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Masanta S, Wiesyk A, Panja C, Pilch S, Ciesla J, Sipko M, De A, Enkhbaatar T, Maslanka R, Skoneczna A, Kucharczyk R. Fmp40 ampylase regulates cell survival upon oxidative stress by controlling Prx1 and Trx3 oxidation. Redox Biol 2024; 73:103201. [PMID: 38795545 PMCID: PMC11140801 DOI: 10.1016/j.redox.2024.103201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Reactive oxygen species (ROS), play important roles in cellular signaling, nonetheless are toxic at higher concentrations. Cells have many interconnected, overlapped or backup systems to neutralize ROS, but their regulatory mechanisms remain poorly understood. Here, we reveal an essential role for mitochondrial AMPylase Fmp40 from budding yeast in regulating the redox states of the mitochondrial 1-Cys peroxiredoxin Prx1, which is the only protein shown to neutralize H2O2 with the oxidation of the mitochondrial glutathione and the thioredoxin Trx3, directly involved in the reduction of Prx1. Deletion of FMP40 impacts a cellular response to H2O2 treatment that leads to programmed cell death (PCD) induction and an adaptive response involving up or down regulation of genes encoding, among others the catalase Cta1, PCD inducing factor Aif1, and mitochondrial redoxins Trx3 and Grx2. This ultimately perturbs the reduced glutathione and NADPH cellular pools. We further demonstrated that Fmp40 AMPylates Prx1, Trx3, and Grx2 in vitro and interacts with Trx3 in vivo. AMPylation of the threonine residue 66 in Trx3 is essential for this protein's proper endogenous level and its precursor forms' maturation under oxidative stress conditions. Additionally, we showed the Grx2 involvement in the reduction of Trx3 in vivo. Taken together, Fmp40, through control of the reduction of mitochondrial redoxins, regulates the hydrogen peroxide, GSH and NADPH signaling influencing the yeast cell survival.
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Affiliation(s)
- Suchismita Masanta
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Sylwia Pilch
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Jaroslaw Ciesla
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Marta Sipko
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Abhipsita De
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics PAS, Warsaw, 02-106, Pawinskiego 5A, Poland.
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Adusumilli SH, Alikkam Veetil A, Choudhury C, Chattopadhyaya B, Behera D, Bachhawat AK. Glucose 6-phosphate dehydrogenase variants increase NADPH pools for yeast isoprenoid production. FEBS Open Bio 2024; 14:410-425. [PMID: 38124687 PMCID: PMC10909971 DOI: 10.1002/2211-5463.13755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Isoprenoid biosynthesis has a significant requirement for the co-factor NADPH. Thus, increasing NADPH levels for enhancing isoprenoid yields in synthetic biology is critical. Previous efforts have focused on diverting flux into the pentose phosphate pathway or overproducing enzymes that generate NADPH. In this study, we instead focused on increasing the efficiency of enzymes that generate NADPH. We first established a robust genetic screen that allowed us to screen improved variants. The pentose phosphate pathway enzyme, glucose 6-phosphate dehydrogenase (G6PD), was chosen for further improvement. Different gene fusions of G6PD with the downstream enzyme in the pentose phosphate pathway, 6-phosphogluconolactonase (6PGL), were created. The linker-less G6PD-6PGL fusion displayed the highest activity, and although it had slightly lower activity than the WT enzyme, the affinity for G6P was higher and showed higher yields of the diterpenoid sclareol in vivo. A second gene fusion approach was to fuse G6PD to truncated HMG-CoA reductase, the rate-limiting step and also the major NADPH consumer in the pathway. Both domains were functional, and the fusion also yielded higher sclareol levels. We simultaneously carried out a rational mutagenesis approach with G6PD, which led to the identification of two mutants of G6PD, N403D and S238QI239F, that showed 15-25% higher activity in vitro. The diterpene sclareol yields were also increased in the strains overexpressing these mutants relative to WT G6PD, and these will be very beneficial in synthetic biology applications.
