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Felmlee KR, Macdonald SJ, Everman ER. Pre-adult exposure to three heavy metals leads to changes in the head transcriptome of adult flies. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000591. [PMID: 35856016 PMCID: PMC9287740 DOI: 10.17912/micropub.biology.000591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 11/15/2022]
Abstract
We examined the effect of developmental exposure to three heavy metals - cadmium, copper, and lead - on gene expression in adult head tissue in the model organism Drosophila melanogaster . All metals affected development time and/or gene expression level. While variation in the response to each metal was apparent, two differentially-expressed genes were upregulated in response to all three metal treatments, and 11 genes were downregulated in two of the three treatments. Our work reveals that developmental metal exposure has the potential to have long-lasting, metal-specific effects on gene expression in adults, even after the metal stress has been removed.
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Affiliation(s)
| | - Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas; Center for Computational Biology, University of Kansas
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2
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Dey P, Malik A, Singh DK, Haange SB, von Bergen M, Jehmlich N. Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique. Front Microbiol 2022; 13:872576. [PMID: 35756008 PMCID: PMC9221998 DOI: 10.3389/fmicb.2022.872576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.
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Affiliation(s)
- Priyadarshini Dey
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Department of Biotechnology, MS Ramaiah Institute of Technology, Bengaluru, India
| | - Anushree Malik
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Dileep Kumar Singh
- Department of Zoology, Faculty of Science, University of Delhi, New Delhi, India
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity, Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- *Correspondence: Nico Jehmlich,
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Geetha N, Bhavya G, Abhijith P, Shekhar R, Dayananda K, Jogaiah S. Insights into nanomycoremediation: Secretomics and mycogenic biopolymer nanocomposites for heavy metal detoxification. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124541. [PMID: 33223321 DOI: 10.1016/j.jhazmat.2020.124541] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/02/2020] [Accepted: 11/06/2020] [Indexed: 05/21/2023]
Abstract
Our environment thrives on the subtle balance achieved by the forever cyclical nature of building and rebuilding life through natural processes. Fungi, being the evident armor of bioremediation, is the indispensable element of the soil food web, contribute to be the nature's most dynamic arsenal with non-specific enzymes like peroxidase (POX), glutathione peroxidase (GPx), catalase (CAT), superoxide dismutase (SOD), non-enzymatic compounds like thiol (-SH) groups and non-protein compounds such as glutathione (GSH) and metallothionein (MT). Recently, the area of nanomycoremediation has been gaining momentum as a powerful tool for environmental clean-up strategies with its ability to detoxify heavy metals with its unique characteristics to adapt mechanisms such as biosorption, bioconversion, and biodegradation to harmless end products. The insight into the elaborate secretomic processes provides us with huge opportunities for creating a magnificent living bioremediation apparatus. This review discusses the scope and recent advances in the lesser understood area, nanomycoremediation, the state-of-the-art, innovative, cost-effective and promising tool for detoxification of heavy metal pollutants and focuses on the metabolic capabilities and secretomics with nanobiotechnological interventions.
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Affiliation(s)
- Nagaraja Geetha
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, Karnataka, India
| | - Gurulingaiah Bhavya
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, Karnataka, India
| | - Padukana Abhijith
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, Karnataka, India
| | - Ravikant Shekhar
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, Karnataka, India
| | - Karigowda Dayananda
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, Karnataka, India
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, Karnataka, India.
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Ameen F, Alsamhary K, Alabdullatif JA, ALNadhari S. A review on metal-based nanoparticles and their toxicity to beneficial soil bacteria and fungi. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 213:112027. [PMID: 33578100 DOI: 10.1016/j.ecoenv.2021.112027] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 05/02/2023]
Abstract
The unregulated deposition of metal-based nanoparticles in terrestrial ecosystems particularly in agricultural systems has alarmingly threatened the sustainability of the environment and diversity of beneficial microbial populations such as soil bacteria and fungi. This occurs due to the poor treatment of biosolids during wastewater treatment and their application in agricultural fields to enhance the fertility of soils. Continuous deposition, low biodegradability, and longer persistence of metal nanoparticles in soils adversely impact the population of soil beneficial bacteria and fungi. The current literature suggests the toxic outcome of nanoparticle-fungi and nanoparticle-bacteria interactions based on various toxicity endpoints. Therefore, due to the extreme importance of beneficial soil bacteria and fungi for soil fertility and plant growth, this review summarizes the production, application, release of metal nanoparticles in the soil system and their impact on various soil microbes specifically plant growth-promoting rhizobacteria, cellular toxicity and impact of nanoparticles on bioactive molecule production by microbes, destructive nanoparticle impact on unicellular, mycorrhizal, and cellulose/lignin degrading fungi. This review also highlights the molecular alterations in fungi and bacteria-induced by nanoparticles and suggests a plausible toxicity mechanism. This review advances the understanding of the nano-toxicity aspect as a common outcome of nanoparticles and fungi/bacteria interactions.
