Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals and Bacterial Strains
2.2. ASKA Library Screening and Minimal Inhibitory Concentration (MIC) Determination
2.3. Bioinformatical Analyses
3. Results
3.1. Genome-Wide Screening of Resistance Genes against H2O2
3.2. Genome-Wide Screening of Resistance Genes against HOCl
3.3. Effects of Overexpressing Selected Resistance Genes in the MG1655 Strain
3.4. Effects of Inactivating Selected Resistance Genes in the E. coli Genome
4. Discussion
4.1. Summary of the Study
4.2. H2O2-Resistance Genes
4.3. HOCl-Resistance Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Biological Functions 1 | Genes 2 |
---|---|
Stress responses | btuE, cheA, cheW, evgS, exoX, katE, katG, mepA, osmE, phoA, psiF, radA, rarA, ruvC, sbmC, sodB, sufC, tpx, ttdB, yajQ, ybcM, ybhT (acrZ), ybiJ, ycdO (efeO), ycjU (pgmB), ydjR (ves), yeaD, yegD, yfiD (grcA), yhiO (uspB), yjjX, yodA (zinT), ypdA (pyrS), yraJ |
Membrane components and transporters | amiB, btuD, cmtB, cusC, damX, dmsA, exbD, feoB, fhuA, frvB, ftsH, gatC, hyaA, kefB, kefC, macA, metN, mltC, mtlA, nrfC, nuoB, ompL, ompW, ompX, oppD, rbsA, rfbX, sapC, shiA, slyB, wcaD, ybhC, ycjP, ydcT, ygjQ, yidC, yobA, yrbB (mlaB) |
Metabolism | aceA, aceK, agaS, allB, aroB, aroF, aroL, astD, citG, cobT, eda, fadD, galU, gatD, gloA, guaA, hcr, hisB, hpt, hybD, hypB, ilvA, ispA, kbaZ, kdsA, lacA, lacZ, leuA, lpcA (gmhA), moaA, moeB, paaB, pflA, pflD, phnI, prpD, prpE, puuD, ribA, ribC, ribD, sucA, sucC, tdk, thiL, thrA, ubiD, upp, wbbI, yaiE (ppnP), ybdK, ybiS (ldtB), ycfS (idtC), ydeN, ydiR, ydjA, yeaU (dmlA), yfbB (menH) |
DNA replication, gene expression and regulation | agaR, appY, baeR, cpdA, deoR, dnaX, flhD, fnr, gadE, mngR, pepA, rho, rluA, rna, rpmG, rsgA, stpA, tus, umuD, valS, ydfH, yecO (cmoA), yggD (fumE), yhaJ, yidZ, yjeK (epmB), yjfN, yncC (mcbR), yraO (diaA) |
Cell division and mobility | flgE, flgK, fliS, flxA, minD, minE, motB, ybgF, ydeQ, yfiR, yihG, yraP |
Other and unknown | glf, hokD, mpl, yabQ, yagM, yaiX, ybcH, ybfH, ybhN, ybiI, ybiV, ybiW, yceH, ycgL, yciC, yciK, yddK, ydfA, ydfB, ydfD, ydhL, ydjJ, ydjL, yeaO, yecA, yecI, yedE, yedM, yfdM, yfjM, ygcP, ygcU, ygeR, yhjJ, yihM, yjcF, yjjJ, ykfH, ymcB, yncG, yoaH, yobB, yoeE, yqeK, yqhA, yrbL |
Gene | Known or Projected Functions |
---|---|
kefC | K+: H+ antiporter; plays a role in protecting the cell from electrophile toxicity [28]. |
leuA | 2-isopropylmalate synthase; involved in the first step of leucine biosynthesis [29]. |
metN | L-methionine/D-methionine ABC transporter ATP-binding subunit [30]. |
prpE | Propionyl-CoA synthetase; catalyzes formation of propionyl-CoA, the first reaction in propionate catabolism via the methylcitrate cycle [31]. |
yajQ | A nucleotide binding protein [32]. |
appY | DNA-binding transcriptional activator; induces the expression of energy metabolism genes under anaerobiosis, stationary phase, and phosphate starvation [33]. |
ybhC | An outer membrane lipoprotein [34]. |
katE | Catalase HPII; the primary scavenger at high H2O2 concentrations [35]. |
sapC | Putrescine ABC exporter membrane protein; putrescine efflux [36]. |
mcbR | A member of the FadR C-terminal domain (FCD) family in the GntR superfamily of transcriptional regulators [37]. |
yncG | Putative glutathione S-transferase [38]. |
