Genome-Wide Analysis of Innate Susceptibility Mechanisms of Escherichia coli to Colistin
Abstract
:1. Introduction
2. Results
2.1. Effect of Colistin Stress on the E. coli Mutant Library
2.2. Effect of Colistin on Cell Membranes
2.3. DNA Housekeeping Genes Associated with Colistin Susceptibility
2.4. Small RNA Dependent Regulation
2.5. GlpT Transporter and Phosphonates
2.6. Validation of the Potential Genes
3. Discussion
4. Materials and Methods
4.1. TraDIS-Xpress Library
4.2. Colistin Exposure Conditions and TraDIS-Xpress Sequencing
4.3. Bioinformatics
4.4. Validation Experiments
4.5. Comparing Combinations of Two Antibiotics at Different Concentrations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Pathway | Gene | Annotation | Multiple of MIC | |||
---|---|---|---|---|---|---|
2× | 1× | 0.5× | 0.25× | |||
Lipid biosynthesis and regulation | basR | response regulator in two-component regulatory system with BasS | 4.03 | 0.00 | 0.00 | 0.00 |
basS | sensory histidine kinase in two-component regulatory system with BasR | 17.44 | 5.65 | 1.94 | 5.45 | |
waaB | UDP-D-galactose:(glucosyl)lipopolysaccharide-1 and 6-D-galactosyltransferase | 0.00 | −1.82 | 0.00 | 0.00 | |
waaC | ADP-heptose:LPS heptosyl transferase I | 0.00 | −2.25 | −1.70 | 0.00 | |
waaG | glucosyltransferase I | 0.00 | −3.06 | −1.98 | −1.61 | |
waaP | kinase that phosphorylates core heptose of lipopolysaccharide | 0.00 | −2.46 | −1.92 | 0.00 | |
waaR | UDP-D-galactose:(glucosyl)lipopolysaccharide-alpha-1 and 3-D-galactosyltransferase | 0.00 | −3.83 | −2.01 | −1.11 | |
waaS | lipopolysaccharide core biosynthesis protein | 0.00 | −1.96 | −1.63 | −1.60 | |
waaU | lipopolysaccharide core biosynthesis | 0.00 | −1.10 | 0.00 | 0.00 | |
lptC | lipopolysaccharide export and IM-tethered periplasmic protein of the LptBFGC export complex | 0.00 | 1.57 | 1.50 | 1.42 | |
waaD | ADP-L-glycero-D-mannoheptose-6-epimerase and NAD(P)-binding | 0.00 | −2.66 | −2.16 | 0.00 | |
wbbH | O-antigen polymerase | 0.00 | −1.14 | −1.16 | −1.17 | |
wbbI | d-Galf:alpha-d-Glc beta-1 and 6-galactofuranosyltransferase | 0.00 | 0.00 | −1.08 | 0.00 | |
wbbK | lipopolysaccharide biosynthesis protein | 0.00 | −1.59 | −1.45 | −1.57 | |
Transcription and translation regulation | aspU | tRNA-Asp | 0.00 | 0.00 | 0.00 | −2.70 |
cmoB | tRNA (cmo5U34)-carboxymethyltransferase and carboxy-SAM-dependent | 0.00 | 1.30 | 0.00 | 0.00 | |
valS | valyl-tRNA synthetase | 0.00 | 0.00 | 0.00 | −3.15 | |
truA | tRNA pseudouridine(38–40) synthase | 0.00 | 1.11 | 1.32 | 1.23 | |
hfq | global sRNA chaperone; HF-I and host factor for RNA phage Q beta replication | 0.00 | 1.41 | 1.55 | 1.55 | |
ohsC | sRNA antisense regulator of shoB toxin | 0.00 | −2.49 | −2.81 | −2.55 | |
oxyS | sRNA antisense regulator activates genes that detoxify oxidative damage and Hfq-dependent | 0.00 | 0.00 | −2.27 | 0.00 | |
rpoN | RNA polymerase and sigma 54 (sigma N) factor | 0.00 | 1.99 | 0.00 | 1.81 | |
rydC | sRNA antisense regulator of yejABEF and Hfq-dependent; over-expression causes a thermosensitive growth phenotype on minimal glycerol and maltose and or ribose media | 0.00 | −2.31 | 0.00 | −1.83 | |
