Physiological Response of Corynebacterium glutamicum to Indole
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Molecular Genetic Techniques
2.2. Culture Conditions
2.3. Sequencing of Transcriptomis and Genomic Data
2.3.1. RNA Isolation, qRT-PCR, Preparation of cDNA Libraries for Sequencing and DeSeq Analysis
2.3.2. gDNA Isolation, Library Preparation and Sequencing
2.4. Quantification of Amino Acids and Organic Acids by HPLC or GC–MS
2.5. Protein Purification and Electrophoretic Mobility Shift Assay
2.6. Iron Reduction Assay
2.7. Pseudo-Dipeptid Synthesis
3. Results
3.1. Growth and Global Gene Expression Response of C. glutamicum to Extracellularly Added Indole
3.2. Transtriptome Analysis of C. glutamicum C1* in Response to Indole-Alanine Dipeptide
3.3. Adaptive Laboratory Evolution for Increasing Indole Tolerance
3.4. Investigation of the Transcriptional Regulator Cg3388
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Data Availability
References
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Strains | Description | Source |
---|---|---|
Corynebacterium glutamicum | ||
WT | C. glutamicum wild type ATCC13032 | ATCC |
C1* | Genome-reduced chassis strain derived from WT | [52] |
ΔdtxR | WT containing dtxR deletion | [53] |
ΔrosR | WT containing rosR deletion | [54] |
Δcg3388 | WT containing cg3388/ihtR deletion | [55] |
C1* ΔdtxR | C1* containing dtxR deletion | This study |
C1* ΔrosR | C1* containing rosR deletion | This study |
IVO20 | Strain evolved from WT after 20 transfers in the presence of indole | This study |
IVO38 | Strain evolved from WT after 38 transfers in the presence of indole | This study |
C1* cg3388M1T | C1* with SNP in cg3388/ihtR, resulting in amino acid exchange M1T | This study |
C1* whcBR63L | C1* with SNP in whcB, resulting in amino acid exchange R63L | This study |
C1* cg3388M1T dtxRT8A | C1* with SNP in cg3388/ihtR and dtxR, resulting in amino acid exchange M1T and T8A | This study |
C1* cg3388M1T whcBR63L | C1* with SNP in cg3388/ihtR and whcB, resulting in amino acid exchanges M1T and R63L, respectively | This study |
C1* cg3388M1T dtxRT8A whcBR63L | C1* with SNPs in cg3388/ihtR, dtxR and whcB, resulting in amino acid exchanges M1T, T8A and R63L, respectively | This study |
C1* (pVWEx1) | C1* carrying pVWEx1 | This study |
C1* (pVWEx1-phe) | C1* carrying pVWEx1-phe | This study |
C1* Δphe (pVWEx1) | C1* containing phe deletion, carrying pVWEx1 | This study |
C1* Δphe (pVWEx1-phe) | C1* containing phe deletion, carrying pVWEx1-phe | This study |
C1* (pEKEx3) | C1* carrying pEKEx3 | This study |
C1* (pEKEx3-cg2796-cg2797) | C1* carrying pEKEx3-cg2796-cg2797 | This study |
C1* Δcg2796-cg2797 (pEKEx3) | C1* containing cg2796-cg2797 deletion, carrying pEKEx3 | This study |
C1* Δcg2796-cg2797 (pEKEx3-cg2796-cg2797) | C1* containing cg2796-cg2797 deletion, carrying pEKEx3-cg2796-cg2797 | This study |
Escherichia coli | ||
S17-1 | recA pro hsdR RP4-2-Tc::Mu-Km::Tn7 | [56] |
DH5α | F-thi-1 endA1 hsdr17(r-, m-) supE44 1lacU169 (Φ80lacZ1M15) recA1 gyrA96 | [49] |
BL21 (DE3) | F– ompT gal dcm lon hsdSB(rB–mB–) λ(DE3[lacI lacUV5-T7p07 ind1 sam7 nin5])[malB+]K-12(λS) | [57] |