yqhA | Uncharacterized protein; predicted to be an integral membrane protein. |
katG | Catalase/hydroperoxidase; bifunctional with both catalase and peroxidase activity [39]. |
damX | Non-essential cell division protein [40]. |
yhjJ | Peptidase M16 family protein. |
ilvA | Threonine deaminase; carries out the first step in the synthesis of isoleucine [41]. |
rho | Transcription termination factor; required for one of the two major types of termination of RNA transcription [42]. |
ydhL | DUF1289 domain-containing protein. |
mlaB | Intermembrane phospholipid transport system protein; forms a stable complex with MlaF, MlaE, and MlaD and is required for the stability of this complex [43]. |
citG | Triphosphoribosyl-dephospho-CoA synthase [44]. |
Biological Functions | Genes |
---|---|
Stress responses | cheW, dacB, frmB, gloA, groL, hyaE, hyaF, hybG, inaA, otsA, rfbC, sanA, sbmC, solA, ssuD, ycbB (ldtD), yghW, yhaK, yodA (ZinT), yqjA |
Membrane components and transporters | appC, chbB, exbD, gspK, hyaA, hyaC, hydN, marC, mpaA, nmpC, nrfC, rfe, slyB, tap, ybhC, ybhR, ybiM, ybiO, yceJ, ydgK, yfdY, yggR, ygjE (ttdT), yhiP (dtpB), yoaE, yoeE, ypfJ, yrbB |
Metabolism | acnA, agaS, aspC, bioA, cobS, cynT, dadA, hisA, ilvA, leuA, mtlD, nagD, paaG, prpE, purB, sucC, ubiD, upp, ycdK (rutC), ygbL |
DNA replication, gene expression and regulation | agar, gyrA, lhr, rnc, rpoS, rsuA, trmU, uvrY, yccK (tusE), ydaV, ydcP (rlhA), ydiP, ydjF, yhaJ, yhdJ, ykgM, ymfG (xisE), yneJ |
Cell division & mobility | flip, fliS, motB, ydeQ, yedQ (dgcQ), ygcF (queE), yneF (dgcF) |
Other and unknown | dsrB, elaA, smf, sprT, yagM, ybbV, yccJ, ycgY, yddJ, ydfB, ydfD, ydhL, yeeX, yfiH (pgeF), yhcG, ykfC, ymfE, yncH, yncM, ynfN, ytfI |
Gene | Known or Projected Functions |
---|---|
prpE | Propionate-CoA ligase; catalyzes the synthesis of propionyl-CoA from propionate and CoA [31]. |
frmB | S-formylglutathione hydrolase; hydrolyzes S-formylglutathione to glutathione and formate [45]. |
rutC | Putative aminoacrylate peracid reductase [46]. |
sucC | Succinate-CoA ligase (ADP-forming) subunit beta; functions in the citric acid cycle [47]. |
ycbB | Periplasmic L,D-transpeptidase; plays a role in the protective remodeling of peptidoglycan during cell envelope stress [48]. |
yccJ | PF13993 family protein. |
hyaC | Probable Ni/Fe-hydrogenase 1 b-type cytochrome subunit; functions in anchoring hydrogenase to the membrane [49]. |
hyaE | Hydrogenase-1 operon protein [50]. |
tap | Methyl-accepting chemotaxis protein IV [51]. |
yoaE | UPF0053 inner membrane protein; putative transport protein [52]. |
motB | Motility protein B; comprises the stator element of the flagellar motor complex with MotA [53]. |
rnc | Ribonuclease 3 for rRNA processing [54]. |
elaA | Putative N-acetyltransferase. |
yfdY | DUF2545 domain-containing protein [55]. |
exbD | A component of the energy-transducing Ton system [56]. |
ilvA | Threonine deaminase; carries out the first step in the synthesis of isoleucine [41]. |
yhdJ | Overexpression of YdhJ leads to methylation of genomic DNA at the NsiI recognition sequence (5′-ATGCAT-3′) [57]. |
ytfI | Uncharacterized gene. |
ybhR | One of two integral membrane subunits of a putative ABC exporter [58]. |
yedQ | A probable inner membrane protein whose expression is dependent on σS under a number of stress conditions [59]. |
