New Insights into the Biofilm Lifestyle and Metabolism of Acidithiobacillus Species from Analysis of High Throughput Proteomic Data

2013 ◽  
Vol 825 ◽  
pp. 111-114
Author(s):  
Mario Vera ◽  
Claudia Janosch ◽  
Sören Bellenberg ◽  
Beate Krok ◽  
Wolfgang Sand ◽  
...  
Keyword(s):  
High Throughput ◽  
Extracellular Polymeric Substances ◽  
Sulfur Metabolism ◽  
Outer Membrane Proteins ◽  
Metal Sulfide ◽  
Bacterial Attachment ◽  
Energy Substrate ◽  
Polysaccharide Biosynthesis ◽  
Proteomic Data ◽  
Sulfur Oxidizer

Bioleaching is the extraction of metals, such as copper or gold, from sulfidic ores by microorganisms. Their energy for growth is obtained by oxidation of ferrous iron and/or reduced inorganic sulfur compounds. Bacterial attachment to ores increase leaching activities through the formation of a special microenvironment between the bacterium and the metal sulfide surface, filled by extracellular polymeric substances (EPS). Recently, a high-throughput proteomic comparison from biofilm cells attached to pyrite (FeS2) and planktonic cells of the mesophilic iron and/or sulfur oxidizer Acidithiobacillus ferrooxidans ATCC 23270 was done. Several proteins were found to be up-regulated in biofilm cells. Among them, membrane and outer membrane proteins probably involved in osmotic regulation, polysaccharide biosynthesis and protein secretion, as well as proteins probably involved in cofactor metabolism were present. In order to extend our knowledge of the genus Acidithiobacilli, we started a high-throughput proteomic analysis of the sulfur oxidizer Acidithiobacillus caldus ATCC 51756 by comparing cells grown with an insoluble energy substrate such as elemental sulfur (S°) against cells grown on a soluble energy substrate, such as thiosulfate. The results revealed several differences in proteins related to sulfur metabolism, potential EPS biosynthesis pathways as well as membrane and transport functions. In both microorganisms several conserved hypothetical proteins were found. Some of them were also found to be induced in sessile cells, suggesting their potential involvement in biofilm formation. This study will provide new insights into the biology of Acidithiobacilli and will probably help assigning functions to poorly characterized and unknown proteins. Keywords: Biofilm, Proteomics, Acidithiobacilli

scholarly journals Biofilm Formation in Xanthomonas arboricola pv. pruni: Structure and Development

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 546
Author(s):  
Pilar Sabuquillo ◽  
Jaime Cubero
Keyword(s):  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Environmental Changes ◽  
Nutrient Content ◽  
Infection Process ◽  
Bacterial Attachment ◽  
Key Factors ◽  
Cell Structures ◽  
Microscopy Techniques

Xanthomonasarboricola pv. pruni (Xap) causes bacterial spot of stone fruit and almond, an important plant disease with a high economic impact. Biofilm formation is one of the mechanisms that microbial communities use to adapt to environmental changes and to survive and colonize plants. Herein, biofilm formation by Xap was analyzed on abiotic and biotic surfaces using different microscopy techniques which allowed characterization of the different biofilm stages compared to the planktonic condition. All Xap strains assayed were able to form real biofilms creating organized structures comprised by viable cells. Xap in biofilms differentiated from free-living bacteria forming complex matrix-encased multicellular structures which become surrounded by a network of extracellular polymeric substances (EPS). Moreover, nutrient content of the environment and bacterial growth have been shown as key factors for biofilm formation and its development. Besides, this is the first work where different cell structures involved in bacterial attachment and aggregation have been identified during Xap biofilm progression. Our findings provide insights regarding different aspects of the biofilm formation of Xap which improve our understanding of the bacterial infection process occurred in Prunus spp and that may help in future disease control approaches.

scholarly journals Production of nonulosonic acids in the extracellular polymeric substances of “Candidatus Accumulibacter phosphatis”

