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Wang YJ, Zhou X, Zhang MM, Liu MH, Ding N, Wu QF, Lei CR, Dong ZY, Ren JL, Zhao JR, Jia CL, Liu J, Zhou B, Lu D. Physiological and biochemical characteristics of the carbon ion beam irradiation-generated mutant strain Clostridium butyricum FZM 240 in vitro and in vivo. Enzyme Microb Technol 2024; 178:110447. [PMID: 38626534 DOI: 10.1016/j.enzmictec.2024.110447] [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: 12/12/2023] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/18/2024]
Abstract
Clostridium butyricum (C. butyricum) represents a new generation of probiotics, which is beneficial because of its good tolerance and ability to produce beneficial metabolites, such as short-chain fatty acids and enzymes; however, its low enzyme activity limits its probiotic efficacy. In this study, a mutant strain, C. butyricum FZM 240 was obtained using carbon ion beam irradiation, which exhibited greatly improved enzyme production and tolerance. The highest filter paper, endoglucanase, and amylase activities produced by C. butyricum FZM 240 were 125.69 U/mL, 225.82 U/ mL, and 252.28 U/mL, which were 2.58, 1.95, and 2.21-fold higher, respectively, than those of the original strain. The survival rate of the strain increased by 11.40 % and 5.60 % after incubation at 90 °C for 5 min and with simulated gastric fluid at pH 2.5 for 2 h, respectively, compared with that of the original strain. Whole-genome resequencing and quantitative real-time PCR(qRT-PCR) analysis showed that the expression of genes related to enzyme synthesis (GE000348, GE001963 and GE003123) and tolerance (GE001114) was significantly up-regulated, while that of genes related to acid metabolism (GE003450) was significantly down-regulated. On this basis, homology modeling and functional prediction of the proteins encoded by the mutated genes were performed. According to the results, the properties related to the efficacy of C. butyricum as a probiotic were significantly enhanced by carbon ion beam irradiation, which is a novel strategy for the application of Clostridium spp. as feed additives.
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Affiliation(s)
- Ya-Juan Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China; Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin 730900, China.
| | - Miao-Miao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China; Gansu Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou 730070, China
| | - Mei-Han Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410000, China
| | - Nan Ding
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Qing-Feng Wu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Cai-Rong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Zi-Yi Dong
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Jun-Le Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Jing-Ru Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Cheng-Lin Jia
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Jun Liu
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410000, China
| | - Bo Zhou
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410000, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China; Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin 730900, China; Gansu Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou 730070, China.
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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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Feng Z, Du Y, Chen J, Chen X, Ren W, Wang L, Zhou L. Comparison and Characterization of Phenotypic and Genomic Mutations Induced by a Carbon-Ion Beam and Gamma-ray Irradiation in Soybean ( Glycine max (L.) Merr.). Int J Mol Sci 2023; 24:ijms24108825. [PMID: 37240171 DOI: 10.3390/ijms24108825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/07/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to be highly efficient with high linear energy transfer (LET), and gamma rays have also been widely used for mutation breeding. However, systematic knowledge of the mutagenic effects of these two mutagens during development and on phenotypic and genomic mutations has not yet been elucidated in soybean. To this end, dry seeds of Williams 82 soybean were irradiated with a carbon-ion beam and gamma rays. The biological effects of the M1 generation included changes in survival rate, yield and fertility. Compared with gamma rays, the relative biological effectiveness (RBE) of the carbon-ion beams was between 2.5 and 3.0. Furthermore, the optimal dose for soybean was determined to be 101 Gy to 115 Gy when using the carbon-ion beam, and it was 263 Gy to 343 Gy when using gamma rays. A total of 325 screened mutant families were detected from out of 2000 M2 families using the carbon-ion beam, and 336 screened mutant families were found using gamma rays. Regarding the screened phenotypic M2 mutations, the proportion of low-frequency phenotypic mutations was 23.4% when using a carbon ion beam, and the proportion was 9.8% when using gamma rays. Low-frequency phenotypic mutations were easily obtained with the carbon-ion beam. After screening the mutations from the M2 generation, their stability was verified, and the genome mutation spectrum of M3 was systemically profiled. A variety of mutations, including single-base substitutions (SBSs), insertion-deletion mutations (INDELs), multinucleotide variants (MNVs) and structural variants (SVs) were detected with both carbon-ion beam irradiation and gamma-ray irradiation. Overall, 1988 homozygous mutations and 9695 homozygous + heterozygous genotype mutations were detected when using the carbon-ion beam. Additionally, 5279 homozygous mutations and 14,243 homozygous + heterozygous genotype mutations were detected when using gamma rays. The carbon-ion beam, which resulted in low levels of background mutations, has the potential to alleviate the problems caused by linkage drag in soybean mutation breeding. Regarding the genomic mutations, when using the carbon-ion beam, the proportion of homozygous-genotype SVs was 0.45%, and that of homozygous + heterozygous-genotype SVs was 6.27%; meanwhile, the proportions were 0.04% and 4.04% when using gamma rays. A higher proportion of SVs were detected when using the carbon ion beam. The gene effects of missense mutations were greater under carbon-ion beam irradiation, and the gene effects of nonsense mutations were greater under gamma-ray irradiation, which meant that the changes in the amino acid sequences were different between the carbon-ion beam and gamma rays. Taken together, our results demonstrate that both carbon-ion beam and gamma rays are effective techniques for rapid mutation breeding in soybean. If one would like to obtain mutations with a low-frequency phenotype, low levels of background genomic mutations and mutations with a higher proportion of SVs, carbon-ion beams are the best choice.
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Affiliation(s)
- Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingmin Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liu J, Zhao G, Geng J, Geng Z, Dou H, Liu X, An Z, Zhang H, Wang Y. Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton. FRONTIERS IN PLANT SCIENCE 2023; 14:1056662. [PMID: 36875607 PMCID: PMC9978701 DOI: 10.3389/fpls.2023.1056662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LETmax of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were "hotspot" mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.
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Affiliation(s)
- Jianguang Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Jinpeng Geng
- School of Science, Hebei University of Technology, Tianjin, China
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Haikuan Dou
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Xu Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Zetong An
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Hanshuang Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
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Frequency and Spectrum of Mutations Induced by Gamma Rays Revealed by Phenotype Screening and Whole-Genome Re-Sequencing in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23020654. [PMID: 35054839 PMCID: PMC8775868 DOI: 10.3390/ijms23020654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/26/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M1 generation, large-scale phenotype screening in M2 generation, as well as whole-genome re-sequencing of seven M3 phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M2 plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10−10/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding.
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Du Y, Luo S, Zhao J, Feng Z, Chen X, Ren W, Liu X, Wang Z, Yu L, Li W, Qu Y, Liu J, Zhou L. Genome and transcriptome-based characterization of high energy carbon-ion beam irradiation induced delayed flower senescence mutant in Lotus japonicus. BMC PLANT BIOLOGY 2021; 21:510. [PMID: 34732128 PMCID: PMC8564971 DOI: 10.1186/s12870-021-03283-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants. RESULTS A mutant (C416) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in Lotus japonicus derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of C416 was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that C416 was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in C416, whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in Lotus japonicus. The abscisic acid (ABA) signaling pathway is positively regulated in C416. CONCLUSION So far, C416 might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in Lotus japonicus, rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of Lotus japonicus from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in C416, and lays a foundation for candidate flower senescence gene identification in Lotus japonicus. It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.
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Affiliation(s)
- Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Shanwei Luo
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Jian Zhao
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730000, People's Republic of China
| | - Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Xiao Liu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Zhuanzi Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Lixia Yu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Wenjian Li
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Ying Qu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, 730900, People's Republic of China
| | - Jie Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China.
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, 730900, People's Republic of China.