Locus | Gene | Gene Product | Ind/- |
---|---|---|---|
cg0018 | uncharacterized membrane protein | 4.09 | |
cg0405 | ABC-type Fe3+-siderophore transport systems | 2.57 | |
cg0470 | htaB | heme binding protein | 3.12 |
cg0471 | htaC | heme binding protein | 2.91 |
cg0637 | creC | benzylaldehyde dehydrogenases | 2.85 |
cg0638 | creD | phosphohydrolase | 3.11 |
cg0639 | creE | class I P450 system subunit | 3.59 |
cg0640 | creF | class I P450 system subunit | 3.81 |
cg0641 | creG | NAD+-dependent 4-hydroxybenzyl alcohol dehydrogenase | 3.01 |
cg0642 | creH | 4-methylbenzyl phosphate synthase subunit | 3.60 |
cg0644 | creI | 4-methylbenzyl phosphate synthase subunit | 3.95 |
cg0645 | creJ | class I P450 system subunit | 3.96 |
cg1120 | ripA | AraC-type DNA-binding domain-containing proteins | 2.47 |
cg1152 | seuB | acyl-CoA dehydrogenases | 3.20 |
cg1298 | cydC | ATP-binding/permease protein | 3.69 |
cg1299 | cydD | ATP-binding/permease protein | 3.77 |
cg1300 | cydB | cytochrome bd-type quinol oxidase, subunit 2 | 3.84 |
cg1301 | cydA | cytochrome bd-type quinol oxidase, subunit 1 | 3.72 |
cg1773 | ctaB | polyprenyltransferase | 2.45 |
cg1881 | predicted iron-dependent peroxidase | 3.15 | |
cg1883 | uncharacterized secreted protein | 3.15 | |
cg1884 | copC | membrane-bound copper chaperone | 3.08 |
cg1930 | hypothetical protein | 3.46 | |
cg1931 | hypothetical protein | 2.72 | |
cg2678 | ABC-type transporter. periplasmic component | 2.44 | |
cg2796 | uncharacterized protein involved in propionate catabolism | 6.87 | |
cg2797 | uncharacterized ACR | 6.29 | |
cg2962 | putative enzyme synthesing extracellular polysaccharides | 3.69 | |
cg2966 | phe | putative phenol 2-monooxygenase | 6.14 |
cg3280 | uncharacterized secreted protein | 2.70 | |
cg3281 | copB | cation transport ATPases | 2.67 |
cg3286 | hypothetical protein | 3.09 | |
cg3287 | copO | multicopper oxidase | 3.11 |
cg3289 | thioredoxin-like protein | 3.82 | |
cg3327 | dps | starvation-inducible DNA-binding protein | 4.40 |
Locus | Gene | Gene Product | Ind-Ala/- |
---|---|---|---|
cg0012 | ssuR | transcriptional activator of sulfonate(ester) utilization | 1.84 |
cg0018 | uncharacterized membrane protein | 5.36 | |
cg0120 | putative hydrolase | 1.66 | |
cg0175 | putative secreted protein | 1.85 | |
cg0192 | hypothetical protein | 1.97 | |
cg0286 | putative membrane protein | −2.23 | |
cg0464 | putative Cu2+ transporting P-type ATPase | 1.59 | |
cg0569 | cation transporting ATPase | 2.05 | |
cg0759 | prpD2 | methylcitrate dehydratase, involved in propionate catabolism | 2.38 |
cg0760 | prpB2 | methylisocitrate lyase, involved in propionate metabolism | 2.53 |
cg0762 | prpC2 | methylcitrate synthase, involved in propionate catabolism | 2.57 |
cg0796 | prpD1 | putative (2-methyl) citrate dehydratase | 1.65 |
cg0797 | prpB1 | putative (methyl)isocitrate lyase | 1.82 |
cg0798 | prpC1 | putative (methyl)citrate synthase | 1.76 |
cg1279 | putative secreted protein | 2.05 | |
cg1327 | putative transcriptional regulator, Crp-family | 1.53 | |
cg1328 | putative heavy-metal ion transporting P-type ATPase | 1.72 | |
