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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress. Biometals 2023; 36:1081-1108. [PMID: 37209221 DOI: 10.1007/s10534-023-00506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/24/2023] [Indexed: 05/22/2023]
Abstract
Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María D Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Functional response of Acinetobacter guillouiae SFC 500-1A to tannery wastewater as revealed by a complementary proteomic approach. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118333. [PMID: 37320920 DOI: 10.1016/j.jenvman.2023.118333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/22/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023]
Abstract
Acinetobacter guillouiae SFC 500-1 A is a promising candidate for the bioremediation of tannery wastewater. In this study, we applied shotgun proteomic technology in conjunction with a gel-based assay (Gel-LC) to explore the strain's intracellular protein profile when grown in tannery wastewater as opposed to normal culture conditions. A total of 1775 proteins were identified, 52 of which were unique to the tannery wastewater treatment. Many of them were connected to the degradation of aromatic compounds and siderophore biosynthesis. On the other hand, 1598 proteins overlapped both conditions but were differentially expressed in each. Those that were upregulated in wastewater (109) were involved in the processes mentioned above, as well as in oxidative stress mitigation and intracellular redox state regulation. Particularly interesting were the downregulated proteins under the same treatment (318), which were diverse but mainly linked to the regulation of basic cellular functions (replication, transcription, translation, cell cycle, and wall biogenesis); metabolism (amino acids, lipids, sulphate, energetic processes); and other more complex responses (cell motility, exopolysaccharide production, biofilm formation, and quorum sensing). The findings suggest that SFC 500-1 A engages in survival and stress management strategies to cope with the toxic effects of tannery wastewater, and that such strategies may be mostly oriented at keeping metabolic processes to a minimum. Altogether, the results might be useful in the near future to improve the strain's effectiveness if it will be applied for bioremediation.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), 5800, Río Cuarto, Córdoba, Argentina; Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
| | - María D Paez
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), 5800, Río Cuarto, Córdoba, Argentina; Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Río Cuarto, Córdoba, Argentina.
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), 5800, Río Cuarto, Córdoba, Argentina; Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Río Cuarto, Córdoba, Argentina.
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Paez MD, Callegari EA. Proteomics Analysis of the Estrogen Effects in the Rat Uterus Using Gel-LC and Tandem Mass Spectrometry Approaches. Methods Mol Biol 2022; 2418:289-311. [PMID: 35119672 DOI: 10.1007/978-1-0716-1920-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proteomics-based bottoms-up, at a big scale applied to the protein identification and relative quantification present in complex mixtures (cell lysates, tissues, biological fluids, secretome, etc.) is a useful strategy to identify proteins and analyze their changes. Samples processed through a gel-free approach provide a simple method for protein separation and profile comparison of different conditions, such as using fewer steps in the protocol, reducing excessive sample handling, and covering an extended range of molecular weights and isoelectric points. However, it presents a great limitation related to the management of large dynamic ranges of proteins. There are numerous protocols that allow handling the problem or limitations generated by a high dynamic range of the proteins present in the sample. The Gel-LC technique is a complementary alternative of the gel-free approach available to solve the issue of protein samples with a high dynamic range. The different steps of the protocol involve sample processing through Gel-LC (1D-SDS-PAGE) prior to digestion, 1D-nanoUHPLC coupled to high-resolution/mass accuracy tandem mass spectrometry analysis (1D-nanoUHPLC-HR/MA-MS /MS analysis) and afterward, the protein identification and relative quantification analysis using bioinformatics tools for the data conversion, organization, and interpretation.
