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Guo X, Ren J, Zhou X, Zhang M, Lei C, Chai R, Zhang L, Lu D. Strategies to improve the efficiency and quality of mutant breeding using heavy-ion beam irradiation. Crit Rev Biotechnol 2024; 44:735-752. [PMID: 37455421 DOI: 10.1080/07388551.2023.2226339] [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: 08/09/2022] [Accepted: 04/15/2023] [Indexed: 07/18/2023]
Abstract
Heavy-ion beam irradiation (HIBI) is useful for generating new germplasm in plants and microorganisms due to its ability to induce high mutagenesis rate, broad mutagenesis spectrum, and excellent stability of mutants. However, due to the random mutagenesis and associated mutant breeding modalities, it is imperative to improve HIBI-based mutant breeding efficiency and quality. This review discusses and summarizes the findings of existing theoretical and technical studies and presents a set of tandem strategies to enable efficient and high-quality HIBI-based mutant breeding practices. These strategies: adjust the mutation-inducing techniques, regulate cellular response states, formulate high-throughput screening schemes, and apply the generated superior genetic elements to genetic engineering approaches, thereby, improving the implications and expanding the scope of HIBI-based mutant breeding. These strategies aim to improve the mutagenesis rate, screening efficiency, and utilization of positive mutations. Here, we propose a model based on the integration of these strategies that would leverage the advantages of HIBI while compensating for its present shortcomings. Owing to the unique advantages of HIBI in creating high-quality genetic resources, we believe this review will contribute toward improving HIBI-based breeding.
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Affiliation(s)
- Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Junle Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cairong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Chai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Lingxi Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Ji X, Chen L, Yang G, Tang C, Zhou W, Liu T, Lu X. Mutagenesis and fluorescence-activated cell sorting of oleaginous Saccharomyces cerevisiae and the multi-omics analysis of its high lipid accumulation mechanisms. BIORESOURCE TECHNOLOGY 2024; 406:131062. [PMID: 38964514 DOI: 10.1016/j.biortech.2024.131062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/14/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Acquiring lipid-producing strains of Saccharomyces cerevisiae is necessary for producing high-value palmitoleic acid. This study sought to generate oleaginous S. cerevisiae mutants through a combination of zeocin mutagenesis and fluorescence-activated cell sorting, and then to identify key mutations responsible for enhanced lipid accumulation by multi-omics sequencing. Following three consecutive rounds of mutagenesis and sorting, a mutant, MU310, with the lipid content of 44%, was successfully obtained. Transcriptome and targeted metabolome analyses revealed that a coordinated response involving fatty acid precursor biosynthesis, nitrogen metabolism, pentose phosphate pathway, ethanol conversion, amino acid metabolism and fatty acid β-oxidation was crucial for promoting lipid accumulation. The carbon fluxes of acetyl-CoA and NADPH in lipid biosynthesis were boosted in these pathways. Certain transcriptional regulators may also play significant roles in modulating lipid biosynthesis. Results of this study provide high-quality resource for palmitoleic acid production and deepen the understanding of lipid synthesis in yeast.
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Affiliation(s)
- Xiaotong Ji
- Key Laboratory of Biofuels, Key Laboratory of Shandong Energy Biological Genetic Resources, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Chen
- Key Laboratory of Biofuels, Key Laboratory of Shandong Energy Biological Genetic Resources, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Songling Rd 238, Qingdao 266100, China
| | - Chunlei Tang
- Key Laboratory of Biofuels, Key Laboratory of Shandong Energy Biological Genetic Resources, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China
| | - Wenjun Zhou
- Key Laboratory of Biofuels, Key Laboratory of Shandong Energy Biological Genetic Resources, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China.
