TABLE 2

Description of mutations and their context in the genome of the E. coli 1000G-BA strain

Gene(s)/genomic
location & function
Description or known function(s)Effects of mutations (if any)
yadL ← (intragenic)Adhesion and tissue tropism in E. coli (115, 116)Unknown
acrB ←(intragenic)Antibiotic/drug efflux (86, 117120)V139A is involved in tetracycline resistance in E. coli (81) and in
substrate binding and carbapenem resistance (85)
acrA ← / → acrR
(intergenic)
acrR regulates efflux (acrAB) pump operon,
solvent tolerance (121), motility, flagellar and
biofilm/pellicle formation, and pathogenesis
(122, 123)
Mutation is in the promoter “acrRp,” upstream of acrR; mutation
effect unknown
mdfA → (intragenic)Multidrug resistance, active exclusion of
chloramphenicol (95, 96, 124, 125)
P263S; changes nonreactive proline to serine, is often found in
protein functional centers, occurs in a transmembrane domain
(125, 126), and is a new mutation and an addition to mdfA
mutations as a response(s) to antibiotic stress
ybjG ← / → mdfA
(intergenic)
ybjG—bacitracin resistance (127, 128); mdfA
multidrug resistance (8588)
Mutation is in the promoter “cmrp,” updstream of mdfA; effect
unknown; IS30 insertion occurs only 8 bp away from a (PhosP)
regulator binding region of ybjG.; the 3 changes (on mdfA and
its promoter cmrp and in its immediate neighborhood) are
additions to changes related to mdfA in response to antibiotic
exposure
rpoC → (intragenic)Encodes the RNA polymerase subunit β';
categorized as an essential gene for
E. coli (129)
Unknown
treB ← (intragenic)Encodes trehalose-specific PTS enzyme IIBC,
linked with biofilms in E. coli (130)
Unknown
gltS ← / → xanP
(intergenic)
Flanking genes encode metabolite transport
proteins
Mutation is in the promoter “xanPp5” upstream of xanP
fimE → (intragenic)fimE regulates adhesion protein coding gene fimAUnknown
fimE → / → fimA
(intergenic)
Flanking genes encode metabolite transport proteinsMutation is in the 3rd base upstream of the start codon “ATG”
of the fimA gene
marR → (intragenic)Multidrug resistance (81)E131V is in the DNA-binding domain involved in organic
solvent tolerance (88) regulating
a global network of 80 genes (8991, 131);
fluoroquinolone resistance (9294) in clinically
relevant E. coli strains
ompF ← (intragenic)Encodes outer membrane porin involved in
antibiotic resistance (78, 132, 133), acid stress
response (ASR) (72, 134)
Dysfunctional ompF likely causes increased antibiotic
resistance of 1000-BA
crl → (intragenic
TMR)
Highly conserved in Gram-negative bacteria;
encodes the thin, coiled aggregative surface
filaments called curli (curli mediate adhesion [135138]
and wound colonization and interaction with
the immune system [138, 139] and influence stress
responses, quorum sensing [140], and biofilms
[141] and resistance to gentamicin [54] and
control ASR genes [142, 143])
Loss of the crl gene potentially results in a fitness cost
of antibiotic resistance in 1000-BA
yeaJ → (intragenic
TMR)
Encodes a diguanylate cyclase and regulates
swimming motility and biofilm formation
(144146)
Loss of the yeaJ gene potentially results in a
potential fitness cost of antibiotic resistance in 1000-BA
(flhAB cheZYBR tap
tar cheWA motBA
flhCD) ←
(inter- and
intragenic TMR)
14-gene cluster, central to chemotaxis and biofilm
formation (144, 147); cheR, cheW (chemotaxis),
and motA (motility) are considered essential for
E. coli (129)
Loss of gene cluster potentially results in a fitness cost of
antibiotic resistance in 1000-BA