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Affiliation(s)
- Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Khawla Alsamhary
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Jamila A Alabdullatif
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh ALNadhari
- Deanship of Scientific Research, King Saud University, Riyadh 11451, Saudi Arabia
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5
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Mycoremediation: A Novel Approach to Rescue Soil from Heavy Metal Contamination. Fungal Biol 2021. [DOI: 10.1007/978-3-030-54422-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Okay S, Yildirim V, Büttner K, Becher D, Özcengiz G. Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110694. [PMID: 32388186 DOI: 10.1016/j.ecoenv.2020.110694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/12/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.
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Affiliation(s)
- Sezer Okay
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, Turkey
| | - Volkan Yildirim
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; Department of Biology, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Knut Büttner
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Dörte Becher
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, Greifswald, Germany
| | - Gülay Özcengiz
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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Saprotrophic proteomes of biotypes of the witches' broom pathogen Moniliophthora perniciosa. Fungal Biol 2017; 121:743-753. [PMID: 28800846 DOI: 10.1016/j.funbio.2017.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 05/03/2017] [Accepted: 05/16/2017] [Indexed: 11/23/2022]
Abstract
Nine geographically diverse Moniliophthora perniciosa (witches' broom disease pathogen) isolates were cultured in vitro. They included six C-biotypes differing in virulence on cacao (Theobroma cacao), two S-biotypes (solanaceous hosts), and an L-biotype (liana hosts). Mycelial growth rates and morphologies differed considerably, but no characters were observed to correlate with virulence or biotype. In plant inoculations using basidiospores, one C-biotype caused symptoms on tomato (an S-biotype host), adding to evidence of limited host adaptation in these biotypes. Mycelial proteomes were analysed by two-dimensional gel electrophoresis (2-DE), and 619 gel spots were indexed on all replicate gels of at least one strain. Multivariate analysis of gel spots discriminated the L-biotype, but not the S-biotypes, from the remaining strains. The proteomic similarity of the S- and C-biotypes is consistent with their reported lack of phylogenetic distinction. Sequences from tandem mass spectrometry of tryptic peptides from major 2-DE spots were matched with Moniliophthora genome and transcript sequences on NCBI and WBD Transcriptome Atlas databases. Protein-spot identifications indicated that M. perniciosa saprotrophic mycelial proteomes expressed functions potentially connected with a 'virulence life-style', including peroxiredoxin, heat-shock proteins, nitrilase, formate dehydrogenase, a prominent complement of aldo-keto reductases, mannitol-1-phosphate dehydrogenase, and central metabolism enzymes with proposed pathogenesis functions.
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Fialho MB, de Andrade A, Bonatto JMC, Salvato F, Labate CA, Pascholati SF. Proteomic response of the phytopathogen Phyllosticta citricarpa to antimicrobial volatile organic compounds from Saccharomyces cerevisiae. Microbiol Res 2015; 183:1-7. [PMID: 26805613 DOI: 10.1016/j.micres.2015.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/07/2015] [Accepted: 11/11/2015] [Indexed: 11/26/2022]
Abstract
Volatile organic compounds (VOCs) released by Saccharomyces cerevisiae inhibit plant pathogens, including the filamentous fungus Phyllosticta citricarpa, causal agent of citrus black spot. VOCs mediate relevant interactions between organisms in nature, and antimicrobial VOCs are promising, environmentally safer fumigants to control phytopathogens. As the mechanisms by which VOCs inhibit microorganisms are not well characterized, we evaluated the proteomic response in P. citricarpa after exposure for 12h to a reconstituted mixture of VOCs (alcohols and esters) originally identified in S. cerevisiae. Total protein was extracted and separated by 2D-PAGE, and differentially expressed proteins were identified by LC-MS/MS. About 600 proteins were detected, of which 29 were downregulated and 11 were upregulated. These proteins are involved in metabolism, genetic information processing, cellular processes, and transport. Enzymes related to energy-generating pathways, particularly glycolysis and the tricarboxylic acid cycle, were the most strongly affected. Thus, the data indicate that antimicrobial VOCs interfere with essential metabolic pathways in P. citricarpa to prevent fungal growth.