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Quantitative multi-omics analysis of the effects of mitochondrial dysfunction on lipid metabolism in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2019; 104:1211-1226. [PMID: 31832712 DOI: 10.1007/s00253-019-10260-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
Abstract
In this study, combined genome, transcriptome, and metabolome analysis was performed for eight Saccharomyces cerevisiae mitochondrial respiration-deficient mutants. Each mutant exhibited a unique nuclear genome mutation pattern; the nuclear genome mutations, and thus potentially affected genes and metabolic pathways, showed a co-occurrence frequency of ≤ 3 among the eight mutants. For example, only a lipid metabolism-related pathway was likely to be affected by the nuclear genome mutations in one of the mutants. However, large deletions in the mitochondrial genome were the shared characteristic among the eight mutants. At the transcriptomic level, lipid metabolism was the most significantly enriched Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) co-occurring in both ≥ 4 and ≥ 5 mutants. Any identified DEG enriched in lipid metabolism showed the same up-/down-regulated pattern among nearly all eight mutants. Further, 126 differentially expressed lipid species (DELS) were identified, which also showed the same up-/down-regulated pattern among nearly all investigated mutants. It was conservatively demonstrated that the similar change pattern of lipid metabolism in the entire investigated mutant population was attributed to mitochondrial dysfunction. The change spectrum of lipid species was presented, suggesting that the number and change degree of up-regulated lipid species were higher than those of down-regulated lipid species. Additionally, energy storage lipids increased in content and plasma-membrane phospholipid compositions varied in the relative proposition. The results for the genome, transcriptome, and lipidome were mutually validated, which provides quantitative data revealing the roles of mitochondria from a global cellular perspective.
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Chen X, Feng H, Du Y, Luo S, Li W, Yu L, Feng Z, Cui T, Zhou L. Genetic polymorphisms in mutagenesis progeny of Arabidopsis thaliana irradiated by carbon-ion beams and γ-rays irradiations. Int J Radiat Biol 2019; 96:267-275. [PMID: 31692404 DOI: 10.1080/09553002.2020.1688412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: Heavy-ion beams and γ-rays are popular physical mutagenesis to generate mutations in higher plants. It has been found that they show different mutation frequencies and spectrums of phenotype induction, however, the characteristics of heavy-ion beams on genetic polymorphism have not been clarified by comparing with γ-rays.Materials and methods: In the present study, seeds of Arabidopsis thaliana were exposed to carbon-ion beams (with linear energy transfer (LET) of 50 keV/μm) and γ-rays (with average LET of 0.2 keV/μm) irradiation. By using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analysis, the genetic polymorphism of both M1 and M3 plants were investigated, respectively.Results: Carbon-ion beams induced relatively higher polymorphism rate in both M1 and M3 generation than γ-rays: the polymorphism rates of M1 plants derived from carbon-ion beams irradiation are 12.87% (ISSR-C) and 9.01% (RAPD-C), while are 7.67% (ISSR-γ) and 1.45% (RAPD-γ) of plants derived from γ-rays. In M3 generation, the polymorphism rates of ISSR-C, RAPD-C, ISSR-γ, and RAPD-γ are 17.64%, 22.79%, 12.10%, and 2.82%, respectively.Conclusions: In summary, the exposure to carbon-ion beams and γ-rays lead to the change of genomic DNA of A. thaliana, which could be tested in M1 plants and M3 plants by ISSR and RAPD technology. So, both carbon-ion beams and γ-rays can induce variations of genetic polymorphisms in M1 plants and M3 plants. The genetic polymorphisms of M1 plants and M3 plants induced by carbon-ion beams are higher than γ-rays, indicating that heavy-ion beams irradiations mutation breeding is more advantageous than conventional ionizing radiations. Average molecular polymorphism of M1 plants is lower than M3 mutants, by nearly 4.77% (ISSR-C), 13.78% (RAPD-C), 4.43% (ISSR-γ), and 1.37% (RAPD-γ). We hope our study will provide basic information for understanding the effects of carbon-ion beams and γ-rays for plant mutation breeding.
