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Chen MM, Shi GH, Dai Y, Fang WX, Wu Q. Identifying genetic variants associated with amphotericin B (AMB) resistance in Aspergillus fumigatus via k-mer -based GWAS. Front Genet 2023; 14:1133593. [PMID: 37229189 PMCID: PMC10203564 DOI: 10.3389/fgene.2023.1133593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/10/2023] [Indexed: 05/27/2023] Open
Abstract
Aspergillus fumigatus is one of the most common pathogenic fungi, which results in high morbidity and mortality in immunocompromised patients. Amphotericin B (AMB) is used as the core drug for the treatment of triazole-resistant A. fumigatus. Following the usage of amphotericin B drugs, the number of amphotericin B-resistant A. fumigatus isolates showed an increasing trend over the years, but the mechanism and mutations associated with amphotericin B sensitivity are not fully understood. In this study, we performed a k-mer-based genome-wide association study (GWAS) in 98 A. fumigatus isolates from public databases. Associations identified with k-mers not only recapitulate those with SNPs but also discover new associations with insertion/deletion (indel). Compared to SNP sites, the indel showed a stronger association with amphotericin B resistance, and a significant correlated indel is present in the exon region of AFUA_7G05160, encoding a fumarylacetoacetate hydrolase (FAH) family protein. Enrichment analysis revealed sphingolipid synthesis and transmembrane transport may be related to the resistance of A. fumigatus to amphotericin B. The expansion of variant types detected by the k-mer method increases opportunities to identify and exploit complex genetic variants that drive amphotericin B resistance, and these candidate variants help accelerate the selection of prospective gene markers for amphotericin B resistance screening in A. fumigatus.
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Affiliation(s)
- Meng-Meng Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guo-Hui Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yi Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xia Fang
- Guangxi Biological Sciences and Biotechnology Center, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Xie Q, Liu B, Dong W, Li J, Wang D, Liu Z, Gao C. Comparative transcriptomic and metabolomic analyses provide insights into the responses to NaCl and Cd stress in Tamarix hispida. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 884:163889. [PMID: 37142042 DOI: 10.1016/j.scitotenv.2023.163889] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Salinity and heavy metal pollution seriously affect plant growth. Tamarix hispida (T. hispida) has the potential to remediate soil saline-alkali and heavy metal pollution. In this study, the response mechanisms of T. hispida under NaCl, CdCl2 (Cd) and combined CdCl2 and NaCl (Cd-NaCl) stresses were explored. Overall, the antioxidant system showed changes under the three stresses. The addition of NaCl inhibited the absorption of Cd2+. However, there were obvious differences in the transcripts and metabolites identified among the three stress responses. Interestingly, the number of DEGs was greatest under NaCl stress (929), but the number of differentially expressed metabolites (DEMs) was lowest (48), with 143 and 187 DEMs identified under Cd and Cd-NaCl stress, respectively. It is worth noting that both DEGs and DEMs were enriched in the linoleic acid metabolism pathway under Cd stress. In particular, the content of lipids changed significantly under Cd and Cd-NaCl stress, suggesting that maintaining normal lipid synthesis and metabolism may be an important way to improve the Cd tolerance of T. hispida. Flavonoids may also play an important role in the response to NaCl and Cd stress. These results provide a theoretical basis for cultivating plants with improved salt and cadmium repair abilities.
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Affiliation(s)
- Qingjun Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Baichao Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenfang Dong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jinghang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Danni Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhongyuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.
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Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O. Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. SCIENCE ADVANCES 2022; 8:eabo6467. [PMID: 36112690 PMCID: PMC9481131 DOI: 10.1126/sciadv.abo6467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/02/2022] [Indexed: 05/25/2023]
Abstract
Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.
