Proteomic analysis of temperature dependent extracellular proteins from Aspergillus fumigatus grown under solid-state culture condition

Engineering Caldicellulosiruptor bescii with Surface Layer Homology Domain-Linked Glycoside Hydrolases Improves Plant Biomass Solubilization

Extremely thermophilic Caldicellulosiruptor species solubilize carbohydrates from lignocellulose through glycoside hydrolases (GHs) that can be extracellular, intracellular, or cell surface layer (S-layer) associated. Caldicellulosiruptor genomes sequenced so far encode at least one surface layer homology domain glycoside hydrolase (SLH-GH), representing six different classes of these enzymes; these can have multiple binding and catalytic domains. Biochemical characterization of a representative from each class was done to determine their biocatalytic features: four SLH-GHs from Caldicellulosiruptor kronotskyensis (Calkro_0111, Calkro_0402, Calkro_0072, and Calkro_2036) and two from Caldicellulosiruptor hydrothermalis (Calhy_1629 and Calhy_2383). Calkro_0111, Calkro_0072, and Calhy_2383 exhibited β-1,3-glucanase activity, Calkro_0402 was active on both β-1,3/1,4-glucan and β-1,4-xylan, Calkro_2036 exhibited activity on both β-1,3/1,4-glucan and β-1,4-glucan, and Calhy_1629 was active only on arabinan. Caldicellulosiruptor bescii, the only species with molecular genetic tools as well as already a strong cellulose degrader, contains only one SLH-GH, Athe_0594, a glucanase that is a homolog of Calkro_2036; the other 5 classes of SLH-GHs are absent in C. bescii. The C. bescii secretome, supplemented with individual enzymes or cocktails of SLH-GHs, increased in vitro sugar release from sugar cane bagasse and poplar. Expression of non-native SLH-GHs in vivo, either associated with the S-layer or as freely secreted enzymes, improved total carbohydrate solubilization of sugar cane bagasse and poplar by up to 45% and 23%, respectively. Most notably, expression of Calkro_0402, a xylanase/glucanase, improved xylose solubilization from poplar and bagasse by over 70% by C. bescii. While Caldicellulosiruptor species are already prolific lignocellulose degraders, they can be further improved by the strategy described here. IMPORTANCE Caldicellulosiruptor species hold promise as microorganisms that can solubilize the carbohydrate portion of lignocellulose and subsequently convert fermentable sugars into bio-based chemicals and fuels. Members of the genus have surface layer (S-layer) homology domain-associated glycoside hydrolases (SLH-GHs) that mediate attachment to biomass as well as hydrolysis of carbohydrates. Caldicellulosiruptor bescii, the most studied member of the genus, has only one SLH-GH. Expression of SLH-GHs from other Caldicellulosiruptor species in C. bescii significantly improved degradation of sugar cane bagasse and poplar. This suggests that this extremely thermophilic bacterium can be engineered to further improve its ability to degrade specific plant biomasses by inserting genes encoding SLH-GHs recruited from other Caldicellulosiruptor species.

Functional Specificity of Three α-Arabinofuranosidases from Different Glycoside Hydrolase Families in Aspergillus niger An76

α-l-Arabinofuranosidase (Abf), a debranching enzyme that can remove arabinose substituents from arabinoxylan, promotes the hydrolysis of hemicellulose in plant biomass. However, the functional specificity of Abfs from different glycoside hydrolase (GH) families on the digestion of arabinoxylan and their synergistic interaction with xylanase have not been systematically studied. In this work, we characterized three Abfs (AxhA, AbfB, and AbfC) from GH62, GH54, and GH51 families in Aspergillus niger An76. Quantitative transcriptional analysis showed that expression of the axhA gene was upregulated as a result of induction by xylose substrates, whereas expression of the abfB gene was mainly induced by arabinose. Recombinant AxhA, AbfB, and AbfC exhibited different hydrolytic performances. AxhA showed the highest catalytic activity toward wheat arabinoxylan (WAX) and tended to hydrolyze monosubstituted arabinofuranose units, whereas AbfB had higher catalytic activity on AN and debranched arabinan (DAN), having the ability to cope with mono- and disubstituted arabinofuranose units. Furthermore, AbfC had greater arabinofuranosidase activity on p-nitrophenyl-α-l-arabinofuranoside (pNP-AraF) than on other substrates. Moreover, three Abfs displayed obvious synergistic action with GH11 xylanase XynB against WAX and barley husk residues. The elucidation of the degradation mechanisms of Abfs will lay a theoretical foundation for the efficient industrialized transformation of arabinoxylans.