cg1393 | putative acetyltransferase, GNAT family | 1.78 | |
cg1470 | hypothetical protein | 2.58 | |
cg1471 | hypothetical protein | 1.51 | |
cg1635 | putative membrane protein | 1.51 | |
cg1710 | bacA | undecaprenol kinase | −1.77 |
cg2096 | putative membrane protein | −1.59 | |
cg2391 | aroG | 3-deoxy-7-phosphoheptulonate synthase | −1.54 |
cg2500 | putative transcriptional regulator. ArsR-family | 1.59 | |
cg2559 | aceB | malate synthase | 1.79 |
cg2560 | aceA | isocitrate lyase | 2.34 |
cg2719 | putative enterochelin esterase | −1.6 | |
cg2836 | sucD | succinate-CoA ligase (ADP-forming), alpha subunit | 2.06 |
cg2837 | sucC | succinate-CoA ligase (ADP-forming), beta subunit | 2.23 |
cg2962 | putative enzyme synthesing extracellular polysaccharides | 2.12 | |
cg2966 | phe | putative phenol 2-monooxygenase | 2.08 |
cg3169 | pck | phosphoenolpyruvate carboxykinase (GTP) | 2.00 |
cg3195 | putative flavin-containing monooxygenase | 1.60 | |
cg3202 | farR | transcriptional regulator. GntR-family | 1.88 |
cg3226 | putative MFS-type L-lactate permease | 2.05 | |
cg3303 | putative PadR-family transcriptional regulator | 2.26 | |
cg3327 | dps | starvation-inducible DNA-binding protein | 1.85 |
cg3367 | ABC-type multidrug transport system, ATPase | 1.72 | |
cg3402 | copper chaperone | 2.03 | |
cg3431 | rnpA | ribonuclease P | −1.70 |
cg4019 | hypothetical protein | 3.57 | |
cg4028 | hypothetical protein | 2.05 |
Locus | Gene Name | Amino Acid Exchange | Gene Product |
---|---|---|---|
cg0695 | whcB | R63L in IVO20 | Stationary phase repressor protein |
cg2103 | dtxR | T8A in IVO20 | Transcriptional iron homeostasis repressor |
cg3388 | - | M1T in IVO20 | Putative transcriptional regulator. IclR-family |
cg0566 | gabT | insertion in IVO20 (ACCGCAT pos. 17 to 23) | 4-aminobutyrate aminotransferase |
cg1324 | rosR | T2I in IVO38 | Transcriptional regulator of oxidative stress response |
cg1420 | gatB | D452G in IVO38 | Glutamyl-tRNA (Gln) amidotransferase. subunit B |
cg2103 | dtxR | R103H in IVO38 | Transcriptional iron homeostasis repressor |
cg3132 | - | V310A in IVO38 | Putative membrane protein |
cg3388 | - | G69D in IVO38 | Putative transcriptional regulator. IclR-family |
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Walter, T.; Veldmann, K.H.; Götker, S.; Busche, T.; Rückert, C.; Kashkooli, A.B.; Paulus, J.; Cankar, K.; Wendisch, V.F. Physiological Response of Corynebacterium glutamicum to Indole. Microorganisms 2020, 8, 1945. https://doi.org/10.3390/microorganisms8121945
Walter T, Veldmann KH, Götker S, Busche T, Rückert C, Kashkooli AB, Paulus J, Cankar K, Wendisch VF. Physiological Response of Corynebacterium glutamicum to Indole. Microorganisms. 2020; 8(12):1945. https://doi.org/10.3390/microorganisms8121945
Chicago/Turabian StyleWalter, Tatjana, Kareen H. Veldmann, Susanne Götker, Tobias Busche, Christian Rückert, Arman Beyraghdar Kashkooli, Jannik Paulus, Katarina Cankar, and Volker F. Wendisch. 2020. "Physiological Response of Corynebacterium glutamicum to Indole" Microorganisms 8, no. 12: 1945. https://doi.org/10.3390/microorganisms8121945