Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry

Author(s):  
Robert J. Gruninger ◽  
Adrian Tsang ◽  
Tim A. McAllister
2019 ◽  
Vol 85 (23) ◽  
Author(s):  
Sarah Ganter ◽  
Guylaine Miotello ◽  
Lucía Manso-Silván ◽  
Jean Armengaud ◽  
Florence Tardy ◽  
...  

ABSTRACT Many mycoplasma species are isolated from the ruminant lungs as either saprophytes or true pathogens. These wall-less bacteria possess a minimal genome and reduced metabolic capabilities. Accordingly, they rely heavily on their hosts for the supply of essential metabolites and, notably, peptides. Seven of 13 ruminant lung-associated Mycoplasma (sub)species were shown to possess caseinolytic activity when grown in rich media and assessed with a quantitative fluorescence test. For some species, this activity was detected in spent medium, an indication that proteases were secreted outside the mycoplasma cells. To identify these proteases, we incubated concentrated washed cell pellets in a defined medium and analyzed the supernatants by tandem mass spectrometry. Secreted-protease activity was detected mostly in the species belonging to the Mycoplasma mycoides cluster (MMC) and, to a lesser extent, in Mycoplasma bovirhinis. Analyzing a Mycoplasma mycoides subsp. capri strain, chosen as a model, we identified 35 expressed proteases among 55 predicted coding genes, of which 5 were preferentially found in the supernatant. Serine protease S41, acquired by horizontal gene transfer, was responsible for the caseinolytic activity, as demonstrated by zymography and mutant analysis. In an M. capricolum mutant, inactivation of the S41 protease resulted in marked modification of the expression or secretion of 17 predicted surface-exposed proteins. This is an indication that the S41 protease could have a role in posttranslational cleavage of surface-exposed proteins and ectodomain shedding, whose physiological impacts still need to be explored. IMPORTANCE Few studies pertaining to proteases in ruminant mycoplasmas have been reported. Here, we focus on proteases that are secreted outside the mycoplasma cell using a mass spectrometry approach. The most striking result is the identification, within the Mycoplasma mycoides cluster, of a serine protease that is exclusively detected outside the mycoplasma cells and is responsible for casein digestion. This protease may also be involved in the posttranslational processing of surface proteins, as suggested by analysis of mutants showing a marked reduction in the secretion of extracellular proteins. By analogy, this finding may help increase understanding of the mechanisms underlying this ectodomain shedding in other mycoplasma species. The gene encoding this protease is likely to have been acquired via horizontal gene transfer from Gram-positive bacteria and sortase-associated surface proteases. Whether this protease and the associated ectodomain shedding are related to virulence has yet to be ascertained.


2020 ◽  
Vol 17 ◽  
Author(s):  
Juliana Abigail Leite ◽  
Nathalia Gonsales da Rosa-Garzon ◽  
Helen Julie Laure ◽  
José Cesar Rosa ◽  
Octavio Luiz Franco ◽  
...  

Background: Proteomics facilitates understanding of the complexity of molecular and physiological mechanisms involved in the metabolic and biological fungal adaptations to pH changes. Proteomics enables the identification of enzymes and fungal proteins involved in these adaptations. This approach may be used to investigate such fungi as Aspergillus niveus, whose proteome has not yet been analyzed, changes the intra- and extracellular protein profiles in response to extracellular pH. Objective: In the current study, we used two-dimensional gel electrophoresis (2DE) and mass spectrometry to evaluate the response of A. niveus to grow at pH 5, 6, 7, and 8 for 96 hours submerged bioprocess culturing. Methods: This study evaluated the response of A. niveus to grow at pH 5, 6, 7, and 8 for 96 h submerged bioprocess culturing, by analysis of two-dimensional gel electrophoresis (2DE), of the intracellular proteomes and the secretome, protein spots of interest were submitted to tryptic digestion and analyzed by matrix-assisted laser desorption/ionization time-offlight tandem mass spectrometry (MALDI-TOF/TOF-MS). Results: This approach revealed substantial differences between the functions of intra- and extracellular proteins of A. niveus. The data suggested that pH-modulated global proteins are involved in important, mainly metabolic, processes, in the pentose phosphate pathway, protein regulation, cell wall maintenance, and others. Moreover, the change in extracellular pH could have altered the availability of nutrients, and induced the production of enzymes that respond to oxidative and other stresses. Conclusion: Proteomic facilitates understanding of the complexity of molecular and physiological mechanisms involved in the metabolic and biological adaptations of fungi to pH changes.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 236-236
Author(s):  
Qi Da ◽  
Jennifer Nolasco ◽  
Tanvir Khatlani ◽  
Fernandez Maria ◽  
Miguel A. Cruz ◽  
...  