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Affiliation(s)
- Maria D Paez
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
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Li SW, Wen Y, Leng Y. Transcriptome analysis provides new insights into the tolerance and reduction of Lysinibacillus fusiformis 15-4 to hexavalent chromium. Appl Microbiol Biotechnol 2021; 105:7841-7855. [PMID: 34546405 DOI: 10.1007/s00253-021-11586-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022]
Abstract
Microbial bioremediation of Cr(VI)-contaminated environments has drawn extensive concern. However, the molecular processes underlying the microbial Cr(VI) tolerance and reduction remain unclear. We isolated a Cr(VI)-reducing Lysinibacillus fusiformis strain 15-4 from soil on the Qinghai-Tibet Plateau. When grown in 1 mM and 2 mM Cr(VI)-containing medium, strain 15-4 could reduce 100% and 93.7% of Cr(VI) to Cr(III) after 36 h and 60 h of incubation, respectively. To know the molecular processes in response to Cr(VI), transcriptome sequencing was carried out using RNA-Seq technology. The results annotated a total of 3913 expressed genes in the strain. One thousand ninety-eight genes (28.1%) were significantly (fold change ≥ 2, false discovery rate ≤ 0.05) expressed in response to Cr(VI), of which 605 (55.1%) were upregulated and 493 (44.9%) were downregulated. The enrichment analysis showed that a total of 630 differentially expressed genes (DEGs) were enriched to 122 KEGG pathways, of which 8 pathways were significantly (p < 0.05) enriched in Cr(VI)-treated sample, including ATP-binding cassette (ABC) transporters (97 DEGs), ribosome (40), sulfur metabolism (16), aminoacyl-tRNA biosynthesis (19), porphyrin metabolism (20), quorum sensing (44), oxidative phosphorylation (17), and histidine metabolism (10), suggesting that these pathways play key roles to cope with Cr(VI) in the strain. The highly upregulated DEGs consisted of 29 oxidoreductase, 18 dehydrogenase, 14 cell redox homeostasis and stress response protein, and 10 DNA damage and repair protein genes. However, seven Na+:H+ antiporter complex-coding DEGs and most of transcriptional regulator-coding DEGs were significantly downregulated in the Cr-treated sample. Many of FMN/NAD(P)H-dependent reductase-encoding genes were greatly induced by Cr, suggesting the involvement of these genes in Cr(VI) reduction in strain 15-4. Sulfur and iron ions as well as the thiol-disulfide exchange reactions might play synergistic roles in Cr reduction.Key points• Lysinibacillus fusiformis 15-4 was able to tolerate and reduce Cr(VI) to Cr(III).• Transcriptome analysis revealed that 1098 DEGs and 8 key KEGG pathways significantly responded to Cr(VI).• Sulfur metabolism, protein biosynthesis, and porphyrin metabolism were the key pathways associated with the survival of strain 15-4 in response to Cr(VI).
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Affiliation(s)
- Shi-Weng Li
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, People's Republic of China. .,School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China. .,Key Laboratory of Extreme Environmental Microbial Resources and Engineering in Gansu Province, Lanzhou, 730000, People's Republic of China.
| | - Ya Wen
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China
| | - Yan Leng
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China
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Bonilla JO, Callegari EA, Paez MD, Gil RA, Villegas LB. Characterization of copper stress response in Fusarium tricinctum M6: A metal-resistant microorganism isolated from an acid mine drainage-affected environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 412:125216. [PMID: 33951861 PMCID: PMC8108702 DOI: 10.1016/j.jhazmat.2021.125216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 05/30/2023]
Abstract
Acid mine drainage-affected environments are interesting microbial niches for the isolation of metal-resistant microorganisms. In this sense, the aim of the present work is to isolate and characterize metal-resistant microorganisms from sediments of an abandoned gold mine located in San Luis (Argentina). For these purposes, the metal removal capacity and the microelemental composition of the biomass exposed to metals were evaluated. Likewise, proteomic techniques were applied to understand the removal and resistance mechanisms. Fusarium tricinctum M6 was isolated and identified as tolerant to Cu(II), Fe(II) and Cr(VI). When faced with 40 µg mL-1 Cu(II), the growth was affected by 60% and the removal capacity was 30-35%. Copper was found uniformly distributed in the biomass (5.23% w/w) and variations in the proportion of other biomass constituent elements were detected. When exposed to Cu(II), F. tricinctum M6 showed differential expression of intra and extracellular proteins involved in different metabolic processes. A large number of proteins with metal ion binding sites were detected both at intra and extracellular levels. The results obtained in the present work indicated bioadsorption of the metal on the cell surface and an important readjustment of the protein expression to counteract the stress produced by Cu(II).
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Affiliation(s)
- José Oscar Bonilla
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | - Eduardo Alberto Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María Daniela Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Raúl Andrés Gil
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | - Liliana Beatriz Villegas
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina.