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Affiliation(s)
- Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hiba Waldman Ben-Asher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gal Eyal
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland St. Lucia, Queensland 4072, Australia
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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Wang C, Fang C, Wang C, Jin C, Qian M, Jin Y. Maternal Sodium p-Perfluorous Nonenoxybenzene Sulfonate Exposure Disturbed Lipid Metabolism and Induced an Imbalance in Tyrosine Metabolism in the F1 Generation of Mice. Chem Res Toxicol 2022; 35:651-662. [PMID: 35377151 DOI: 10.1021/acs.chemrestox.1c00424] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The toxicity of perfluorinated compounds (PFCs) to mammals has recently received increasing attention. However, the effects of maternal sodium p-perfluorous nonenoxybenzene sulfonate (OBS) exposure during pregnancy and lactation on the liver function of dams (F0) and offspring (F1) mice are still unknown. The results demonstrated that maternal OBS treatment could not only induce lipid metabolism dysfunction but also disrupt amino acid metabolism in the liver of F0 and F1 generations. OBS had marked accumulation in the liver, and the serum and liver triglyceride (TG) levels increased in the F0 and F1 generations after maternal OBS exposure. Moreover, maternal OBS exposure changed the transcriptional levels of genes related to lipid metabolism (fatty acid (FA) synthesis, TG synthesis, and transport) and induced changes in the amino acid level in dams and 20-day-old mice offspring (F1-20 d). Additionally, the regulation of lipid metabolism by OBS was mainly dependent on the activation of peroxisome proliferator-activated receptor γ (PPARγ) and cluster of differentiation 36 (CD36). Interestingly, OBS could also disturb tyrosine (TYR) metabolism by increasing the TYR level and downregulating fumarate acetoacetate hydrolase (FAH). Together, these results indicated that the liver can be perceived as the major target tissue of OBS, which strongly affected metabolic function and ultimately led to an imbalance in the metabolism of lipids and TYR. In summary, maternal OBS exposure during pregnancy and lactation has toxic effects on the hepatic metabolism of dams and offspring, indicating that the toxic effects could obviously cross generations of mice, and we should pay more attention to understanding the health risk to both dams and offspring.
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Affiliation(s)
- Caiyun Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18, Chaowang Road, Hangzhou 310014, China
| | - Chanlin Fang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18, Chaowang Road, Hangzhou 310014, China
| | - Caihong Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18, Chaowang Road, Hangzhou 310014, China
| | - Cuiyuan Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18, Chaowang Road, Hangzhou 310014, China.,Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou 310015, China
| | - Mingrong Qian
- Interdisciplinary Research Academy, Zhejiang Shuren University, 8, Shuren Street, Gongshu District, Hangzhou 310015, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18, Chaowang Road, Hangzhou 310014, China
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Reimer JJ, Thiele B, Biermann RT, Junker-Frohn LV, Wiese-Klinkenberg A, Usadel B, Wormit A. Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species. PLANT MOLECULAR BIOLOGY 2021; 107:177-206. [PMID: 34677706 PMCID: PMC8553704 DOI: 10.1007/s11103-021-01194-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/16/2021] [Indexed: 05/03/2023]
Abstract
Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.
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Affiliation(s)
- Julia J Reimer
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, PtJ, 52425, Jülich, Germany
| | - Björn Thiele
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Agrosphere (IBG-3), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Robin T Biermann
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., 14979, Großbeeren, Germany
| | - Laura V Junker-Frohn
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Anika Wiese-Klinkenberg
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Bioinformatics (IBG-4), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Björn Usadel
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Bioinformatics (IBG-4), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Heinrich-Heine-University, Chair of Biological Data Science, 40225, Düsseldorf, Germany
| | - Alexandra Wormit
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Hu C, Huang L, Chen Y, Liu J, Wang Z, Gao B, Zhu Q, Ren C. Fumarylacetoacetate hydrolase is required for fertility in rice. PLANTA 2021; 253:122. [PMID: 34003383 DOI: 10.1007/s00425-021-03632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
The rice OsFAH gene functions identically to that of Arabidopsis SSCD1 encoding FAH. Loss of OsFAH causes rice sterility. Fumarylacetoacetate hydrolase (FAH) is the last enzyme in the tyrosine (Tyr) degradation pathway that is crucial for animals. By genetic analysis of the mutant of Short-day Sensitive Cell Death 1 gene encoding Arabidopsis FAH, we first found the pathway also plays a critical role in plants (Han et al., Plant Physiol 162:1956-1964, 2013). To further understand the role of the Tyr degradation pathway in plants, we investigated a biological function of the rice FAH. Firstly, the cDNA of rice FAH gene (OsFAH) was cloned and confirmed to be able to rescue the Arabidopsis Short-day Sensitive Cell Death 1 mutant defective in the FAH. Then, we identified the OsFAH T-DNA insertion mutant and generated the OsFAH RNA interference lines, and found that loss of OsFAH results in rice sterility. Furthermore, we analyzed expression of the OsFAH gene in roots, stems, leaves and young panicles at booting stage of rice and found that its transcript level was highest in young panicles and lowest in roots. In addition, the expression analysis of β-glucuronidase driven by OsFAH promoter in transgenic Arabidopsis showed that the OsFAH promoter was highly active in aerial tissues in vegetative stage, and sepals, filaments and stigma in reproductive stage. These results suggested that FAH plays an important role in rice fertility.
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Affiliation(s)
- Chao Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lihua Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Yancheng Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture, Hunan Rice Research Institute, Changsha, 410125, China
| | - Jinling Liu
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Zhilong Wang
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Bida Gao
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Zhu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Chunmei Ren
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China.
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