TABLE 2.

Identified genotypic changes of recovered L. plantarum strains compared to NZ3400B^f

SNP positiona	SNP location within gene	AA changeb	AA chargec	AA polarityd	Immobilized adaptation cycle											Planktonic adaptation cycle														Recovered L. plantarum IA_10					Locus tage	Description
																TR1, period 2			TR2								TR1, period 1
					IA01	IA02	IA03	IA04	IA05	IA06	IA07	IA08	IA09	IA10	IA11	PA1.2̱01	PA1.2̱02	PA1.2̱03	PA2̱01	PA2̱02	PA2̱03	PA2̱04	PA2̱05	PA2̱06	PA2̱07	PA2̱08	PA1.1̱01	PA1.1̱02	PA1.2̱03	IA̱10.1	IA̱10.2	A̱10.3	IA̱10.4	IA̱10.5
					(i)	(i)		(ii)	(ii)	(ii)	(ii)	(ii)	(ii)	(ii)						(iii)	(iii)	(iv)	(iv)	(iv)
3197325	C979T	Glu→Lys	− = +	P = P	x	x	x									x	x	x																	LP_RS14990	GHLK domain-containing protein
1441981	G645T	Met→Ile	N = N	A = A																								x							LP_RS06730	Glycerophosphodiester phosphodiesterase
2635801	A487C	Thr→Pro	N = N	P = A																									x						LP_RS12455	Lipase/esterase
2832369	C328T	Thr→Ile	N = N	P = A																									x						LP_RS13325	Class I SAM-dependent methyltransferase
3244391	C837A	Leu→Phe	N = N	A = A																		x	x	x							x				LP_RS15205	ROK family protein
945932	C2340T	None																x																	LP_RS04385	rpoC; DNA-directed RNA polymerase subunit beta
488529	G1192A	Asp→Asn	− = N	P = P																								x							LP_RS02260	Aminoacetyl-tRNA hydrolase
1536407	G881A	None																								x									LP_RS07205	rsgA; ribosome small subunit-dependent GTPase A
1737654	G173A	Ala→Val	N = N	A = A																							x								LP_RS08140	HAD_IC family P-type ATPase
3261513	C749T	None																	x	x	x														LP_RS15260	Extracellular solute-binding protein
1286590	A767G	Ile→Thr	N = N	A = P																						x									LP_RS05980	MFS transporter
300072	C995T	Thr→Met	N = N	P = A																							x								LP_RS01370	Acetoin ABC transporter permease
332157	G382A	Ala→Thr	N = N	A = P												x	x	x																	LP_RS01530	Hypothetical protein
2947006	G39T	Met→ Ile	N = N	A = A			x																												LP_RS13860	VanZ family protein
3025391	C569A	Gly→Val	N = N	A = A				x	x	x	x	x	x																	x	ϕ	x	x	x	LP_RS14255	WxL domain-containing protein
2307096	G984A	Met→Ile	N = N	A = A																											x				LP_RS10985	LPXTG cell wall anchor domain-containing protein
1116951		N.A.	N.A.	N.A.													x		x																gen. DNA	Intergenic; LP_RS05100 < LP_RS05095
67503		N.A.	N.A.	N.A.											x																				gen. DNA	Intergenic; LP_RS00275 < LP_RS00270

^aIndicates SNP position in relation to the L. plantarum WCFS1 genome.

^bIndicates amino acid change in the mutant compared to NZ3400B caused by the SNP. None, no change in amino acid; N.A., amino acid change not identifiable.

^cIndicates change of the amino acid charge compared to NZ3400B caused by the SNP. N, neutral; +, positive charge; −, negative charge.

^dAmino acid polarity. P, polar; A, apolar.

^eLocation of the SNP. Intergenic SNPs are labeled with genomic (gen.) DNA.

^f“x” indicates an SNP; ϕ indicates loss of a mutation; Roman numerals in parentheses represent isogenic strains. AA, amino acid; SAM, S-adenosylmethionine; MFS, major facilitator superfamily.