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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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Ravanfar R, Sheng Y, Gray HB, Winkler JR. Tryptophan extends the life of cytochrome P450. Proc Natl Acad Sci U S A 2023; 120:e2317372120. [PMID: 38060561 PMCID: PMC10722969 DOI: 10.1073/pnas.2317372120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Powerfully oxidizing enzymes need protective mechanisms to prevent self-destruction. The flavocytochrome P450 BM3 from Priestia megaterium (P450BM3) is a self-sufficient monooxygenase that hydroxylates fatty acid substrates using O2 and NADPH as co-substrates. Hydroxylation of long-chain fatty acids (≥C14) is well coupled to O2 and NADPH consumption, but shorter chains (≤C12) are more poorly coupled. Hydroxylation of p-nitrophenoxydodecanoic acid by P450BM3 produces a spectrophotometrically detectable product wherein the coupling of NADPH consumption to product formation is just 10%. Moreover, the rate of NADPH consumption is 1.8 times that of O2 consumption, indicating that an oxidase uncoupling pathway is operative. Measurements of the total number of enzyme turnovers before inactivation (TTN) indicate that higher NADPH concentrations increase TTN. At lower NADPH levels, added ascorbate increases TTN, while a W96H mutation leads to a decrease. The W96 residue is about 7 Å from the P450BM3 heme and serves as a gateway residue in a tryptophan/tyrosine (W/Y) hole transport chain from the heme to a surface tyrosine residue. The data indicate that two oxidase pathways protect the enzyme from damage by intercepting the powerfully oxidizing enzyme intermediate (Compound I) and returning it to its resting state. At high NADPH concentrations, reducing equivalents from the flavoprotein are delivered to Compound I by the usual reductase pathway. When NADPH is not abundant, however, oxidizing equivalents from Compound I can traverse a W/Y chain, arriving at the enzyme surface where they are scavenged by reductants. Ubiquitous tryptophan/tyrosine chains in highly oxidizing enzymes likely perform similar protective functions.
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Affiliation(s)
- Raheleh Ravanfar
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Yuling Sheng
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
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Singleton AH, Bergum OET, Søgaard CK, Røst LM, Olsen CE, Blindheim FH, Ræder SB, Bjørnstad FA, Sundby E, Hoff BH, Bruheim P, Otterlei M. Activation of multiple stress responses in Staphylococcus aureus substantially lowers the minimal inhibitory concentration when combining two novel antibiotic drug candidates. Front Microbiol 2023; 14:1260120. [PMID: 37822747 PMCID: PMC10564113 DOI: 10.3389/fmicb.2023.1260120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
The past few decades have been plagued by an increasing number of infections caused by antibiotic resistant bacteria. To mitigate the rise in untreatable infections, we need new antibiotics with novel targets and drug combinations that reduce resistance development. The novel β-clamp targeting antimicrobial peptide BTP-001 was recently shown to have a strong additive effect in combination with the halogenated pyrrolopyrimidine JK-274. In this study, the molecular basis for this effect was examined by a comprehensive proteomic and metabolomic study of the individual and combined effects on Staphylococcus aureus. We found that JK-274 reduced activation of several TCA cycle enzymes, likely via increasing the cellular nitric oxide stress, and BTP-001 induced oxidative stress in addition to inhibiting replication, translation, and DNA repair processes. Analysis indicated that several proteins linked to stress were only activated in the combination and not in the single treatments. These results suggest that the strong additive effect is due to the activation of multiple stress responses that can only be triggered by the combined effect of the individual mechanisms. Importantly, the combination dose required to eradicate S. aureus was well tolerated and did not affect cell viability of immortalized human keratinocyte cells, suggesting a species-specific response. Our findings demonstrate the potential of JK-274 and BTP-001 as antibiotic drug candidates and warrant further studies.
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Affiliation(s)
- Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Cecilie Elisabeth Olsen
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Fredrik Heen Blindheim
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Synnøve Brandt Ræder
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Frithjof A. Bjørnstad
- Department of Materials Science and Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eirik Sundby
- Department of Materials Science and Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bård Helge Hoff
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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García-Calvo L, Rane DV, Everson N, Humlebrekk ST, Mathiassen LF, Mæhlum AHM, Malmo J, Bruheim P. Central carbon metabolite profiling reveals vector-associated differences in the recombinant protein production host Escherichia coli BL21. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2023.1142226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used host for recombinant protein production, both as an industrial expression platform and as a model system at laboratory scale. The recombinant protein production industry generates proteins with direct applications as biopharmaceuticals and in technological processes central to a plethora of fields. Despite the increasing economic significance of recombinant protein production, and the importance of E. coli as an expression platform and model organism, only few studies have focused on the central carbon metabolic landscape of E. coli during high-level recombinant protein production. In the present work, we applied four targeted CapIC- and LC-MS/MS methods, covering over 60 metabolites, to perform an in-depth metabolite profiling of the effects of high-level recombinant protein production in strains derived from E. coli BL21, carrying XylS/Pm vectors with different characteristics. The mass-spectrometric central carbon metabolite profiling was complemented with the study of growth kinetics and protein production in batch bioreactors. Our work shows the robustness in E. coli central carbon metabolism when introducing increased plasmid copy number, as well as the greater importance of induction of recombinant protein production as a metabolic challenge, especially when strong promoters are used.
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Thorfinnsdottir LB, Bø GH, Booth JA, Bruheim P. Survival of Escherichia coli after high-antibiotic stress is dependent on both the pregrown physiological state and incubation conditions. Front Microbiol 2023; 14:1149978. [PMID: 36970700 PMCID: PMC10036391 DOI: 10.3389/fmicb.2023.1149978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
IntroductionThe survival of bacterial cells exposed to antibiotics depends on the mode of action, the antibiotics concentration, and the duration of treatment. However, it also depends on the physiological state of the cells and the environmental conditions. In addition, bacterial cultures contain sub-populations that can survive high antibiotic concentrations, so-called persisters. Research on persisters is challenging due to multiple mechanisms for their formation and low fractions, down to and below one millionth of the total cell population. Here, we present an improved version of the persister assay used to enumerate the amount of persisters in a cell population.MethodsThe persister assay with high antibiotic stress exposure was performed at both growth supporting and non-supporting conditions. Escherichia coli cells were pregrown to various growth stages in shake flasks and bench-top bioreactors. In addition, the physiological state of E. coli before antibiotic treatment was determined by quantitative mass spectrometry-based metabolite profiling.ResultsSurvival of E. coli strongly depended on whether the persister assay medium supported growth or not. The results were also highly dependent on the type of antibiotic and pregrown physiological state of the cells. Therefore, applying the same conditions is critical for consistent and comparable results. No direct connection was observed between antibiotic efficacy to the metabolic state. This also includes the energetic state (i.e., the intracellular concentration of ATP and the adenylate energy charge), which has earlier been hypothesized to be decisive for persister formation.DiscussionThe study provides guides and suggestions for the design of future experimentation in the research fields of persisters and antibiotic tolerance.
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Affiliation(s)
| | - Gaute Hovde Bø
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - James Alexander Booth
- Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- *Correspondence: Per Bruheim,
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