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Affiliation(s)
- Xia Chen
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Feng
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Yan Du
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Wenjian Li
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Zhuo Feng
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Cui
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Libin Zhou
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,Baiyin Innovation Academy for Heavy Ion Bioindustry, Baiyin, China
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Guo X, Zhang M, Gao Y, Cao G, Yang Y, Lu D, Li W. A genome-wide view of mutations in respiration-deficient mutants of Saccharomyces cerevisiae selected following carbon ion beam irradiation. Appl Microbiol Biotechnol 2019; 103:1851-1864. [PMID: 30661110 DOI: 10.1007/s00253-019-09626-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 12/15/2022]
Abstract
Mitochondrial dysfunction in Saccharomyces cerevisiae was selected as a marker of ion penetration following carbon ion beam (CIB) irradiation. Respiration-deficient mutants were screened. Following confirmation of negligible spontaneous mutation, eight genetically stable S. cerevisiae respiration-deficient mutant strains and a control strain were resequenced with ~ 200-fold read depth. Strategies were established to identify and validate the particular mutations induced by CIB irradiation. In the nuclear genome, CIB irradiation mainly caused base substitutions and some small (< 100 bp) insertions/deletions (indels), which were widely distributed across the chromosomes. Although mitochondrial dysfunction was selected as a screening marker, variants in the nuclear genome were detected at a high frequency (10-7) relative to spontaneous mutations (10-9). The transition to transversion ratio for base substitutions was 0.746, which was less than that of spontaneous mutations. In the mitochondrial genome, there were very large deletions including substantial gene areas, resulting in extremely low read coverage. Meanwhile, every mutant possessed a distinctive mutation pattern, for both the nuclear and the mitochondrial genome. Nuclear genomes contained scanty mitochondrial respiration-related genes that were potentially affected by verified mutations, suggesting that variants in the mitochondrial genome may be the main drivers of respiratory deficiencies. Our study confirmed the previous finding that heavy ion beam (HIB) irradiation mainly induces substantial base substitutions and some small indels but also yielded some novel findings, in particular, novel structural variants in the mitochondrial genomes. These data will enhance the understanding of HIB-induced damage and mutations and aid in the HIB-based microbial mutation breeding.
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Affiliation(s)
- Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.,Gansu Key Laboratory of Microbial Resources Exploition and Application, Lanzhou, 730000, China
| | - Yue Gao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guozhen Cao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Department of Pharmacology, School of Preclinical Medicine of Xinjiang Medical University, Urumqi, 830011, China
| | - Yang Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Gansu Key Laboratory of Microbial Resources Exploition and Application, Lanzhou, 730000, China.
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Gansu Key Laboratory of Microbial Resources Exploition and Application, Lanzhou, 730000, China.
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Nikitaki Z, Holá M, Donà M, Pavlopoulou A, Michalopoulos I, Angelis KJ, Georgakilas AG, Macovei A, Balestrazzi A. Integrating plant and animal biology for the search of novel DNA damage biomarkers. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:21-38. [DOI: 10.1016/j.mrrev.2018.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
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11
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Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing. Mutat Res 2017; 807:21-30. [PMID: 29268080 DOI: 10.1016/j.mrfmmm.2017.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/08/2017] [Accepted: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Heavy-ion beam irradiation is a powerful physical mutagen that has been used to create numerous mutant materials in plants. These materials are an essential resource for functional genomics research in the post-genome era. The advent of Next-Generation Sequencing (NGS) technology has promoted the study of functional genomics and molecular breeding. A wealth of information can be gathered from whole genome re-sequencing; however, understanding the molecular mutation profile at genome wide, as well as identifying causal genes for a given phenotype are big challenging issues for researchers. The huge outputs created by NGS make it difficult to capture key information. It is worthy to explore an effective and efficient data-sieving strategy for mutation scanning at whole genome scale. Re-sequencing data from one laboratory wild type (Columbia) and eleven M3Arabidopsis thaliana lines derived from carbon-ion beam irradiation were used in present study. Both the number and different combinations of samples used for analysis affected the sieving results. The result indicated that using six samples was sufficient to filter out the shared mutation (background interference) sites as well as to identify the true mutation sites in the whole genome. The final number of candidate mutation sites could be further narrowed down by combining traditional rough map-based cloning. Our results demonstrated the feasibility of a parallel sequencing analysis as an efficient tool for the identification of mutations induced by carbon-ion beam irradiation. For the first time, we presented different analysis strategies for handling massive parallel sequencing data sets to detect the mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana with low false-positive rate, as well as to identify the causative nucleotide changes responsible for a mutant phenotype.