| | - Tianzhong Liu
- Key Laboratory of Biofuels, Key Laboratory of Shandong Energy Biological Genetic Resources, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Key Laboratory of Shandong Energy Biological Genetic Resources, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China
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3
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González-Vidal A, Mercado-Sáenz S, Burgos-Molina AM, Alamilla-Presuel JC, Alcaraz M, Sendra-Portero F, Ruiz-Gómez MJ. Molecular Mechanisms of Resistance to Ionizing Radiation in S. cerevisiae and Its Relationship with Aging, Oxidative Stress, and Antioxidant Activity. Antioxidants (Basel) 2023; 12:1690. [PMID: 37759994 PMCID: PMC10525530 DOI: 10.3390/antiox12091690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The repair of the damage produced to the genome and proteome by the action of ionizing radiation, oxidizing agents, and during aging is important to maintain cellular homeostasis. Many of the metabolic pathways influence multiple processes. In this way, this work aims to study the relationship between resistance/response to ionizing radiation, cellular aging, and the response mechanisms to oxidative stress, free radicals, reactive oxygen species (ROS), and antioxidant activity in the yeast S. cerevisiae. Systems biology allows us to use tools that reveal the molecular mechanisms common to different cellular response phenomena. The results found indicate that homologous recombination, non-homologous end joining, and base excision repair pathways are the most important common processes necessary to maintain cellular homeostasis. The metabolic routes of longevity regulation are those that jointly contribute to the three phenomena studied. This study proposes eleven common biomarkers for response/resistance to ionizing radiation and aging (EXO1, MEC1, MRE11, RAD27, RAD50, RAD51, RAD52, RAD55, RAD9, SGS1, YKU70) and two biomarkers for response/resistance to radiation and oxidative stress, free radicals, ROS, and antioxidant activity (NTG1, OGG1). In addition, it is important to highlight that the HSP104 protein could be a good biomarker common to the three phenomena studied.
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Affiliation(s)
- Alejandro González-Vidal
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; (A.G.-V.); (J.C.A.-P.); (F.S.-P.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Parque Tecnológico de Andalucía (PTA), 29590 Málaga, Spain; (S.M.-S.); (A.M.B.-M.)
| | - Silvia Mercado-Sáenz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Parque Tecnológico de Andalucía (PTA), 29590 Málaga, Spain; (S.M.-S.); (A.M.B.-M.)
- Departamento de Fisiología Humana, Histología Humana, Anatomía Patológica y Educación Físico Deportiva, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
| | - Antonio M. Burgos-Molina
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Parque Tecnológico de Andalucía (PTA), 29590 Málaga, Spain; (S.M.-S.); (A.M.B.-M.)
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
| | - Juan C. Alamilla-Presuel
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; (A.G.-V.); (J.C.A.-P.); (F.S.-P.)
| | - Miguel Alcaraz
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Murcia, 30100 Murcia, Spain;
| | - Francisco Sendra-Portero
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; (A.G.-V.); (J.C.A.-P.); (F.S.-P.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Parque Tecnológico de Andalucía (PTA), 29590 Málaga, Spain; (S.M.-S.); (A.M.B.-M.)
| | - Miguel J. Ruiz-Gómez
- Departamento de Radiología y Medicina Física, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain; (A.G.-V.); (J.C.A.-P.); (F.S.-P.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Parque Tecnológico de Andalucía (PTA), 29590 Málaga, Spain; (S.M.-S.); (A.M.B.-M.)