New Perspectives in the Diagnosis and Management of Allergic Fungal Airway Disease

Allergy to airway-colonising, thermotolerant, filamentous fungi represents a distinct eosinophilic endotype of often severe lung disease. This endotype, which particularly affects adult asthma, but also complicates other airway diseases and sometimes occurs de novo, has a heterogeneous presentation ranging from severe eosinophilic asthma to lobar collapse. Its hallmark is lung damage, characterised by fixed airflow obstruction (FAO), bronchiectasis and lung fibrosis. It has a number of monikers including severe asthma with fungal sensitisation (SAFS) and allergic bronchopulmonary aspergillosis/mycosis (ABPA/M), but these exclusive terms constitute only sub-sets of the condition. In order to capture the full extent of the syndrome we prefer the inclusive term allergic fungal airway disease (AFAD), the criteria for which are IgE sensitisation to relevant fungi in association with airway disease. The primary fungus involved is Aspergillus fumigatus, but a number of other thermotolerant species from several genera have been implicated. The unifying mechanism involves germination of inhaled fungal spores in the lung in the context of IgE sensitisation, leading to a persistent and vigorous eosinophilic inflammatory response in association with release of fungal proteases. Most allergenic fungi, including Alternaria and Cladosporium species, are not thermotolerant and cannot germinate in the airways so only act as aeroallergens and do not cause AFAD. Studies of the airway mycobiome have shown that A. fumigatus colonises the normal as much as the asthmatic airway, suggesting it is the tendency to become IgE-sensitised that is the critical triggering factor for AFAD rather than colonisation per se. Treatment is aimed at preventing exacerbations with glucocorticoids and increasingly by the use of anti-T2 biological therapies. Anti-fungal therapy has a limited place in management, but is an effective treatment for fungal bronchitis which complicates AFAD in about 10% of cases.

Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions

Filamentous fungi have been associated with extreme habitats, including nuclear power plant accident sites and the International Space Station (ISS). Due to their immense adaptation and phenotypic plasticity capacities, fungi may thrive in what seems like uninhabitable niches. This study is the first report of fungal survival after exposure of monolayers of conidia to simulated Mars conditions (SMC). Conidia of several Chernobyl nuclear accident-associated and ISS-isolated strains were tested for UV-C and SMC sensitivity, which resulted in strain-dependent survival. Strains surviving exposure to SMC for 30 min, ISSFT-021-30 and IMV 00236-30, were further characterized for proteomic, and metabolomic changes. Differential expression of proteins involved in ribosome biogenesis, translation, and carbohydrate metabolic processes was observed. No significant metabolome alterations were revealed. Lastly, ISSFT-021-30 conidia re-exposed to UV-C exhibited enhanced UV-C resistance when compared to the conidia of unexposed ISSFT-021.

Effective one-step saccharification of lignocellulosic biomass using magnetite-biocatalysts containing saccharifying enzymes

Lignocellulosic biomass, packed with sugars, is one of the most available renewable resources for biofuels and bioproducts production. To release the sugars for the production, enzymatic hydrolysis (saccharification) of pretreated lignocellulosic biomass are required. However, the saccharification process is costly, inefficient, and requires multi-step operations. This is in part due to the high cost and the limited selection of commercial enzymes which commonly have different optimal pH and temperatures. Here we reported a one-step saccharification of pretreated lignocellulosic biomass using immobilized biocatalysts containing five different saccharifying enzymes (SEs) with a similar optimum pH and temperature. The five SEs - endo-1,4-β-d-glucanase (an endoglucanase, eglS), cellobiohydrolase (an exoglucanase, cbhA), and β-glucosidase (bglH), endo-1,4-β-xylanase (an endoxylanase, xynC) and β-xylosidase (bxlB) - were successfully expressed and produced by E. coli BL21. Better saccharification of pretreated corn husks was observed when using the five crude SE enzymes than those using two commonly used SEs, endo-1,4-β-d-glucanase and β-glucosidase. The five SEs were cross-linked in the absence or the presence of magnetic nanoparticles (hereafter referred as SE-CLEAs and M-SE-CLEAs, respectively). By using SE-CLEAs, the highest amount of reduced sugar (250 mg/g biomass) was measured. The activity of immobilized SEs is better than free crude SEs. The M-SE-CLEAs can be reused at least 3 times for effective saccharification of pretreated lignocellulosic biomass.

Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles

BACKGROUND

As a ubiquitous filamentous fungal, Aspergillus spp. play a critical role in lignocellulose degradation, which was also defined as considerable cell factories for organic acids and industrially relevant enzymes producer. Nevertheless, the production of various extracellular enzymes can be influenced by different factors including nitrogen source, carbon source, cultivation temperature, and initial pH value. Thus, this study aims to reveal how amino acids affect the decomposition of lignocellulose by Aspergillus fumigatus Z5 through transcriptional and proteomics methods.

RESULTS

The activities of several lignocellulosic enzymes secreted by A. fumigatus Z5 adding with cysteine, methionine, and ammonium sulfate were determined with the chromatometry method. The peak of endo-glucanase (7.33 ± 0.03 U mL-1), exo-glucanase (10.50 ± 0.07 U mL-1), β-glucosidase (21.50 ± 0.22 U mL-1), and xylanase (76.43 ± 0.71 U mL-1) were all obtained in the Cys treatment. The secretomes of A. fumigatus Z5 under different treatments were also identified by LC-MS/MS, and 227, 256 and 159 different proteins were identified in the treatments of Cys, Met, and CK (Control, treatment with ammonium sulfate as the sole nitrogen source), respectively. Correlation analysis results of transcriptome and proteome data with fermentation profiles showed that most of the cellulose-degrading enzymes including cellulases, hemicellulases and glycoside hydrolases were highly upregulated when cysteine was added to the growth medium. In particular, the enzymes that convert cellulose into cellobiose appear to be upregulated. This study could increase knowledge of lignocellulose bioconversion pathways and fungal genetics.

CONCLUSIONS

Transcriptome and proteome analyses' results indicated that cysteine could significantly promote the secretion of lignocellulosic enzymes of an efficient lignocellulosic decomposing strain, A. fumigatus Z5. The possible reason for these results is that Z5 preferred to use amino acids such as cysteine to adapt to the external environment through upregulating carbon-related metabolism pathways.

Isolation, identification and characterization of lignocellulolytic aerobic and anaerobic fungi in one- and two-phase biogas plants

Aerobic and anaerobic fungi are among the most effective plant biomass degraders known and have high potential to increase the efficiency of lignocellulosic biomass utilization, such as for biogas generation. However, limited information is available on their contribution to such industrial processes. Therefore, the presence of fungi along the biogas production chain of one-phase and two-phase biogas plants in Germany was analyzed. Seventeen aerobic species of Zygomycota, Ascomycota and Basidiomycota were identified, including efficient producers of lignocellulases, such as Trichoderma capillare isolated from a hydrolysis tank and Coprinopsis cinerea from fibers separated from pressed digestate. Five anaerobic fungal species of the phylum Neocallimastigomycota (comprising two novel clades) were present in an slightly acidic fermenter of a biogas plant fed with cow manure displaying endoglucanase transcriptional activity. The broad fungal presence demonstrated in this study can serve developing bioaugmentation systems with relevant lignocellulolytic fungi to improve biogas production from recalcitrant fiber material.

Proteomic researches for lignocellulose-degrading enzymes: A mini-review

Protective action of lignin/hemicellulose networks and crystalline structures of embedded cellulose render lignocellulose material resistant to external enzymatic attack. To eliminate this bottleneck, research has been conducted in which advanced proteomic techniques are applied to identify effective commercial hydrolytic enzymes. This mini-review summarizes researches on lignocellulose-degrading enzymes, the mechanisms of the responses of various lignocellulose-degrading strains and microbial communities to various carbon sources and various biomass substrates, post-translational modifications of lignocellulose-degrading enzymes, new lignocellulose-degrading strains, new lignocellulose-degrading enzymes and a new method of secretome analysis. The challenges in the practical use of enzymatic hydrolysis process to realize lignocellulose biorefineries are discussed, along with the prospects for the same.

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

Aspergillus fumigatus and multiple other Aspergillus species cause a wide range of lung infections, collectively termed aspergillosis. Aspergilli are ubiquitous in environment with healthy immune systems routinely eliminating inhaled conidia, however, Aspergilli can become an opportunistic pathogen in immune-compromised patients. The aspergillosis mortality rate and emergence of drug-resistance reveals an urgent need to identify novel targets. Secreted and cell membrane proteins play a critical role in fungal-host interactions and pathogenesis. Using a computational pipeline integrating data from high-throughput experiments and bioinformatic predictions, we have identified secreted and cell membrane proteins in ten Aspergillus species known to cause aspergillosis. Small secreted and effector-like proteins similar to agents of fungal-plant pathogenesis were also identified within each secretome. A comparison with humans revealed that at least 70% of Aspergillus secretomes have no sequence similarity with the human proteome. An analysis of antigenic qualities of Aspergillus proteins revealed that the secretome is significantly more antigenic than cell membrane proteins or the complete proteome. Finally, overlaying an expression dataset, four A. fumigatus proteins upregulated during infection and with available structures, were found to be structurally similar to known drug target proteins in other organisms, and were able to dock in silico with the respective drug.