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12
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Hu W, Li W, Chen H, Liu J, Wang S, Chen J. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger. PLoS One 2017. [PMID: 28650980 PMCID: PMC5484496 DOI: 10.1371/journal.pone.0180120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research.
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Affiliation(s)
- Wei Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
- * E-mail: (WH); (JC)
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
| | - Hao Chen
- College of food science and engineering, Gansu Agricultural University, Lanzhou city, Gansu Province, China
| | - Jing Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
| | - Shuyang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
| | - Jihong Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
- * E-mail: (WH); (JC)
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13
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Du Y, Luo S, Li X, Yang J, Cui T, Li W, Yu L, Feng H, Chen Y, Mu J, Chen X, Shu Q, Guo T, Luo W, Zhou L. Identification of Substitutions and Small Insertion-Deletions Induced by Carbon-Ion Beam Irradiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1851. [PMID: 29163581 PMCID: PMC5665000 DOI: 10.3389/fpls.2017.01851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Heavy-ion beam irradiation is one of the principal methods used to create mutants in plants. Research on mutagenic effects and molecular mechanisms of radiation is an important subject that is multi-disciplinary. Here, we re-sequenced 11 mutagenesis progeny (M3) Arabidopsis thaliana lines derived from carbon-ion beam (CIB) irradiation, and subsequently focused on substitutions and small insertion-deletion (INDELs). We found that CIB induced more substitutions (320) than INDELs (124). Meanwhile, the single base INDELs were more prevalent than those in large size (≥2 bp). In details, the detected substitutions showed an obvious bias of C > T transitions, by activating the formation of covalent linkages between neighboring pyrimidine residues in the DNA sequence. An A and T bias was observed among the single base INDELs, in which most of these were induced by replication slippage at either the homopolymer or polynucleotide repeat regions. The mutation rate of 200-Gy CIB irradiation was estimated as 3.37 × 10-7 per site. Different from previous researches which mainly focused on the phenotype, chromosome aberration, genetic polymorphism, or sequencing analysis of specific genes only, our study revealed genome-wide molecular profile and rate of mutations induced by CIB irradiation. We hope our data could provide valuable clues for explaining the potential mechanism of plant mutation breeding by CIB irradiation.
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Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Jiangyan Yang
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Tao Cui
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjian Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hui Feng
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuze Chen
- College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinhu Mu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xia Chen
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qingyao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Wenlong Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Libin Zhou
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Libin Zhou
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Hu W, Liu J, Chen JH, Wang SY, Lu D, Wu QH, Li WJ. A mutation of Aspergillus niger for hyper-production of citric acid from corn meal hydrolysate in a bioreactor. J Zhejiang Univ Sci B 2015; 15:1006-10. [PMID: 25367793 DOI: 10.1631/jzus.b1400132] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The properties of the screened mutants for hyper-production of citric acid induced by carbon ((12)C(6+)) ion beams and X-ray irradiation were investigated in our current study. Among these mutants, mutant H4002 screened from (12)C(6+) ion irradiation had a higher yield of citric acid production than the parental strain in a 250-ml shaking flash. These expanded submerged experiments in a bioreactor were also carried out for mutant H4002. The results showed that (177.7-196.0) g/L citric acid was accumulated by H4002 through exploiting corn meal hydrolysate (containing initial 200.0-235.7 g/L sugar) with the productivity of (2.96-3.27) g/(L∙h). This was especially true when the initial sugar concentration was 210 g/L, and the best economical citric acid production reached (187.5±0.7) g/L with a productivity of 3.13 g/(L∙h). It was observed that mutant H4002 can utilize low-cost corn meal as a feedstock to efficiently produce citric acid. These results imply that the H4002 strain has the industrial production potentiality for citric acid and offers strong competition for the citric acid industry.
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Affiliation(s)
- Wei Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key laboratory of Microbial Resources Exploition and Application, Lanzhou 730000, China
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