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Starodubtseva MN, Chelnokova IA, Shkliarava NM, Villalba MI, Tapalski DV, Kasas S, Willaert RG. Modulation of the nanoscale motion rate of Candida albicans by X-rays. Front Microbiol 2023; 14:1133027. [PMID: 37025638 PMCID: PMC10070863 DOI: 10.3389/fmicb.2023.1133027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction Patients undergoing cancer treatment by radiation therapy commonly develop Candida albicans infections (candidiasis). Such infections are generally treated by antifungals that unfortunately also induce numerous secondary effects in the patient. Additional to the effect on the immune system, ionizing radiation influences the vital activity of C. albicans cells themselves; however, the reaction of C. albicans to ionizing radiation acting simultaneously with antifungals is much less well documented. In this study, we explored the effects of ionizing radiation and an antifungal drug and their combined effect on C. albicans. Methods The study essentially relied on a novel technique, referred to as optical nanomotion detection (ONMD) that monitors the viability and metabolic activity of the yeast cells in a label and attachment-free manner. Results and discussion Our findings demonstrate that after exposure to X-ray radiation alone or in combination with fluconazole, low-frequency nanoscale oscillations of whole cells are suppressed and the nanomotion rate depends on the phase of the cell cycle, absorbed dose, fluconazole concentration, and post-irradiation period. In a further development, the ONMD method can help in rapidly determining the sensitivity of C. albicans to antifungals and the individual concentration of antifungals in cancer patients undergoing radiation therapy.
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Affiliation(s)
- Maria N. Starodubtseva
- Department of Medical and Biological Physics, Gomel State Medical University, Gomel, Belarus
- Laboratory of Bionanoscopy, Institute of Radiobiology of NAS of Belarus, Gomel, Belarus
- *Correspondence: Maria N. Starodubtseva,
| | - Irina A. Chelnokova
- Laboratory of Bionanoscopy, Institute of Radiobiology of NAS of Belarus, Gomel, Belarus
| | | | - María Inés Villalba
- Laboratory of Biological Electron Microscopy, École Polytechnique Fédérale de Lausanne (EPFL), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Dmitry V. Tapalski
- Department of Microbiology, Gomel State Medical University, Gomel, Belarus
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy, École Polytechnique Fédérale de Lausanne (EPFL), University of Lausanne (UNIL), Lausanne, Switzerland
- Centre Universitaire Romand de Médecine Légale, Unité Facultaire d’Anatomie et de Morphologie (UFAM), University of Lausanne (UNIL), Lausanne, Switzerland
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel and École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ronnie G. Willaert
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel and École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), Research Group Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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Bai J, Gong Z, Shu M, Zhao H, Ye F, Tang C, Zhang S, Zhou B, Lu D, Zhou X, Lin Q, Liu J. Increased Water-Soluble Yellow Monascus Pigment Productivity via Dual Mutagenesis and Submerged Repeated-Batch Fermentation of Monascus purpureus. Front Microbiol 2022; 13:914828. [PMID: 35756045 PMCID: PMC9218666 DOI: 10.3389/fmicb.2022.914828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Monascus pigments (MPs) have been used in the food industry for more than 2,000 years and are known for their safety, bold coloring, and physiological activity. MPs are mainly yellow (YMPs), orange (OMPs), and red (RMPs). In this study, a mutant strain Monascus purpureus H14 with high production of water-soluble YMPs (WSYMPs, λmax at 370 nm) was generated instead of primary YMPs (λmax at 420 nm), OMPs (λmax at 470 nm), and RMPs (λmax at 510 nm) produced by the parent strain M. purpureus LQ-6 through dual mutagenesis of atmospheric and room-temperature plasma and heavy ion beam irradiation (HIBI), producing 22.68 U/ml extracellular YMPs and 10.67 U/ml intracellular YMPs. WSYMP production was increased by 289.51% in optimal conditions after response surface methodology was applied in submerged fermentation. Application of combined immobilized fermentation and extractive fermentation improved productivity to 16.89 U/ml/day, 6.70 times greater than with conservative submerged fermentation. The produced WSYMPs exhibited good tone stability to environmental factors, but their pigment values were unstable to pH, light, and high concentrations of Ca2+, Zn2+, Fe2+, Cu2+, and Mg2+. Furtherly, the produced exYMPs were identified as two yellow monascus pigment components (monascusone B and C21H27NO7S) by UHPLC-ESI-MS. This strategy may be extended to industrial production of premium WSYMPs using Monascus.