2021 ◽  
Author(s):  
Sergio Tomás-Martínez ◽  
Hugo B.C. Kleikamp ◽  
Thomas R. Neu ◽  
Martin Pabst ◽  
David G. Weissbrodt ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Pathogenic Bacteria ◽  
Extracellular Polymeric Substances ◽  
Lectin Binding ◽  
Wide Distribution ◽  
Sialic Acids ◽  
Animal Cells ◽  
Microbial Life ◽  
Proteomic Data ◽  
Accumulibacter Phosphatis

Abstract Nonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as an important compound in the extracellular matrix of virtually all microbial life and in “Candidatus Accumulibacter phosphatis”, a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of “Ca. Accumulibacter” to produce different types of NulOs. Proteomic analysis showed the ability of “Ca. Accumulibacter” to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of “Ca. Accumulibacter” in particular, and biofilms in general. Key Points •“Ca. Accumulibacter” has the potential to produce a range of nonulosonic acids. •Mass spectrometry and lectin binding can reveal the presence and location of nonulosonic acids. •The role of nonulosonic acid in non-pathogenic bacteria needs to be studied in detail.

scholarly journals Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit

2020 ◽  
Author(s):  
Thierry Balliau ◽  
Harold Duruflé ◽  
Nicolas Blanchet ◽  
Mélisande Blein-Nicolas ◽  
Nicolas B. Langlade ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Deficit ◽  
High Throughput ◽  
Molecular Basis ◽  
Inbred Lines ◽  
Vegetative Stage ◽  
Valuable Resource ◽  
Proteomic Data ◽  
High Throughput Phenotyping

AbstractThis article describes how the proteomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower. They included both inbred lines and their hybridsWater deficit was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide proteomic data from sunflower leaves corresponding to the identification of 3062 proteins and the quantification of 1211 of them in these 24 genotypes grown in two watering conditions. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the molecular basis of heterosis.

scholarly journals Rendering Bio-Inert Low Density Polyethylene Amenable For Biodegradation Via Fast High Throughput Reactive Extrusion Assisted Oxidation

2021 ◽  
Author(s):  
Pablo Ferrero ◽  
Olivia A. Attallah ◽  
Miguel Ángel Valera ◽  
Ivana Aleksic ◽  
Muhammad Azeem ◽  
...  
Keyword(s):  
High Throughput ◽  
Operating Temperature ◽  
Crystallinity Index ◽  
Reactive Extrusion ◽  
Bacterial Attachment ◽  
Low Density Polyethylene ◽  
Low Density ◽  
Carbonyl Index ◽  
Pre Treatment ◽  
Pretreatment Conditions

Abstract An energy efficient high throughput pre-treatment of low density polyethylene (LDPE) using a fast reactive extrusion (REX) assisted oxidation technique followed by bacterial attachment as an indicator for bio-amenability was studied. Silicon dioxide (SiO2) was selected as a model oxidizing and catalytic reagent with the REX process demonstrated to be effective both in the presence and absence of the catalyst. Optimized 5-minute duration pretreatment conditions were determined using Box-Behnken design (BBD) with respect to screws speed, operating temperature, and concentration of SiO2. The crystallinity index, carbonyl index and weight loss (%) of LDPE were used as the studied responses for BDD. FTIR and DSC spectra of the residual LDPE obtained after pretreatment with the REX assisted oxidation technique showed a significant increase in residual LDPE carbonyl index from 0 to 1.04 and a decrease of LDPE crystallinity index from 29% to 18%. Up to 5-fold molecular weight reductions were also demonstrated using GPC. Optimum LDPE pretreatment with a duration of 5 minutes was obtained at low screw speed (50 rpm), operating temperature of 380-390⁰C and variable concentration of SiO2 (0 and 2% (w/w)) indicating that effective pretreatment can occur under noncatalytic and catalysed conditions. Biofilms were successfully formed on pretreated LDPE samples after 14 days of incubation.Furthermore, the technique proposed in this study is expected to provide a high throughput approach for pretreatment of pervasive recalcitrant PE based plastics to reduce their bio inertness.

