Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strains and Culture Conditions
2.2. RNA-Seq Quantification of Gene Expression Levels
2.3. Construction of the WCGNA Network
2.4. Hub Gene Determination
2.5. GO and KEGG Enrichment Analysis
2.6. PPI Analysis
2.7. Data Visualization
3. Results
3.1. Growth and Transcriptome Changes under Mild Acid Stress
3.2. Differential Gene Expression Analysis
3.3. WGCNA Analysis
3.3.1. Soft Threshold Determination, Network Topology Analysis of Adjacency Matrices Based on WGCNA
3.3.2. Gene Clustering and Module–Trait Relationships
3.3.3. Functional Enrichment Analysis of Hub Genes Highly Correlated with Traits
3.4. OD600
3.5. SC3124 and WT
3.6. pH 6.0 and pH 6.8
3.7. PPI Analysis of Hub Genes in Blue and Pink Modules
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Subnetwork | Gene | Product | GO Pathway 1 | KEGG Pathway 1 |
---|---|---|---|---|
SN.1 | dppF | dipeptide ABC transporter ATP binding subunit DppF | Transporter activity; transmembrane transporter activity; nitrogen compound transport; establishment of localization; amino acid transport; carboxylic acid transport; monoatomic cation transmembrane transport; monoatomic ion transmembrane transport. | ABC transporters |
lolE | lipoprotein release complex—inner membrane subunit | |||
lolD | lipoprotein release complex—ATP binding subunit | |||
artQ | L-arginine ABC transporter membrane subunit ArtQ | |||
dppD | dipeptide ABC transporter ATP binding subunit DppD | |||
artI | putative ABC transporter periplasmic binding protein ArtI | |||
proX | glycine betaine ABC transporter periplasmic binding protein ProX | |||
cydC | glutathione/L-cysteine ABC exporter subunit CydC | |||
ydcS | putative ABC transporter periplasmic binding protein/polyhydroxybutyrate synthase | |||
dppB | dipeptide ABC transporter membrane subunit DppB | |||
potC | spermidine preferential ABC transporter membrane subunit PotC | |||
hisM | lysine, arginine, ornithine ABC transporter/histidine ABC transporter, membrane subunit HisM | |||
lolC | lipoprotein release complex—inner membrane subunit | |||
potB | spermidine preferential ABC transporter membrane subunit PotB | |||
hisQ | lysine, arginine, ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ | |||
osmF | glycine betaine ABC transporter periplasmic binding protein OsmF | |||
dppC | dipeptide ABC transporter membrane subunit DppC | |||
dppA | dipeptide ABC transporter periplasmic binding protein | |||
SN.2 | nuoJ | NADH:quinone oxidoreductase subunit J | NAD(P)H dehydrogenase (quinone) activity; oxidoreductase activity, acting on NAD(P)H; electron transfer activity. | Oxidative phosphorylation; citrate cycle (TCA cycle). |
sucD | succinyl-CoA synthetase subunit alpha | |||
nuoC | NADH:quinone oxidoreductase subunit CD | |||
nuoN | NADH:quinone oxidoreductase subunit N | |||
nuoF | NADH:quinone oxidoreductase subunit F | |||
sucB | dihydrolipoyltranssuccinylase | |||
nuoH | NADH:quinone oxidoreductase subunit H | |||
nuoG | NADH:quinone oxidoreductase subunit G | |||
sucA | subunit of E1(0) component of 2-oxoglutarate dehydrogenase | |||
nuoL | NADH:quinone oxidoreductase subunit L | |||
sdhB | succinate:quinone oxidoreductase, iron-sulfur cluster binding protein | |||
SN.3 | pxpC | 5-oxoprolinase component C | Purine biosynthesis; pyrimidine nucleotide biosynthesis; glutamate biosynthesis; 5-oxoprolinase (ATP-hydrolyzing) activity; toxin biosynthesis. | Purine, pyrimidine metabolism; glutathione metabolism; alanine, aspartate and glutamate metabolism. |
purR | DNA-binding transcriptional repressor PurR | |||
pyrC | dihydroorotase | |||
purF | amidophosphoribosyltransferase | |||