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Affiliation(s)
- Jie Bai
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Zihan Gong
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Meng Shu
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Hui Zhao
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Fanyu Ye
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Chenglun Tang
- Nanjing Sheng Ming Yuan Health Technology Co. Ltd., Nanjing, China.,Jiangsu Institute of Industrial Biotechnology JITRI Co. Ltd., Nanjing, China
| | - Song Zhang
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Bo Zhou
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Dong Lu
- Biophysics Research Laboratory, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Xiang Zhou
- Biophysics Research Laboratory, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Qinlu Lin
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China
| | - Jun Liu
- National Engineering Research Center of Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, China.,Hunan Provincial Key Laboratory of Food Safety Monitoring and Early Waring, Changsha, China
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Dong M, Wang S, Xu F, Xiao G, Bai J, Wang J, Sun X. Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:63. [PMID: 35658919 PMCID: PMC9166314 DOI: 10.1186/s13068-022-02161-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/18/2022] [Indexed: 01/10/2023]
Abstract
Background The major challenge of facing the efficient utilization of biomass is the high cost of cellulolytic enzyme, while the Trichoderma longibrachiatum plays an essential role in the production of industrial enzymes and biomass recycling. Results The cellulase hyper‑producing mutants of LC-M4 and LC-M16 derived from the wild type T. longibrachiatum LC strain through heavy ion mutagenesis exhibited the high-efficiency secretion ability of cellulase and hemicellulose. The FPase activities of LC-M4 (4.51 IU/mL) and LC-M16 (4.16 IU/mL) mutants increased by 46.91% and 35.5% when compared to the LC strain, respectively. Moreover, these two cellulase hyper-producing mutants showed faster growth rate on the cellulosic substrates (Avicel and CMC-Na) plate than that of LC strain. Therefore, an integrative transcriptome and proteome profiling analysis of T. longibrachiatum LC and its cellulase hyper‑producing mutant LC-M4 and LC-M16 were employed to reveal the key genes involved in cellulolytic enzymes regulation. It was showed that the transcriptome and proteome profiles changed dramatically between the wild strain and mutant strains. Notably, the overlapped genes obtained from integrative analysis identified that the protein processing in ER involved in protein secretory pathway, starch and sucrose metabolism pathway and N-glycan biosynthesis pathway were significantly changed both in cellulase hyper-producing mutants and thereby improving the enzyme secretion efficiency, which maybe the main reason of cellulase hyper-production in LC-M4 and LC-M16 mutants. In addition, the three DEGs/DEPs (PDI, Sec61, VIP36) related with protein secretion in ER and two DEGs/DEPs (OST, MOGS) related with N-glycan biosynthesis were identified as key candidate genes participating in enzyme protein biosynthesis and secretion. Conclusions In this study, a hypothetical secretory model of cellulase protein in filamentous fungi was established on the basis of DEGs/DEPs and key genes identified from the omics analysis, which were of great guidance on the rational genetic engineering and/or breeding of filamentous fungi for improving cellulase production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02161-7.
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Affiliation(s)
- Miaoyin Dong
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Shuyang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China. .,Institute of Biology, Gansu Academy of Sciences, 197 Dingxi South Rd, Lanzhou, 730000, Gansu, People's Republic of China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China.
| | - Fuqiang Xu
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Guoqing Xiao
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China.