marC | An inner membrane protein with six predicted transmembrane domains [52]. |
sanA | Multi-copy expression of sanA complements the vancomycin sensitivity of an E. coli K-12 mutant with outer membrane permeability defects [60]. |
rsuA | Pseudo-uridine synthase that is responsible for pseudouridylation of 16S rRNA at position 516 [61]. |
Gene | Known or Projected Functions |
---|---|
leuA | 2-isopropylmalate synthase; involved in the first committed step in leucine biosynthesis [29]. |
prpE | Propionyl-CoA synthetase; catalyzes formation of propionyl-CoA via the methylcitrate cycle [31]. |
sucC | β subunit of succinyl-CoA synthetase [47]. |
ybhC | An outer membrane lipoprotein [34]. |
hyaA | Small subunit of hydrogenase-1; contains a unique proximal [4Fe-3S] cluster that is essential for oxygen tolerance [63]. |
ydeQ | Uncharacterized gene. |
cheW | Chemotaxis protein; in the ternary receptor complexes of two-component signaling pathways [64]. |
motB | Motility protein B; comprises the stator element of the flagellar motor complex with MotA [53]. |
yodA | Metal-binding protein; may function as a periplasmic zinc chaperone delivering zinc to apo-enzymes in this compartment [65]. |
ydfB | Uncharacterized gene. |
fliS | Flagellar biosynthesis protein; substrate-specific chaperones of the flagellar export system [66]. |
gloA | Glyoxalase I; catalyzes the first of two sequential steps in the conversion of methylglyoxal to D-lactate [67]. |
ydfD | A lysis protein encoded by the Qin prophage [68]. |
slyB | Outer membrane lipoprotein [69]. |
yoeE | TonB-dependent receptor plug domain-containing protein; may be regulated by Fur regulon [70]. |
sbmC | DNA gyrase inhibitor; protects cell from DNA damage cause by DNA-bound gyrase [71]. |
upp | Uracil phosphoribosyltransferase; a pyrimidine salvage enzyme that catalyzes the synthesis of uridine 5′-monophosphate from uracil and 5-phospho-α-D-ribose 1-diphosphate [72]. |
yhaJ | DNA-binding transcriptional activator; a member of the LysR protein family [73]. |
agaR | DNA-binding transcriptional repressor [74]. |
exbD | A component of the energy-transducing Ton system [56]. |
agaS | Putative galactosamine-6-phosphate deaminase/isomerase. |
ilvA | Threonine deaminase; carries out the first step in the synthesis of isoleucine [41]. |
ubiD | 3-octaprenyl-4-hydroxybenzoate decarboxylase; an enzyme of the ubiquinol-8 biosynthesis pathway that catalyzes the decarboxylation of 3-octaprenyl-4-hydroxybenzoate [75]. |
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Chen, H.; Wilson, J.; Ercanbrack, C.; Smith, H.; Gan, Q.; Fan, C. Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. Antioxidants 2021, 10, 861. https://doi.org/10.3390/antiox10060861
Chen H, Wilson J, Ercanbrack C, Smith H, Gan Q, Fan C. Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. Antioxidants. 2021; 10(6):861. https://doi.org/10.3390/antiox10060861
Chicago/Turabian StyleChen, Hao, Jessica Wilson, Carson Ercanbrack, Hannah Smith, Qinglei Gan, and Chenguang Fan. 2021. "Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli" Antioxidants 10, no. 6: 861. https://doi.org/10.3390/antiox10060861
APA StyleChen, H., Wilson, J., Ercanbrack, C., Smith, H., Gan, Q., & Fan, C. (2021). Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. Antioxidants, 10(6), 861. https://doi.org/10.3390/antiox10060861