Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains

McGuire, Bailey E.; Nano, Francis E.

doi:10.1186/s12864-023-09266-9

BMC Genomics

Table 1 IS10R insertions, frameshifts and truncations in BM28 and BM28 ΔlysU

From: Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains

Gene(s)^a	B number(s)^b	Gene product(s)	Change(s)^c	Codon(s) affected / total codons^d
nmpC#	b0553	DLP12 prophage; putative outer membrane porin NmpC	I	44/346
-ycaD- > / *-ycaM-* >	b0898/b0899	putative transporter YcaD / putative transporter YcaM	I
ydfJ	b1543	putative transporter YdfJ	I	411/427
ydjO	b1730	protein YdjO	I	175/267
ynjI	b1762	DUF1266 domain-containing protein YnjI	I	310/346
fliZ*	b1921	DNA-binding transcriptional regulator FliZ	I	12/183
yedP	b1955	putative mannosyl-3-phosphoglycerate phosphatase	I	105/271
gatA	b2094	galactitol-specific PTS enzyme IIA component	I	69/150
< *-rbfA-* / < -infB-	b3167/ b3168	30S ribosome binding factor / translation initiation factor IF-2	I
yhjY	b3548	conserved protein YhjY	I	158/232
wecH	b3561	O-acetyltransferase WecH	I	196/331
yidP	b3684	putative DNA-binding transcriptional regulator YidP	I	19/238
-nrfG- > / *-gltP-* >	b4076/ b4077	putative formate-dependent nitrite reductase complex subunit NrfG / glutamate/aspartate: H( +) symporter GltP	I
fimE	b4313	regulator for fimA	I	166/198
< *-mcrB-* / < -symE-	b4346/ b4347	5-methylcytosine-specific restriction enzyme subunit McrB / toxic protein SymE	I
caiT	b0040	L-carnitine:gamma-butyrobetaine antiporter	T	68/504
ampE	b0111	protein AmpE	FS	235/284
arfB	b0191	peptidyl-tRNA hydrolase, ribosome rescue factor	FS	103/140
mltD	b0211	membrane-bound lytic murein transglycosylase D	FS	110/452
fadE	b0221	acyl-CoA dehydrogenase	FS	611/814
mdlA	b0448	ABC transporter family protein MdlA	FS	234/590
ybbD#	b0501	putative uncharacterized protein YbbD	FS	139/86
fepE	b0587	polysaccharide co-polymerase family protein FepE	FS	42/377
pagP	b0622	Lipid IVA palmitoyltransferase	FS(79), T(112)	79 and 112/186
galK	b0757	galactokinase	FS	271/382
clsB*	b0789	cardiolipin synthase B	FS	15/413
ybjL	b0847	putative transport protein YbjL	FS	81/561
potG	b0855	putrescine ABC transporter ATP binding subunit	FS	92/377
elfG	b0941	putative fimbrial-like adhesin protein	FS	140/356
narX	b1222	sensory histidine kinase NarX	FS	586/598
yciE	b1257	DUF892 domain-containing protein YciE	T	139/168
recE*	b1350	Rac prophage; exonuclease VIII, ds DNA exonuclease, 5′ → 3’ specific	FS	496/866
ydaU*	b1359	Rac prophage; DUF1376 domain-containing protein YdaU	FS	178/285
ydcO	b1433	putative transport protein YdcO	FS	256/391
lsrF	b1517	3-hydroxy-2,4-pentadione 5-phosphate thiolase	FS	21/291
marB	b1532	multiple antibiotic resistance protein	T	23/72
slyA	b1642	DNA-binding transcriptional dual regulator SlyA	FS	70/144
nimR	b1790	DNA-binding transcriptional repressor NimR	FS	174/273
cheR	b1884	chemotaxis protein methyltransferase	FS	221/286
fliR‡	b1950	flagellar biosynthesis protein FliR	FS (52.9%)	67/261
gatC#	b2092	galactitol-specific PTS enzyme IIC component	FS	305/311
menC	b2261	o-succinylbenzoate synthase	FS	15/320
evgS‡	b2370	sensory histidine kinase EvgS	FS	315/1197
bcp	b2480	thiol peroxidase	FS	44/156
upp	b2498	uracil phosphoribosyltransferase	FS	147/208
ypjA	b2647	adhesin-like autotransporter YpjA	FS	112/1526
umpG	b2744	broad specificity 5'(3')-nucleotidase and polyphosphatase	FS	33/253
yggN	b2958	putative EcfF	FS	195/239
mtr	b3161	tryptophan:H( +) symporter Mtr	FS	335/414
glpR#	b3423	DNA-binding transcriptional repressor GlpR	FS	51/105
pitA	b3493	metal phosphate:H( +) symporter PitA	T	385/499
gadW	b3515	DNA-binding transcriptional dual regulator GadW	FS	86/242
bcsB	b3532	cellulose synthase periplasmic subunit	FS	13/779
xylB	b3564	xylulokinase	FS	418/484
atpC	b3731	ATP synthase F1 complex subunit epsilon	FS	136/139
gpp	b3779	guanosine-5'-triphosphate,3'-diphosphate phosphatase	FS	387/494
cytR	b3934	DNA-binding transcriptional repressor CytR	FS	112/341
yjdI*	b4126	PF06902 family protein YjdI	FS	9/76
cutA*	b4137	copper binding protein CutA	T	106/112
dcuA*	b4138	C4-dicarboxylate transporter DcuA	FS	19/433
serB	b4388	phosphoserine phosphatase	FS	311/322

^aArrows surrounding genes indicate their directions and genes in bold have the insertion upstream of their start codons, meaning the insertions may affect the promoters or ribosome-binding sites of the genes. Mutations only present in BM28 are indicated with an asterisk (*) and mutations only present in BM28 ΔlysU are indicated with a double dagger (‡). Genes that are already interrupted in the wildtype are marked with a number sign (#)
^bThe b number is shown in bold if the encoded protein was detected in an E. coli protein melting temperature study and determined to have a melting temperature ≤ 53.5 °C (≤ 5 °C above the T_max of BM28) [36]
^cI represents an IS10R insertion, FS represents frame shift, T represents truncation, and if a change is at < 75% frequency the percent frequency is shown in brackets
^dIS10R insertions, frame shifts and truncations which result in loss of > 10% of the amino acids are shown in bold

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ISSN: 1471-2164

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