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Affiliation(s)
- Mauricio Batista Fialho
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba, SP, Brazil
| | - Alexander de Andrade
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba, SP, Brazil
| | - José Matheus Camargo Bonatto
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba, SP, Brazil
| | - Fernanda Salvato
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba, SP, Brazil
| | - Carlos Alberto Labate
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba, SP, Brazil
| | - Sérgio Florentino Pascholati
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Avenida Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba, SP, Brazil.
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9
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Zhao WJ, Song Q, Zhang ZJ, Mao L, Zheng WJ, Hu X, Lian HZ. The Kinetic Response of the Proteome in A549 Cells Exposed to ZnSO4 Stress. PLoS One 2015; 10:e0133451. [PMID: 26196515 PMCID: PMC4510299 DOI: 10.1371/journal.pone.0133451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022] Open
Abstract
Zinc, an essential trace element, is involved in many important physiological processes. Cell responses to zinc stress show time-dependent effects besides concentration-dependence and tissue-specificity. Herein, we investigated the time-dependent differential expression of the proteome in A549 cells after administered with ZnSO4 for both 9 and 24 h using 2DE. 123 differentially expressed protein spots were detected, most of which were up-regulated by Zn2+ treatment. Interestingly, 49 proteins exhibited significant differential expression repeatedly during these two treatment periods, and moreover showed a conserved change with different ratios and four time-dependent expression patterns. Pattern 1 (up-regulated with rapid initial induction and subsequent repression) and pattern 4 (down-regulated with steady repression) were the predominant expression patterns. The abundances of the proteins in patterns 1 and 4 after 24 h of zinc treatment are always lower than that after 9 h, indicating that exogenous zinc reduced the expression of proteins in cells after 24 h or longer. Importantly, these findings could also reflect the central challenge in detecting zinc homeostasis proteins by 2DE or other high throughput analytical methods resulting from slight variation in protein expression after certain durations of exogenous zinc treatment and/or low inherent protein content in cells. These time-dependent proteome expression patterns were further validated by measuring dynamic changes in protein content in cells and in expression of two proteins using the Bradford method and western blotting, respectively. The time-dependent changes in total zinc and free Zn2+ ion contents in cells were measured using ICP-MS and confocal microscopy, respectively. The kinetic process of zinc homeostasis regulated by muffling was further revealed. In addition, we identified 50 differentially expressed proteins which are predominantly involved in metabolic process, cellular process or developmental process, and function as binding, catalytic activity or structural molecule activity. This study further elucidates our understanding of dynamic nature of the cellular response to zinc stress and the mechanism of zinc homeostasis.
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Affiliation(s)
- Wen-jie Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Qun Song
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Zi-jin Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Li Mao
- MOE Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Wei-juan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, Jiangsu, PR China
| | - Xin Hu
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
| | - Hong-zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, Jiangsu, PR China
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Bak JS. Complementary substrate-selectivity of metabolic adaptive convergence in the lignocellulolytic performance by Dichomitus squalens. Microb Biotechnol 2014; 7:434-45. [PMID: 24894915 PMCID: PMC4229324 DOI: 10.1111/1751-7915.12134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 05/04/2014] [Indexed: 11/26/2022] Open
Abstract
The lignocellulolytic platform of the wood-decaying organism Dichomitus squalens is important for production of biodegradable elements; however, the system has not yet been fully characterized. In this study, using statistical target optimization, we analysed substrate selectivity based on a variety of D. squalens metabolic pathways using combined omics tools. As compared with the alkali-lignin (AL) programme, the rice straw (RS) programme has the advantage of multilayered signalling to regulate cellulolytic-related genes or to connect their pathways. The spontaneous instability of the AL programme was accelerated by harsh starvation as compared with that of the RS programme. Therefore, the AL programme converged on cellular maintenance much easier and more rapidly. However, regardless of external substrate/concentration type, the compensatory pattern of the major targets (especially peroxidases and growth regulators) was similar, functioning to maintain cellular homeostasis. Interestingly, ligninolytic-mediated targets under non-kaleidoscopic conditions were induced by a substrate-input-control, and especially this mechanism had an important effect on the early stages of the biodegradation process. This optimized target analysis could be used to understand lignocellulolytic network and to improve downstream efficiency.