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Affiliation(s)
- Sri Harsha Adusumilli
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliManauliIndia
- Present address:
Department of Chemical and Biological EngineeringUniversity of Wisconsin‐MadisonWIUSA
| | - Anuthariq Alikkam Veetil
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliManauliIndia
- Present address:
Department of Chemistry and Biomedical SciencesLinnaeus universityKalmarSweden
| | | | - Banani Chattopadhyaya
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliManauliIndia
| | - Diptimayee Behera
- Department of Earth and Environmental SciencesIndian Institute of Science Education and Research MohaliManauliIndia
| | - Anand Kumar Bachhawat
- Department of Biological SciencesIndian Institute of Science Education and Research MohaliManauliIndia
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Bysani VR, Alam AS, Bar-Even A, Machens F. Engineering and evolution of the complete Reductive Glycine Pathway in Saccharomyces cerevisiae for formate and CO 2 assimilation. Metab Eng 2024; 81:167-181. [PMID: 38040111 DOI: 10.1016/j.ymben.2023.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
Using captured CO2 and C1-feedstocks like formate and methanol derived from electrochemical activation of CO2 are key solutions for transforming industrial processes towards a circular carbon economy. Engineering formate and CO2-based growth in the biotechnologically relevant yeast Saccharomyces cerevisiae could boost the emergence of a formate-mediated circular bio-economy. This study adopts a growth-coupled selection scheme for modular implementation of the Reductive Glycine Pathway (RGP) and subsequent Adaptive Laboratory Evolution (ALE) to enable formate and CO2 assimilation for biomass formation in yeast. We first constructed a serine biosensor strain and then implemented the serine synthesis module of the RGP into yeast, establishing glycine and serine synthesis from formate and CO2. ALE improved the RGP-dependent growth by 8-fold. 13C-labeling experiments reveal glycine, serine, and pyruvate synthesis via the RGP, demonstrating the complete pathway activity. Further, we re-established formate and CO2-dependent growth in non-evolved biosensor strains via reverse-engineering a mutation in GDH1 identified from ALE. This mutation led to significantly more 13C-formate assimilation than in WT without any selection or overexpression of the RGP. Overall, we demonstrated the activity of the complete RGP, showing evidence for carbon transfer from formate to pyruvate coupled with CO2 assimilation.
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Affiliation(s)
- Viswanada R Bysani
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Ayesha S Alam
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Fabian Machens
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Bhatia M, Thakur J, Suyal S, Oniel R, Chakraborty R, Pradhan S, Sharma M, Sengupta S, Laxman S, Masakapalli SK, Bachhawat AK. Allosteric inhibition of MTHFR prevents futile SAM cycling and maintains nucleotide pools in one-carbon metabolism. J Biol Chem 2020; 295:16037-16057. [PMID: 32934008 PMCID: PMC7681022 DOI: 10.1074/jbc.ra120.015129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/12/2020] [Indexed: 01/05/2023] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) links the folate cycle to the methionine cycle in one-carbon metabolism. The enzyme is known to be allosterically inhibited by SAM for decades, but the importance of this regulatory control to one-carbon metabolism has never been adequately understood. To shed light on this issue, we exchanged selected amino acid residues in a highly conserved stretch within the regulatory region of yeast MTHFR to create a series of feedback-insensitive, deregulated mutants. These were exploited to investigate the impact of defective allosteric regulation on one-carbon metabolism. We observed a strong growth defect in the presence of methionine. Biochemical and metabolite analysis revealed that both the folate and methionine cycles were affected in these mutants, as was the transsulfuration pathway, leading also to a disruption in redox homeostasis. The major consequences, however, appeared to be in the depletion of nucleotides. 13C isotope labeling and metabolic studies revealed that the deregulated MTHFR cells undergo continuous transmethylation of homocysteine by methyltetrahydrofolate (CH3THF) to form methionine. This reaction also drives SAM formation and further depletes ATP reserves. SAM was then cycled back to methionine, leading to futile cycles of SAM synthesis and recycling and explaining the necessity for MTHFR to be regulated by SAM. The study has yielded valuable new insights into the regulation of one-carbon metabolism, and the mutants appear as powerful new tools to further dissect out the intersection of one-carbon metabolism with various pathways both in yeasts and in humans.
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Affiliation(s)
- Muskan Bhatia
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Jyotika Thakur
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Shradha Suyal
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Ruchika Oniel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Rahul Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shalini Pradhan
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Shantanu Sengupta
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), NCBS-TIFR Campus, Bangalore, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Anand Kumar Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India.
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