Secretome profiling reveals temperature-dependent growth of Aspergillus fumigatus

Aspergillus fumigatus is a ubiquitous opportunistic fungus. In this study, systematic analyses were carried out to study the temperature adaptability of A. fumigatus. A total of 241 glycoside hydrolases and 69 proteases in the secretome revealed the strong capability of A. fumigatus to degrade plant biomass and protein substrates. In total, 129 pathogenesis-related proteins detected in the secretome were strongly correlated with glycoside hydrolases and proteases. The variety and abundance of proteins remained at temperatures of 34°C-45°C. The percentage of endo-1,4-xylanase increased when the temperature was lowered to 20°C, while the percentage of cellobiohydrolase increased as temperature was increased, suggesting that the strain obtains carbon mainly by degrading xylan and cellulose, and the main types of proteases in the secretome were aminopeptidases and carboxypeptidases. Only half of the proteins were retained and their abundance declined to 9.7% at 55°C. The activities of the remaining β-glycosidases and proteases were merely 35% and 24%, respectively, when the secretome was treated at 60°C for 2 h. Therefore, temperatures >60°C restrict the growth of A. fumigatus.

Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse

Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62A_wt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62A_wt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62A_wt and the non-glycosylated enzyme from E. coli (AnAbf62A_deglyc) were highly similar. In addition, the designed glycomutant AnAbf62A_N83Q presented similar patterns of secretion and activity to the AnAbf62A_wt, indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62A_deglyc was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62A_Y312F and AnAbf62A_Y312S showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.

Proteomics as a Tool to Identify New Targets Against Aspergillus and Scedosporium in the Context of Cystic Fibrosis

Cystic fibrosis (CF) is a genetic disorder that increases the risk of suffering microbial, including fungal, infections. In this paper, proteomics-based information was collated relating to secreted and cell wall proteins with potential medical applications from the most common filamentous fungi in CF, i.e., Aspergillus and Scedosporium/Lomentospora species. Among the Aspergillus fumigatus secreted allergens, β-1,3-endoglucanase, the alkaline protease 1 (Alp1/oryzin), Asp f 2, Asp f 13/15, chitinase, chitosanase, dipeptidyl-peptidase V (DppV), the metalloprotease Asp f 5, mitogillin/Asp f 1, and thioredoxin reductase receive a special mention. In addition, the antigens β-glucosidase 1, catalase, glucan endo-1,3-β-glucosidase EglC, β-1,3-glucanosyltransferases Gel1 and Gel2, and glutaminase A were also identified in secretomes of other Aspergillus species associated with CF: Aspergillus flavus, Aspergillus niger, Aspergillus nidulans, and Aspergillus terreus. Regarding cell wall proteins, cytochrome P450 and eEF-3 were proposed as diagnostic targets, and alkaline protease 2 (Alp2), Asp f 3 (putative peroxiredoxin pmp20), probable glycosidases Asp f 9/Crf1 and Crf2, GPI-anchored protein Ecm33, β-1,3-glucanosyltransferase Gel4, conidial hydrophobin Hyp1/RodA, and secreted aspartyl protease Pep2 as protective vaccines in A. fumigatus. On the other hand, for Scedosporium/Lomentospora species, the heat shock protein Hsp70 stands out as a relevant secreted and cell wall antigen. Additionally, the secreted aspartyl proteinase and an ortholog of Asp f 13, as well as the cell wall endo-1,3-β-D-glucosidase and 1,3-β-glucanosyl transferase, were also found to be significant proteins. In conclusion, proteins mentioned in this review may be promising candidates for developing innovative diagnostic and therapeutic tools for fungal infections in CF patients.

A comparative secretome analysis of industrial Aspergillus oryzae and its spontaneous mutant ZJGS-LZ-21

Aspergillus oryzae koji plays a crucial role in fermented food products due to the hydrolytic activities of secreted enzymes. In the present study, we performed a comparative secretome analysis of the industrial strain of Aspergillus oryzae 3.042 and its spontaneous mutantZJGS-LZ-21. One hundred and fifty two (152) differential protein spots were excised (p<0.05), and 25 proteins were identified. Of the identified proteins, 91.3% belonged to hydrolytic enzymes acting on carbohydrates or proteins. Consistent with their enzyme activities, the expression of 14 proteins involved in the degradation of cellulose, hemicellulose, starch and proteins, increased in the ZJGS-LZ-21isolate. In particular, increased levels of acid protease (Pep) may favor the degradation of soy proteins in acidic environments and promote the cleavage of allergenic soybean proteins in fermentation, resulting in improvements of product safety and quality. The ZJGS-LZ-21 isolate showed higher protein secretion and increased hydrolytic activities than did strain 3.042, indicating its promising application in soybean paste fermentation.