appY | global transcriptional activator; DLP12 prophage | 0.00 | −1.66 | −1.66 | −1.69 | |
Membrane associated genes | bhsA | biofilm and cell surface and signaling protein | 0.00 | −1.86 | 0.00 | −2.21 |
ariR | RcsB connector protein for regulation of biofilm and acid-resistance | 0.00 | −1.04 | −1.26 | −1.23 | |
ompA | outer membrane protein A (3a;II*;G;d) | 0.00 | −1.32 | 0.00 | 0.00 | |
surA | peptidyl-prolyl cis-trans isomerase (PPIase) | 0.00 | −3.29 | 0.00 | −1.38 | |
flgA | assembly protein for flagellar basal-body periplasmic P ring | 0.00 | 1.22 | 0.00 | 0.00 | |
Transporters | glpT | sn-glycerol-3-phosphate transporter | 3.26 | 1.08 | 1.15 | 1.14 |
phnE | 4312259_4313047 | 3.84 | 1.44 | 1.35 | 1.29 | |
phnF | putative DNA-binding transcriptional regulator of phosphonate uptake and biodegradation | 4.14 | 1.05 | 1.02 | 0.00 | |
ygcS | putative transporter | 12.28 | 0.00 | 0.00 | 0.00 | |
DNA associated proteins | hrpA | putative ATP-dependent helicase | 16.12 | 2.80 | 0.00 | 2.99 |
recF | gap repair protein | 7.68 | 4.60 | 0.00 | 0.00 | |
uvrD | DNA-dependent ATPase I and helicase II | 8.10 | 0.00 | 0.00 | 0.00 | |
dinI | DNA damage-inducible protein I | 0.00 | 0.00 | 0.00 | −1.28 | |
recG | ATP-dependent DNA helicase | 0.00 | 10.51 | 4.98 | 0.00 | |
dcd | 2′-deoxycytidine 5′-triphosphate deaminase | 0.00 | 3.54 | 2.94 | 3.74 | |
dnaG | DNA primase | 0.00 | −4.65 | −3.74 | 0.00 | |
uspC | universal stress protein | 0.00 | −1.14 | −1.09 | 0.00 | |
seqA | negative modulator of initiation of replication | 0.00 | 1.73 | 1.74 | 0.00 | |
Miscellaneous | ybbC | putative immunity protein | 0.00 | −2.21 | −2.03 | −2.08 |
ybcV | DLP12 prophage; uncharacterized protein | 0.00 | −1.74 | −1.37 | −1.48 | |
ydcD | uncharacterized protein | 0.00 | −2.86 | 0.00 | 0.00 | |
ygeN | 2988672_2989379 | 0.00 | −1.84 | −1.87 | −1.76 | |
yjbL | uncharacterized protein | 0.00 | −2.44 | −2.44 | −2.48 | |
yjbS | uncharacterized protein | 0.00 | −2.22 | −2.04 | −2.39 | |
yfcZ | UPF0381 family protein | 0.00 | 2.99 | 0.00 | 0.00 | |
ycjS | putative NADH-binding oxidoreductase | 0.00 | 1.19 | 1.09 | 1.19 |
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Yasir, M.; Turner, A.K.; Bastkowski, S.; Lott, M.; Holden, E.R.; Telatin, A.; Page, A.J.; Webber, M.A.; Charles, I.G. Genome-Wide Analysis of Innate Susceptibility Mechanisms of Escherichia coli to Colistin. Antibiotics 2022, 11, 1668. https://doi.org/10.3390/antibiotics11111668
Yasir M, Turner AK, Bastkowski S, Lott M, Holden ER, Telatin A, Page AJ, Webber MA, Charles IG. Genome-Wide Analysis of Innate Susceptibility Mechanisms of Escherichia coli to Colistin. Antibiotics. 2022; 11(11):1668. https://doi.org/10.3390/antibiotics11111668
Chicago/Turabian StyleYasir, Muhammad, A. Keith Turner, Sarah Bastkowski, Martin Lott, Emma R. Holden, Andrea Telatin, Andrew J. Page, Mark A. Webber, and Ian G. Charles. 2022. "Genome-Wide Analysis of Innate Susceptibility Mechanisms of Escherichia coli to Colistin" Antibiotics 11, no. 11: 1668. https://doi.org/10.3390/antibiotics11111668