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Affiliation(s)
- Jin Seop Bak
- Department of Chemical and Biomolecular Engineering, Advanced Biomass R&D Center, KAIST, Daejeon, 305-701, Republic of Korea
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11
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Chen G, Zhou Y, Zeng G, Liu H, Yan M, Chen A, Guan S, Shang C, Li H, He J. Alteration of culture fluid proteins by cadmium induction inPhanerochaete chrysosporium. J Basic Microbiol 2013; 55:141-7. [DOI: 10.1002/jobm.201300398] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/14/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Guiqiu Chen
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Ying Zhou
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Hongyu Liu
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Ming Yan
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Anwei Chen
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Song Guan
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Cui Shang
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Huanke Li
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Jianmin He
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
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12
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Singh S, Brocker C, Koppaka V, Ying C, Jackson B, Matsumoto A, Thompson DC, Vasiliou V. Aldehyde dehydrogenases in cellular responses to oxidative/electrophilic stress. Free Radic Biol Med 2013; 56. [PMID: 23195683 PMCID: PMC3631350 DOI: 10.1016/j.freeradbiomed.2012.11.010] [Citation(s) in RCA: 395] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reactive oxygen species (ROS) are continuously generated within living systems and the inability to manage ROS load leads to elevated oxidative stress and cell damage. Oxidative stress is coupled to the oxidative degradation of lipid membranes, also known as lipid peroxidation. This process generates over 200 types of aldehydes, many of which are highly reactive and toxic. Aldehyde dehydrogenases (ALDHs) metabolize endogenous and exogenous aldehydes and thereby mitigate oxidative/electrophilic stress in prokaryotic and eukaryotic organisms. ALDHs are found throughout the evolutionary gamut, from single-celled organisms to complex multicellular species. Not surprisingly, many ALDHs in evolutionarily distant, and seemingly unrelated, species perform similar functions, including protection against a variety of environmental stressors such as dehydration and ultraviolet radiation. The ability to act as an "aldehyde scavenger" during lipid peroxidation is another ostensibly universal ALDH function found across species. Upregulation of ALDHs is a stress response in bacteria (environmental and chemical stress), plants (dehydration, salinity, and oxidative stress), yeast (ethanol exposure and oxidative stress), Caenorhabditis elegans (lipid peroxidation), and mammals (oxidative stress and lipid peroxidation). Recent studies have also identified ALDH activity as an important feature of cancer stem cells. In these cells, ALDH expression helps abrogate oxidative stress and imparts resistance against chemotherapeutic agents such as oxazaphosphorine, taxane, and platinum drugs. The ALDH superfamily represents a fundamentally important class of enzymes that contributes significantly to the management of electrophilic/oxidative stress within living systems. Mutations in various ALDHs are associated with a variety of pathological conditions in humans, highlighting the fundamental importance of these enzymes in physiological and pathological processes.
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Affiliation(s)
- Surendra Singh
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chad Brocker
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Vindhya Koppaka
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chen Ying
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Brian Jackson
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Akiko Matsumoto
- Department of Social Medicine, Saga University School of Medicine, Saga 849-8501, Japan
| | - David C. Thompson
- Department of Clinical Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Vasilis Vasiliou
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Corresponding author: Vasilis Vasiliou, Ph.D., , phone: 1 (303) 724-3520, fax: 1 (303) 724-7266
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Proteomics shows new faces for the old penicillin producer Penicillium chrysogenum. J Biomed Biotechnol 2012; 2012:105109. [PMID: 22318718 PMCID: PMC3270403 DOI: 10.1155/2012/105109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/30/2011] [Accepted: 10/14/2011] [Indexed: 12/14/2022] Open
Abstract
Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as β-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new “omics” era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus.
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