| | - Jin Bai
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Junkai Wang
- College of Physics and Electronic Engineering, Northwest Normal University, 967Anning East Rd, Lanzhou, 730000, Gansu, People's Republic of China
| | - Xisi Sun
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
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Vanderwaeren L, Dok R, Voordeckers K, Vandemaele L, Verstrepen KJ, Nuyts S. An Integrated Approach Reveals DNA Damage and Proteotoxic Stress as Main Effects of Proton Radiation in S. cerevisiae. Int J Mol Sci 2022; 23:ijms23105493. [PMID: 35628303 PMCID: PMC9145671 DOI: 10.3390/ijms23105493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Proton radiotherapy (PRT) has the potential to reduce the normal tissue toxicity associated with conventional photon-based radiotherapy (X-ray therapy, XRT) because the active dose can be more directly targeted to a tumor. Although this dosimetric advantage of PRT is well known, the molecular mechanisms affected by PRT remain largely elusive. Here, we combined the molecular toolbox of the eukaryotic model Saccharomyces cerevisiae with a systems biology approach to investigate the physiological effects of PRT compared to XRT. Our data show that the DNA damage response and protein stress response are the major molecular mechanisms activated after both PRT and XRT. However, RNA-Seq revealed that PRT treatment evoked a stronger activation of genes involved in the response to proteotoxic stress, highlighting the molecular differences between PRT and XRT. Moreover, inhibition of the proteasome resulted in decreased survival in combination with PRT compared to XRT, not only further confirming that protons induced a stronger proteotoxic stress response, but also hinting at the potential of using proteasome inhibitors in combination with proton radiotherapy in clinical settings.
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Affiliation(s)
- Laura Vanderwaeren
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
| | - Karin Voordeckers
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Laura Vandemaele
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
- Correspondence: (K.J.V.); (S.N.); Tel.: +32-(0)16-75-1393 (K.J.V.); +32-1634-7600 (S.N.); Fax: +32-1634-7623 (S.N.)
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium
- Correspondence: (K.J.V.); (S.N.); Tel.: +32-(0)16-75-1393 (K.J.V.); +32-1634-7600 (S.N.); Fax: +32-1634-7623 (S.N.)
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8
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Li X, Chen L, Zhou H, Gu S, Wu Y, Wang B, Zhang M, Ding N, Sun J, Pang X, Lu D. LsrB, the hub of ABC transporters involved in the membrane damage mechanisms of heavy ion irradiation in Escherichia coli. Int J Radiat Biol 2021; 97:1731-1740. [PMID: 34597255 DOI: 10.1080/09553002.2021.1987565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Ionizing radiation, especially heavy ion (HI) beams, has been widely used in biology and medicine. However, the mechanism of membrane damage by such radiation remains primarily uncharacterized. PURPOSE Transcriptomic profiles of Escherichia coli (E. coli) treated with HI illustrated the response mechanisms of the membrane, mainly ABC transporters, related genes regulated by antibiotics treatment through enrichment analyses of GO and KEGG. The networks of protein-protein interactions indicated that LsrB was the crucial one among the ABC transporters specially regulated by HI through the calculation of plugins MCODE and cytoHubba of Cytoscape. Finally, the expression pattern, GO/KEGG enrichment terms, and the interaction between nine LuxS/AI-2 quorum sensing system members were investigated. CONCLUSIONS Above all, results suggested that HI might perform membrane damage through regulated material transport, inhibited LuxS/AI-2 system, finally impeded biofilm formation. This work provides further evidence for the role of ABC transporters, especially LsrB, in membrane damage of E. coli to HI. It will provide new strategies for improving the precise application of HI.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China.,Key Laboratory of Microbial Resources Exploitation and Utilization, Luoyang, China.,National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, China
| | - Lei Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Haitao Zhou
- Neurology Department, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Ying Wu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Bing Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Nan Ding
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiaju Sun
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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9
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Schultzhaus Z, Chen A, Shuryak I, Wang Z. The Transcriptomic and Phenotypic Response of the Melanized Yeast Exophiala dermatitidis to Ionizing Particle Exposure. Front Microbiol 2021; 11:609996. [PMID: 33510728 PMCID: PMC7835796 DOI: 10.3389/fmicb.2020.609996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/14/2020] [Indexed: 01/20/2023] Open
Abstract