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Rahman Z, Thomas L. Chemical-Assisted Microbially Mediated Chromium (Cr) (VI) Reduction Under the Influence of Various Electron Donors, Redox Mediators, and Other Additives: An Outlook on Enhanced Cr(VI) Removal. Front Microbiol 2021; 11:619766. [PMID: 33584585 PMCID: PMC7875889 DOI: 10.3389/fmicb.2020.619766] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Chromium (Cr) (VI) is a well-known toxin to all types of biological organisms. Over the past few decades, many investigators have employed numerous bioprocesses to neutralize the toxic effects of Cr(VI). One of the main process for its treatment is bioreduction into Cr(III). Key to this process is the ability of microbial enzymes, which facilitate the transfer of electrons into the high valence state of the metal that acts as an electron acceptor. Many underlying previous efforts have stressed on the use of different external organic and inorganic substances as electron donors to promote Cr(VI) reduction process by different microorganisms. The use of various redox mediators enabled electron transport facility for extracellular Cr(VI) reduction and accelerated the reaction. Also, many chemicals have employed diverse roles to improve the Cr(VI) reduction process in different microorganisms. The application of aforementioned materials at the contaminated systems has offered a variety of influence on Cr(VI) bioremediation by altering microbial community structures and functions and redox environment. The collective insights suggest that the knowledge of appropriate implementation of suitable nutrients can strongly inspire the Cr(VI) reduction rate and efficiency. However, a comprehensive information on such substances and their roles and biochemical pathways in different microorganisms remains elusive. In this regard, our review sheds light on the contributions of various chemicals as electron donors, redox mediators, cofactors, etc., on microbial Cr(VI) reduction for enhanced treatment practices.
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Affiliation(s)
- Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
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Biogenic nanoparticles: Synthesis, stability and biocompatibility mediated by proteins of Pseudomonas aeruginosa. Colloids Surf B Biointerfaces 2019; 184:110517. [DOI: 10.1016/j.colsurfb.2019.110517] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 11/19/2022]
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Bonilla JO, Callegari EA, Estevéz MC, Villegas LB. Intracellular Proteomic Analysis of Streptomyces sp. MC1 When Exposed to Cr(VI) by Gel-Based and Gel-Free Methods. Curr Microbiol 2019; 77:62-70. [PMID: 31705393 DOI: 10.1007/s00284-019-01790-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The actinobacterium Streptomyces sp. MC1 has previously shown the capacity to resist and remove Cr(VI) from liquid culture media. The aim of this work is to analyze the differential expression pattern of intracellular proteins when Streptomyces sp. MC1 is exposed to Cr(VI) in order to explain the molecular mechanisms of resistance that this microorganism possesses. For this purpose, 2D-PAGE and shotgun proteomic analyses (2D-nanoUPLC-ESI-MS/MS) were applied. The presence of Cr(VI) induced the expression of proteins involved in molecular biosynthesis and energy generation, chaperones with a key role in the repair of misfolded proteins and stress response, transcription proteins, proteins of importance in the DNA supercoiling, repair and replication, and dehydrogenases involved in oxidation-reduction processes. These dehydrogenases can be associated with the reduction of Cr(VI) to Cr(III). The results of this study show that proteins from the groups mentioned before are important to face the stress caused by the Cr(VI) presence and help the microorganism to counteract the toxicity of the metal. The use of two proteomic approaches resulted in a larger number of peptides identified, which is also transduced in a significant number of protein ID. This decreased the potential complexity of the sample because of the protein dynamic range, as well as increased the recovery of peptides from the gel after digestion.
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Affiliation(s)
- José O Bonilla
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700, San Luis, Argentina.,Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700, San Luis, Argentina
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María C Estevéz
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, Tucumán, Argentina
| | - Liliana B Villegas
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700, San Luis, Argentina. .,Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700, San Luis, Argentina.
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Treatment of Low Biodegradability Leachates in a Serial System of Aged Refuse-Filled Bioreactors. SUSTAINABILITY 2019. [DOI: 10.3390/su11113193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This paper presents a technology based on the use of aged refuse that has proven to be highly effective in the treatment of low biodegradability leachates. The tests were developed using two filled bioreactors arranged in series and operated at steady state. The aged refuse used as filling material was extracted from a city located in the southeast of Mexico and characterized by particle size, humidity, volatile solids, and volumetric weight. On the other hand, bacterial characterization made it possible to identify the presence of species related to the degradation and mineralization of organic compounds, as well as to processes of nitrification or reduction of phosphates and Cr (VI). The bioreactor system was operated under four hydraulic loads (10, 20, 35, and 50 L/m3·d). Maximum removal efficiencies of 85, 86.1, 87.9, 98.6, 97.8, and 97.4% were achieved in COD, BOD5, Color, TP, TN, and N-NH3, respectively, complying with Mexican regulations (NOM-001-SEMARNAT-1996). The system also proved to be stable against shock loads, such as organic load fluctuations in the influent or pH variations. The results of this study show that, in countries such as Mexico, aged refuse extracted from landfills represents a promising option as a sustainable alternative for leachate treatment.
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