Abstract Protein phosphorylation represents a common mechanism to regulate the structure and function of proteins. Although vast amount of extracellular proteins including secreted plasma proteins are phosphorylated, historically, phosphorylation has been intensively investigated for intracellular proteins. The plasma and subendothelial protein von Willebrand factor (VWF) undergoes post translational modifications such as glycosylation and sulphation to reach the mature protein product. However, phosphorylation of VWF has not been described. We have used mass spectrometry to analyze purified plasma VWF, and identified that serine 1613 within the A2 domain was phosphorylated. A natural occurring mutation on this residue (S1613P) causes von Willebrand disease Type 2A by increasing the susceptibility of VWF to be cleaved by ADAMTS13. Notably, S1613 overlapped with the S-X-E/pS motif, which is the consensus site for phosphorylation by an atypical kinase, FAM20c (family with sequence similarity 20, member C). Localized to the inner lumen of the golgi/endoplasmic reticulum, FAM20c is secreted and likely responsible for the phosphorylation of several secreted proteins bearing the S-X-E/ps motif. Therefore, we further investigated whether VWF can undergo phosphorylation by FAM20c and how such modification impacts the function of VWF, particularly on the activity of ADAMTS13. In vitro, recombinant FAM20c directly phosphorylated recombinant VWF-A1A2A3 domain protein and purified plasma VWF. Further analysis revealed that the isolated A2 domain but not A1 or A3 domain was phosphorylated by FAM20c. Phosphorylation was assessed employing 32P labeling of proteins, protein shift in phospho tag gel and mass spectrometry. Treatment with λ phosphatase diminished phosphorylation and a defective FAM20c kinase mutant failed to phosphorylate A2 and VWF proteins, confirming the phosphorylation event. In addition, FAM20c-mediated phosphorylation was markedly reduced in a non-phosphorylatable A2 S1613A mutant. Thus, all these outcomes indicate that the secreted kinase FAM20c can phosphorylate S1613 in the A2 domain of VWF. To explore the functional effect of S1613 phosphorylation, we compared the plasma-mediated cleavage of wild type (WT)A2, phosphomimetic S1613D mutant and the nonphosphorylatable A2 S1613A mutant. Unexpectedly, and in sharp contrast to the WT and S1613A variants, the S1613D mutant was effectively cleaved in the presence of the enzyme inhibitor, EDTA. In addition, cleavage of the S1613D mutant was robust and slightly faster than that of the WT and S1613A. These studies suggest that phosphorylation of S1613 in VWF may facilitate the cleavage of VWF multimers. To further explore the physiological relevance of phosphorylated VWF in thrombosis, we generated phospho VWF S1613 and nonphosphorylated S1613 VWF antibodies and studied their effect on thrombus formation. In a microfluidic perfusion system, whole blood supplemented with 50 μg/ml of phosphoVWF antibody but not the nonphosphoVWF antibody, markedly potentiated thrombus formation on a collagen-coated surface. Collectively, these studies suggest that S1613 phosphorylation of VWF suppress thrombus formation, in part by facilitating cleavage of the VWF multimers. These studies identify for the first time that VWF can undergo phosphorylation and opens new avenues for regulation of VWF function by phosphorylation. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 17 (1) ◽  
pp. 3-9
Author(s):  
Rajdeep Das ◽  
Nisha D`souza ◽  
Surya K. Choubey ◽  
Sethumadhavan Murlidharan ◽  
Anura V. Kurpad ◽  
...  

Background: Staphylococcus aureus (S. aureus), an important pathogen, causes a wide range of infections in human starting from food poisoning to septicemia. It affects the host cells with various exotoxins, known as virulence factors, which are synthesized in growth phase-dependent manner of the bacteria. S. aureus has been reported to become resistant to antibiotics rapidly. Among two common clinical isolates, Methicillin-sensitive S. aureus (MSSA) and Methicillin-resistant S. aureus (MRSA), MRSA pose major problems across hospitals around the world. Objective: The objective of the present study was to profile the exoproteins of Methicillin-sensitive S. aureus (ATCC 25293) and subsequently to establish a proteomics-based method of characterization of S. aureus that is crucial in treating hospital-acquired infections. Methods: We used two-dimensional nanoLC/ESI-MS based proteomic platform to characterize and quantify the exoproteins isolated from Methicillin-sensitive S. aureus (ATCC 25293) strain. Results: A total of 69 proteins were identified from extracellular proteome pool of ATCC 25293 strain that includes 18 extracellular proteins, 40 cytoplasmic proteins, 2 membrane proteins, 3 cell wall proteins and 6 uncharacterized proteins. Conclusion: We propose that this mass spectrometry-based proteomics method of characterization of exoproteins might be useful to identify S. aureus strains that are resistant to antibiotics.


2014 ◽  
Vol 9 (7) ◽  
pp. 708-716
Author(s):  
Raimonda Petkauskaite ◽  
Dangiras Lukosius ◽  
Janusz Dębski ◽  
Andrius Jasilionis ◽  
Michał Dadlez ◽  
...  