Fungi can tolerate extremely high doses of ionizing radiation compared with most other eukaryotes, a phenomenon encompassing both the recovery from acute exposure and the growth of melanized fungi in chronically contaminated environments such as nuclear disaster sites. This observation has led to the use of fungi in radiobiology studies, with the goal of finding novel resistance mechanisms. However, it is still not entirely clear what underlies this phenomenon, as genetic studies have not pinpointed unique responses to ionizing radiation in the most resistant fungi. Additionally, little work has been done examining how fungi (other than budding yeast) respond to irradiation by ionizing particles (e.g., protons, α-particles), although particle irradiation may cause distinct cellular damage, and is more relevant for human risks. To address this paucity of data, in this study we have characterized the phenotypic and transcriptomic response of the highly radioresistant yeast Exophiala dermatitidis to irradiation by three separate ionizing radiation sources: protons, deuterons, and α-particles. The experiment was performed with both melanized and non-melanized strains of E. dermatitidis, to determine the effect of this pigment on the response. No significant difference in survival was observed between these strains under any condition, suggesting that melanin does not impart protection to acute irradiation to these particles. The transcriptomic response during recovery to particle exposure was similar to that observed after γ-irradiation, with DNA repair and replication genes upregulated, and genes involved in translation and ribosomal biogenesis being heavily repressed, indicating an attenuation of cell growth. However, a comparison of global gene expression showed clear clustering of particle and γ-radiation groups. The response elicited by particle irradiation was, in total, more complex. Compared to the γ-associated response, particle irradiation resulted in greater changes in gene expression, a more diverse set of differentially expressed genes, and a significant induction of gene categories such as autophagy and protein catabolism. Additionally, analysis of individual particle responses resulted in identification of the first unique expression signatures and individual genes for each particle type that could be used as radionuclide discrimination markers.
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Affiliation(s)
- Zachary Schultzhaus
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | - Amy Chen
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States
| | - Zheng Wang
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
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10
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Schultzhaus ZS, Schultzhaus JN, Romsdahl J, Chen A, Hervey IV WJ, Leary DH, Wang Z. Proteomics Reveals Distinct Changes Associated with Increased Gamma Radiation Resistance in the Black Yeast Exophiala dermatitidis. Genes (Basel) 2020; 11:genes11101128. [PMID: 32992890 PMCID: PMC7650708 DOI: 10.3390/genes11101128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
The yeast Exophiala dermatitidis exhibits high resistance to γ-radiation in comparison to many other fungi. Several aspects of this phenotype have been characterized, including its dependence on homologous recombination for the repair of radiation-induced DNA damage, and the transcriptomic response invoked by acute γ-radiation exposure in this organism. However, these findings have yet to identify unique γ-radiation exposure survival strategies-many genes that are induced by γ-radiation exposure do not appear to be important for recovery, and the homologous recombination machinery of this organism is not unique compared to more sensitive species. To identify features associated with γ-radiation resistance, here we characterized the proteomes of two E. dermatitidis strains-the wild type and a hyper-resistant strain developed through adaptive laboratory evolution-before and after γ-radiation exposure. The results demonstrate that protein intensities do not change substantially in response to this stress. Rather, the increased resistance exhibited by the evolved strain may be due in part to increased basal levels of single-stranded binding proteins and a large increase in ribosomal content, possibly allowing for a more robust, induced response during recovery. This experiment provides evidence enabling us to focus on DNA replication, protein production, and ribosome levels for further studies into the mechanism of γ-radiation resistance in E. dermatitidis and other fungi.
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Affiliation(s)
- Zachary S. Schultzhaus
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Janna N. Schultzhaus
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Jillian Romsdahl
- National Research Council, Postdoctoral Fellowship Program, US Naval Research Laboratory, Washington, DC 20744, USA;
| | - Amy Chen
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA;
| | - W. Judson Hervey IV
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Dagmar H. Leary
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
| | - Zheng Wang
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.S.); (J.N.S.); (W.J.H.IV); (D.H.L.)
- Correspondence: ; Tel.: +1-202-404-1007
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