| 1. |
- Bellenberg, Sören, et al.
(författare)
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Proteomics Reveal Enhanced Oxidative Stress Responses and Metabolic Adaptation in Acidithiobacillus ferrooxidans Biofilm Cells on Pyrite
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 10, s. 1-14
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Tidskriftsartikel (refereegranskat)abstract
- Reactive oxygen species (ROS) cause oxidative stress and growth inhibition by inactivation of essential enzymes, DNA and lipid damage in microbial cells. Acid mine drainage (AMD) ecosystems are characterized by low pH values, enhanced levels of metal ions and low species abundance. Furthermore, metal sulfides, such as pyrite and chalcopyrite, generate extracellular ROS upon exposure to acidic water. Consequently, oxidative stress management is especially important in acidophilic leaching microorganisms present in industrial biomining operations, especially when forming biofilms on metal sulfides. Several adaptive mechanisms have been described, but the molecular repertoire of responses upon exposure to pyrite and the presence of ROS are not thoroughly understood in acidophiles. In this study the impact of the addition of H2O2 on iron oxidation activity in Acidithiobacillus ferrooxidans DSM 14882(T) was investigated. Iron(II)- or sulfur-grown cells showed a higher sensitivity toward H2O2 than pyrite-grown ones. In order to elucidate which molecular responses may be involved, we used shot-gun proteomics and compared proteomes of cells grown with iron(II)-ions against biofilm cells, grown for 5 days in presence of pyrite as sole energy source. In total 1157 proteins were identified. 213 and 207 ones were found to have increased levels in iron(II) ion-grown or pyrite-biofilm cells, respectively. Proteins associated with inorganic sulfur compound (ISC) oxidation were among the latter. In total, 80 proteins involved in ROS degradation, thiol redox regulation, macromolecule repair mechanisms, biosynthesis of antioxidants, as well as metal and oxygen homeostasis were found. 42 of these proteins had no significant changes in abundance, while 30 proteins had increased levels in pyrite-biofilm cells. New insights in ROS mitigation strategies, such as importance of globins for oxygen homeostasis and prevention of unspecific reactions of free oxygen that generate ROS are presented for A. ferrooxidans biofilm cells. Furthermore, proteomic analyses provide insights in adaptations of carbon fixation and oxidative phosphorylation pathways under these two growth conditions.
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| 2. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
- 2020
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Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 21:1, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. Methods: We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. Results: The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. Conclusions: The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.
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| 3. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Systems biology of acidophile biofilms for efficient metal extraction
- 2020
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 7:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput "omics" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.
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| 4. |
- Christel, Stephan, et al.
(författare)
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Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT
- 2018
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Ingår i: Applied and Environmental Microbiology. - : American society for microbiology. - 0099-2240 .- 1098-5336. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilumT applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as substrate and bioleaching cultures containing chalcopyrite (CuFeS2). Leptospirillum ferriphilumT adaptations to growth on chalcopyrite included a possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, expression and translation of genes responsible for chemotaxis and motility were enhanced.
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| 5. |
- Christel, Stephan, et al.
(författare)
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Systems Biology of Acidophile Biofilms for Efficient Metal Extraction
- 2015
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Ingår i: Biotechnologies in Mining Industry and Environmental Engineering. - 9783038356783 ; , s. 312-315
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Konferensbidrag (refereegranskat)abstract
- This European Union ERASysApp funded study will investigate one of the major drawbacks of bioleaching of the copper containing mineral chalcopyrite, namely the long lag phase between construction and inoculation of bioleaching heaps and the release of dissolved metals. In practice, this lag phase can be up to three years and the long time period adds to the operating expenses of bioheaps for chalcopyrite dissolution. One of the major time determining factors in bioleaching heaps is suggested to be the speed of mineral colonization by the acidophilic microorganisms present. By applying confocal microscopy, metatranscriptomics, metaproteomics, bioinformatics, and computer modeling the authors aim to investigate the processes leading up to, and influencing the attachment of three moderately thermophilic sulfur-and/or iron-oxidizing model species:Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. Stirred tank reactors containing chalcopyrite concentrate will be inoculated with these species in various orders and proportions and the effects on the lag phase and rates of metal release will be compared. Meanwhile, confocal microscopy studies of cell attachment to chalcopyrite mineral particles, as well as metatranscriptomics and metaproteomics of the formed biofilms will further increase understanding of the attachment process and help develop a model thereof. By fulfilling our goal to decrease the length of the lag phase of chalcopyrite bioleaching heaps we hope to increase their economic feasibility and therefore, industrial interest in bioleaching as a sustainable technology.
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| 6. |
- Christel, Stephan, et al.
(författare)
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Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching
- 2018
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidicores that provides a more environmentally friendly alternative to many traditional metal extractionmethods, such as roasting or smelting. Industrial interest increases steadily and today, circa 15-20%of the world’s copper production can be traced back to this method. However, bioleaching of theworld’s most abundant copper mineral chalcopyrite suffers from low dissolution rates, oftenattributed to passivating layers, which need to be overcome to use this technology to its full potential.To prevent these passivating layers from forming, leaching needs to occur at a lowoxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult andcostly. As an alternative, selected weak iron-oxidizers could be employed that are incapable ofscavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onsetof bioleaching, but not high enough to allow for the occurrence of passivation. In this study, wereport that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications.Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole ironoxidizer exhibited significantly lower redox potentials and higher release of copper compared tocommunities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic responseto single and co-culture of these two iron oxidizers was studied and revealed a greatly decreasednumber of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured inthe presence of L. ferriphilum. This allowed for the identification of genes potentially responsible forS. thermosulfidooxidans’ weaker iron oxidation to be studied in the future, as well as underlined theneed for mechanisms to control the microbial population in bioleaching heaps
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| 7. |
- Rafati, Nima, et al.
(författare)
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Reconstruction of the birth of a male sex chromosome present in Atlantic herring
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy Of Sciences. - 0027-8424 .- 1091-6490. ; 117:39, s. 24359-24368
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Tidskriftsartikel (refereegranskat)abstract
- The mechanisms underlying sex determination are astonishingly plastic. Particularly the triggers for the molecular machinery, which recalls either the male or female developmental program, are highly variable and have evolved independently and repeatedly. Fish show a huge variety of sex determination systems, including both genetic and environmental triggers. The advent of sex chromosomes is assumed to stabilize genetic sex determination. However, because sex chromosomes are notoriously cluttered with repetitive DNA and pseudogenes, the study of their evolution is hampered. Here we reconstruct the birth of a Y chromosome present in the Atlantic herring. The region is tiny (230 kb) and contains only three intact genes. The candidate male-determining gene BMPR1BBY encodes a truncated form of a BMP1B receptor, which originated by gene duplication and translocation and underwent rapid protein evolution. BMPR1BBY phosphorylates SMADs in the absence of ligand and thus has the potential to induce testis formation. The Y region also contains two genes encoding subunits of the sperm-specific Ca2+ channel CatSper required for male fertility. The herring Y chromosome conforms with a characteristic feature of many sex chromosomes, namely, suppressed recombination between a sex-determining factor and genes that are beneficial for the given sex. However, the herring Y differs from other sex chromosomes in that suppression of recombination is restricted to an ∼500-kb region harboring the male-specific and sex-associated regions. As a consequence, any degeneration on the herring Y chromosome is restricted to those genes located in the small region affected by suppressed recombination.
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