AbstractPlant biomass in the form of cheap wastes, such as straw, corn stalks, wood chips, sawdust, bagasse, pomace, etc., is abundant throughout the world. To convert these wastes into the useful value-added compounds microbial enzymes are the preferred choice. In this paper, we identify enzymes involved in the degradation of starch and polygalacturonic acid using liquid chromatography/mass spectrometry based analysis. We analysed total protein from soil and compost samples. Extracellular proteins from enrichment cultures were analysed in parallel and used as controls in the sample preparation and identification of proteins. In general, both protein sequence coverage and the number of identified peptides were higher in the samples obtained from the enrichment cultures than from the total protein from soil and compost. The influence of the nature of gel (zymography vs. SDS/polyacrylamide) was negligible. Thus, starch and polygalacturonic acid degradation associated proteins can be directly excised from the zymograms without the need to align zymograms with the SDS/polyacrylamide gels. A range of starch and polygalacturonic acid degradation associated enzymes were identified in both total protein samples and extracellular proteins from the enrichment cultures. Our results show that proteins involved in starch and polygalacturonic acid degradation can be identified by liquid chromatography/mass spectrometry from the complex protein mixtures both with and without cultivation of microorganism


Author(s):  
George H. Herbener ◽  
Antonio Nanci ◽  
Moise Bendayan

Protein A-gold immunocytochemistry is a two-step, post-embedding labeling procedure which may be applied to tissue sections to localize intra- and extracellular proteins. The key requisite for immunocytochemistry is the availability of the appropriate antibody to react in an immune response with the antigenic sites on the protein of interest. During the second step, protein A-gold complex is reacted with the antibody. This is a non- specific reaction in that protein A will combine with most IgG antibodies. The ‘label’ visualized in the electron microscope is colloidal gold. Since labeling is restricted to the surface of the tissue section and since colloidal gold is particulate, labeling density, i.e., the number of gold particles per unit area of tissue section, may be quantitated with ease and accuracy.


Author(s):  
Philippe Fragu

The identification, localization and quantification of intracellular chemical elements is an area of scientific endeavour which has not ceased to develop over the past 30 years. Secondary Ion Mass Spectrometry (SIMS) microscopy is widely used for elemental localization problems in geochemistry, metallurgy and electronics. Although the first commercial instruments were available in 1968, biological applications have been gradual as investigators have systematically examined the potential source of artefacts inherent in the method and sought to develop strategies for the analysis of soft biological material with a lateral resolution equivalent to that of the light microscope. In 1992, the prospects offered by this technique are even more encouraging as prototypes of new ion probes appear capable of achieving the ultimate goal, namely the quantitative analysis of micron and submicron regions. The purpose of this review is to underline the requirements for biomedical applications of SIMS microscopy.Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue.


Author(s):  
K.K. Soni ◽  
D.B. Williams ◽  
J.M. Chabala ◽  
R. Levi-Setti ◽  
D.E. Newbury

In contrast to the inability of x-ray microanalysis to detect Li, secondary ion mass spectrometry (SIMS) generates a very strong Li+ signal. The latter’s potential was recently exploited by Williams et al. in the study of binary Al-Li alloys. The present study of Al-Li-Cu was done using the high resolution scanning ion microprobe (SIM) at the University of Chicago (UC). The UC SIM employs a 40 keV, ∼70 nm diameter Ga+ probe extracted from a liquid Ga source, which is scanned over areas smaller than 160×160 μm2 using a 512×512 raster. During this experiment, the sample was held at 2 × 10-8 torr.In the Al-Li-Cu system, two phases of major importance are T1 and T2, with nominal compositions of Al2LiCu and Al6Li3Cu respectively. In commercial alloys, T1 develops a plate-like structure with a thickness <∼2 nm and is therefore inaccessible to conventional microanalytical techniques. T2 is the equilibrium phase with apparent icosahedral symmetry and its presence is undesirable in industrial alloys.


Author(s):  
Bruno Schueler ◽  
Robert W. Odom

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) provides unique capabilities for elemental and molecular compositional analysis of a wide variety of surfaces. This relatively new technique is finding increasing applications in analyses concerned with determining the chemical composition of various polymer surfaces, identifying the composition of organic and inorganic residues on surfaces and the localization of molecular or structurally significant secondary ions signals from biological tissues. TOF-SIMS analyses are typically performed under low primary ion dose (static SIMS) conditions and hence the secondary ions formed often contain significant structural information.This paper will present an overview of current TOF-SIMS instrumentation with particular emphasis on the stigmatic imaging ion microscope developed in the authors’ laboratory. This discussion will be followed by a presentation of several useful applications of the technique for the characterization of polymer surfaces and biological tissues specimens. Particular attention in these applications will focus on how the analytical problem impacts the performance requirements of the mass spectrometer and vice-versa.


Sign in / Sign up

Export Citation Format

Share Document