scholarly journals Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

2021 ◽  
Author(s):  
Oliver M. Crook ◽  
Colin T. R. Davies ◽  
Laurent Gatto ◽  
Paul D.W. Kirk ◽  
Kathryn S. Lilley
Keyword(s):  
Steady State ◽  
High Throughput ◽  
Statistical Power ◽  
Subcellular Localisation ◽  
Type I ◽  
Disease States ◽  
Proteomic Data ◽  
Rational Drug ◽  
Context Specific ◽  
Type Ii Errors

AbstractThe steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different sub-cellular niches upon perturbation of the subcellular environment. Differential localisation provides a step towards mechanistic insight of subcellular protein dynamics. Aberrant localisation has been implicated in a number of pathologies, thus differential localisation may help characterise disease states and facilitate rational drug discovery by suggesting novel targets. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we propose a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation, as well quantifying the uncertainty in these estimates. Furthermore, BANDLE allows information to be shared across spatial proteomics datasets to improve statistical power. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to datasets studying EGF stimulation and AP-4 dependent localisation recovers well studied translocations, using only two-thirds of the provided data. Moreover, we implicate TMEM199 with AP-4 dependent localisation. In an application to cytomegalovirus infection, we obtain novel insights into the rewiring of the host proteome. Integration of high-throughput transcriptomic and proteomic data, along with degradation assays, acetylation experiments and a cytomegalovirus interactome allows us to provide the functional context of these data.

Combinatorial Computational Chemistry Approach to the High-Throughput Screening of Metal Sulfide Catalysts for CO Hydrogenation Process

2003 ◽  
Vol 17 (4) ◽  
pp. 857-861 ◽  
Author(s):  
Momoji Kubo ◽  
Tsuguo Kubota ◽  
Changho Jung ◽  
Kotaro Seki ◽  
Seiichi Takami ◽  
...  
Keyword(s):  
Computational Chemistry ◽  
High Throughput ◽  
High Throughput Screening ◽  
Co Hydrogenation ◽  
Metal Sulfide ◽  
Hydrogenation Process ◽  
Sulfide Catalysts

scholarly journals The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2421
Author(s):  
Sara Motta ◽  
Davide Vecchietti ◽  
Alessandra M. Martorana ◽  
Pietro Brunetti ◽  
Giovanni Bertoni ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Outer Membrane ◽  
Protein Identification ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Protein Domains ◽  
Host Cells ◽  
Inner Membrane ◽  
Proteomic Data ◽  
Associated Proteins

Background: Pseudomonas aeruginosa cell envelope-associated proteins play a relevant role in infection mechanisms. They can contribute to the antibiotic resistance of the bacterial cells and be involved in the interaction with host cells. Thus, studies contributing to elucidating these key molecular elements are of great importance to find alternative therapeutics. Methods: Proteins and peptides were extracted by different methods and analyzed by Multidimensional Protein Identification Technology (MudPIT) approach. Proteomic data were processed by Discoverer2.1 software and multivariate statistics, i.e., Linear Discriminant Analysis (LDA), while the Immune Epitope Database (IEDB) resources were used to predict antigenicity and immunogenicity of experimental identified peptides and proteins. Results: The combination of 29 MudPIT runs allowed the identification of 10,611 peptides and 2539 distinct proteins. Following application of extraction methods enriching specific protein domains, about 15% of total identified peptides were classified in trans inner-membrane, inner-membrane exposed, trans outer-membrane and outer-membrane exposed. In this scenario, nine outer membrane proteins (OprE, OprI, OprF, OprD, PagL, OprG, PA1053, PAL and PA0833) were predicted to be highly antigenic. Thus, they were further processed and epitopes target of T cells (MHC Class I and Class II) and B cells were predicted. Conclusion: The present study represents one of the widest characterizations of the P. aeruginosa membrane-associated proteome. The feasibility of our method may facilitates the investigation of other bacterial species whose envelope exposed protein domains are still unknown. Besides, the stepwise prioritization of proteome, by combining experimental proteomic data and reverse vaccinology, may be useful for reducing the number of proteins to be tested in vaccine development.

