dppF*	ATP-binding component of the dipeptide ABC transporter.	CAC	CgC	680	227 H-R
	fdhD*	Protein with unknown function, required for wild-type formate dehydrogenase-N activity.	AGT	gGT	652	218 S-G
	fimH*	Minor fimbrial subunit, D-mannose specific adhesin, subunit of fimbrial complex.	ACT	gCT	535	179 T-A
	glpT*	Major uptake transporter for glycerol-3-phosphate, belongs to the major facilitator superfamily (MFS).	CCG	CtG	416	139 P-L
	rfe*	Undecaprenyl-phosphate α-N-acetylglucosaminyl transferase .	GCC	aCC	238	80 A-T
	+sucA*	E1(0) component of the oxoglutarate dehydrogenase complex.	GAT	GAa	372	124 D-E
	ydiQ*	Putative subunit of YdiQ-YdiR flavoprotein.	GTG	GcG	218	73 V-A
		Regulatory and putative regulatory genes	JM101 and PB11	PB12	Nucleotide	Pos/Change
	+arcB*	Hybrid protein sensory kinase, member of two-component system.	TAC	TgC	212	71 Y-C
	+barA*	Hybrid protein sensory kinase, member of two-component system.	TTC	cTC	1096	366 F-L
	+rna*	RNase I, cleaves phosphodiester bond between any two nucleotides.	GCC	aCC	268	90 A-T
	+rpoD*	Sigma 70 factor, subunit of RNA polymerase.	GTT	aTT	1744	582 V-I
	+rssA*	Hypothetical protein, coded by a gene that is part of the *rssAB* operon.	CGC	CaC	773	258 R-H
	+yjjU*	Conserved hypothetical protein, could work as a transcriptional protein.	ACT	gCT	338	179 T-A
	+ypdA*	Predicted sensory kinase member of two-component system.	GCG	tCC	598	200 A-S
B)	Gene	Basic description	Mutations
	ptsP	Member of a second PTS chain involved in nitrogen metabolism	Present	Absent	---	---
	*rppH*	RNA pyrophosphohydrolase that initiates mRNA degradation by hydrolysis of the 5'-triphosphate end.	Present	Absent	---	---
	ygdT	Hypothetical protein.	Present	Absent	---	---
	*mutH*	dGATC endonuclease in the MutHLS complex, the methyl-directed mismatch repair pathway.	Present	Absent	---	---
	ygdQ	Putative transport protein.	Present	Absent	---	---
	ygdR	Predicted protein.	Present	Absent	---	---
	tas	Putative NAD(P)-linked reductase that acts in starvation-associated mutations.	Present	Absent	---	---
	lplT	Lysophospholipid transporter (LplT).	Present	Absent	---	---
	aas	2-acylglycerophosphoethanolamine acyltransferase/acyl-ACP synthetase.	Present	Absent	---	---
	omrA	Small RNA that is involved in regulating the protein composition of the outer membrane.	Present	Absent	---	---
	omrB	Small RNA that is involved in regulating the protein composition of the outer membrane.	Present	Absent	---	---
	*galR*	DNA-binding transcription factor; represses transcription of the operons involved in transport and catabolism of D-galactose.	Present	Absent	---	---

Table 1A presents the 23 non synonymous point mutations in structural genes that changed the code for a different amino acid when compared to the parental PB11 and JM101 strains genomes. The asterisks in the table indicate the 21 non-synonymous point mutations detected by both Roche NimbleGen Inc. (RN) and Winter Genomics Inc. (WG) methods. In addition 22 synonymous point mutations in different genes were also detected (Tables S1 and S2 in Additional file 1 and Additional file 2). The regulatory and possible regulatory genes analyzed in this study are in bold letters. The mutations in these seven regulatory and possible regulatory genes and in seven additional genes were confirmed by the Sanger methodology and are labeled with a +. 26 (21+5) point mutations in 26 genes were detected by RN, 5 of them were false positive. 27 (21+6) point mutations in 27 genes were detected by WG. In addition to the 21 mutations shared with RN, only two of these point mutations (noted as WG) were confirmed by the Sanger methodology. Additional file 1 and Additional file 2 (Tables S1 and S2) include the data from RN and WG. Table 1B presents the absent genes in the largest deletion reported by both companies. (Figures. 2, 3, 4 and S1, presented in Additional file 3). Basic descriptions of these genes were taken from www.ecocyc.org.

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ISSN: 1471-2164

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