pxpA | 5-oxoprolinase component A | |||
purK | 5-(carboxyamino)imidazole ribonucleotide synthase | |||
purL | phosphoribosylformylglycinamide synthetase | |||
cvpA | colicin V production protein | |||
gltD | glutamate synthase subunit GltD | |||
SN.4 | epmC | EF-P-Lys34 hydroxylase | Not available. | Not available. |
yfcA | putative transporter YfcA | |||
yfcL | PF08891 family protein YfcL | |||
mepA | peptidoglycan DD-endopeptidase/peptidoglycan LD-endopeptidase | |||
SN.5 | alaA | glutamate--pyruvate aminotransferase AlaA | L-alanine biosynthesis; glutamate biosynthesis; serine biosynthesis; purine nucleotide biosynthesis; plasma membrane. | Alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism; purine metabolism. |
ycdX | zinc-binding phosphatase YcdX | |||
serC | phosphoserine/phosphohydroxythreonine aminotransferase | |||
ghrA | glyoxylate/hydroxypyruvate reductase A | |||
purU | formyltetrahydrofolate deformylase | |||
ycdY | chaperone protein YcdY | |||
gltB | glutamate synthase subunit GltB | |||
ycdZ | inner membrane protein YcdZ | |||
SN.6 | prfA | peptide chain release factor RF1 | Not available. | Not available. |
ispE | 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase | |||
hemA | glutamyl-tRNA reductase | |||
SN.7 | folC | bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase | Folic acid biosynthetic process. | Folate biosynthesis. |
folP | dihydropteroate synthase | |||
folX | dihydroneopterin triphosphate 2′-epimerase | |||
SN.8 | yegS | lipid kinase YegS | Not available | Not available |
ymgG | PF13488 family protein YmgG | |||
ymgD | PF16456 family protein YmgD |
Subnetwork | Gene | Product | GO Pathway 1 | KEGG Pathway 1 |
---|---|---|---|---|
SN.9 | yidC | membrane protein insertase YidC | Not available | Not available |
gltX | glutamate-tRNA ligase | |||
rnpA | RNase P protein component | |||
bipA | 50S ribosomal subunit assembly factor BipA | |||
SN.10 | frmR | DNA-binding transcriptional repressor FrmR | Formaldehyde catabolic process | Microbial metabolism in diverse environments |
frmB | S-formylglutathione hydrolase FrmB | |||
frmA | S-(hydroxymethyl)glutathione dehydrogenase | |||
SN.11 | cysP | thiosulfate/sulfate ABC transporter periplasmic binding protein CysP | Thiosulfate/sulfate transporter; sulfur metabolism; xenobiotic transmembrane transporter | Sulfur metabolism; ABC transporters |
cysU | sulfate/thiosulfate ABC transporter inner membrane subunit CysU | |||
ybhS | probable multidrug ABC transporter permease | |||
SN.12 | amiC | N-acetylmuramoyl-L-alanine amidase C | Not available | Cationic antimicrobial peptide (CAMP) resistance |
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Qin, J.; Guo, H.; Wu, X.; Ma, S.; Zhang, X.; Yang, X.; Liu, B.; Feng, L.; Liu, H.; Huang, D. Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain. Microorganisms 2024, 12, 1565. https://doi.org/10.3390/microorganisms12081565
Qin J, Guo H, Wu X, Ma S, Zhang X, Yang X, Liu B, Feng L, Liu H, Huang D. Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain. Microorganisms. 2024; 12(8):1565. https://doi.org/10.3390/microorganisms12081565
Chicago/Turabian StyleQin, Jingliang, Han Guo, Xiaoxue Wu, Shuai Ma, Xin Zhang, Xiaofeng Yang, Bin Liu, Lu Feng, Huanhuan Liu, and Di Huang. 2024. "Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain" Microorganisms 12, no. 8: 1565. https://doi.org/10.3390/microorganisms12081565
APA StyleQin, J., Guo, H., Wu, X., Ma, S., Zhang, X., Yang, X., Liu, B., Feng, L., Liu, H., & Huang, D. (2024). Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain. Microorganisms, 12(8), 1565. https://doi.org/10.3390/microorganisms12081565