scholarly journals Novel Combination of Atomic Force Microscopy and Epifluorescence Microscopy for Visualization of Leaching Bacteria on Pyrite

2007 ◽  
Vol 74 (2) ◽  
pp. 410-415 ◽  
Author(s):  
Stefanie Mangold ◽  
Kerstin Harneit ◽  
Thore Rohwerder ◽  
Günter Claus ◽  
Wolfgang Sand
Keyword(s):  
Atomic Force Microscopy ◽  
Extracellular Polymeric Substances ◽  
Metal Sulfide ◽  
Epifluorescence Microscopy ◽  
Bacterial Cells ◽  
Cell Integrity ◽  
Force Microscopy ◽  
Topographic Features ◽  
Atomic Force ◽  
Leaching Bacteria

ABSTRACT Bioleaching of metal sulfides is an interfacial process comprising the interactions of attached bacterial cells and bacterial extracellular polymeric substances with the surface of a mineral sulfide. Such processes and the associated biofilms can be investigated at high spatial resolution using atomic force microscopy (AFM). Therefore, we visualized biofilms of the meso-acidophilic leaching bacterium Acidithiobacillus ferrooxidans strain A2 on the metal sulfide pyrite with a newly developed combination of AFM with epifluorescence microscopy (EFM). This novel system allowed the imaging of the same sample location with both instruments. The pyrite sample, as fixed on a shuttle stage, was transferred between AFM and EFM devices. By staining the bacterial DNA with a specific fluorescence dye, bacterial cells were labeled and could easily be distinguished from other topographic features occurring in the AFM image. AFM scanning in liquid caused deformation and detachment of cells, but scanning in air had no effect on cell integrity. In summary, we successfully demonstrate that the new microscopic system was applicable for visualizing bioleaching samples. Moreover, the combination of AFM and EFM in general seems to be a powerful tool for investigations of biofilms on opaque materials and will help to advance our knowledge of biological interfacial processes. In principle, the shuttle stage can be transferred to additional instruments, and combinations of AFM and EFM with other surface-analyzing devices can be proposed.

scholarly journals Unraveling the Central Role of Sulfur-Oxidizing Acidiphilium multivorum LMS in Industrial Bioprocessing of Gold-Bearing Sulfide Concentrates

2021 ◽  
Vol 9 (5) ◽  
pp. 984
Author(s):  
Anna Panyushkina ◽  
Aleksandr Bulaev ◽  
Aleksandr V. Belyi
Keyword(s):  
Sulfur Metabolism ◽  
Draft Genome ◽  
Microbial Consortia ◽  
Reduced Sulfur Compounds ◽  
Sulfur Oxidizer ◽  
Sulfur Oxidizing ◽  
Unique Strain ◽  
Sulfide Concentrates ◽  
Gold Bearing

Acidiphilium multivorum LMS is an acidophile isolated from industrial bioreactors during the processing of the gold-bearing pyrite-arsenopyrite concentrate at 38–42 °C. Most strains of this species are obligate organoheterotrophs that do not use ferrous iron or reduced sulfur compounds as energy sources. However, the LMS strain was identified as one of the predominant sulfur oxidizers in acidophilic microbial consortia. In addition to efficient growth under strictly heterotrophic conditions, the LMS strain proved to be an active sulfur oxidizer both in the presence or absence of organic compounds. Interestingly, Ac. multivorum LMS was able to succeed more common sulfur oxidizers in microbial populations, which indicated a previously underestimated role of this bacterium in industrial bioleaching operations. In this study, the first draft genome of the sulfur-oxidizing Ac. multivorum was sequenced and annotated. Based on the functional genome characterization, sulfur metabolism pathways were reconstructed. The LMS strain possessed a complicated multi-enzyme system to oxidize elemental sulfur, thiosulfate, sulfide, and sulfite to sulfate as the final product. Altogether, the phenotypic description and genome analysis unraveled a crucial role of Ac. multivorum in some biomining processes and revealed unique strain-specific characteristics, including the ars genes conferring arsenic resistance, which are similar to those of phylogenetically distinct microorganisms.

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