Proteomics study revealed altered proteome of Dichogaster curgensis upon exposure to fly ash

Fly ash is toxic and its escalating use as a soil amendment and disposal by dumping into environment is receiving alarming attention due to its impact on environment. Proteomics technology is being used for environmental studies since proteins respond rapidly when an organism is exposed to a toxicant, and hence soil engineers such as earthworms are used as model organisms to assess the toxic effects of soil toxicants. This study adopted proteomics technology and profiled proteome of earthworm Dichogaster curgensis that was exposed to fly ash, with main aim to elucidate fly ash effects on cellular and metabolic pathways. The functional classification of identified proteins revealed carbohydrate metabolism (14.36%), genetic information processing (15.02%), folding, sorting and degradation (10.83%), replication and repair (3.95%); environmental information processing (2.19%), signal transduction (9.61%), transport and catabolism (17.27%), energy metabolism (6.69%), etc. in the proteome. Proteomics data and functional assays revealed that the exposure of earthworm to fly ash induced protein synthesis, up-regulation of gluconeogenesis, disturbed energy metabolism, oxidative and cellular stress, and mis-folding of proteins. The regulation of ubiquitination, proteasome and modified alkaline comet assay in earthworm coelomocytes suggested DNA-protein cross link affecting chromatin remodeling and protein folding.

Protein profiling of mefloquine resistant Plasmodium falciparum using mass spectrometry-based proteomics

Malaria is a mosquito borne infectious disease caused by protozoa of genus Plasmodium. There are five species of Plasmodium that are found to infect humans. Plasmodium falciparum can cause severe malaria leading to higher morbidity and mortality of malaria than the other four species. Antimalarial resistance is the major obstacle to control malaria. Mefloquine was used in combination with Artesunate for uncomplicated P. falciparum in South East Asia and it has developed and established mefloquine resistance in this region. Here, gel-enhanced liquid chromatography/tandem mass spectrometry (GeLC-MS/MS)-based proteomics and label-free quantification were used to explore the protein profiles of mefloquine-sensitive and -induced resistant P. falciparum. A Thai P. falciparum isolate (S066) was used as a model in this research. Our data revealed for the first time that 69 proteins exhibited at least 2-fold differences in their expression levels between the two parasite lines. Of these, 36 were up-regulated and 33 were down-regulated in the mefloquine-resistant line compared with the mefloquine-sensitive line. These findings are consistent with those of past studies, where the multidrug resistance protein Pgh1 showed an up-regulation pattern consistent with that expected from its average 3-copy pfmdr1 gene number. Pgh1 and eight other up-regulated proteins (i.e., histo-aspartyl protease protein, exportin 1, eukaryotic translation initiation factor 3 subunit 8, peptidyl-prolyl cis-trans isomerase, serine rich protein homologue, exported protein 1, ATP synthase beta chain and phospholipid scramblase 1) were further validated for their expression levels using reverse transcriptase quantitative real-time PCR. The data support the up-regulation status in the mefloquine-resistant parasite line of all the candidate genes referred to above. Therefore, GeLC-MS/MS-based proteomics combined with label-free quantification is a reliable approach for exploring mefloquine resistance biomarkers in P. falciparum. Identification of these proteins leads to better understanding of mefloquine resistant mechanisms in malaria parasites.

Proteomics profiling of cholangiocarcinoma exosomes: A potential role of oncogenic protein transferring in cancer progression

Cholangiocarcinoma (CCA), a common primary malignant tumor of bile duct epithelia, is highly prevalent in Asian countries and unresponsive to chemotherapeutic drugs. Thus, a newly recognized biological entity for early diagnosis and treatment is highly needed. Exosomes are small membrane bound vesicles found in body fluids and released by most cell types including cancer cells. The vesicles contain specific subset of proteins and nucleic acids corresponding to cell types and play essential roles in pathophysiological processes. The present study aimed to assess the protein profiles of CCA-derived exosomes and their potential roles. We have isolated exosomes from CCA cells namely KKU-M213 and KKU-100 derived from Thai patients and their roles were investigated by incubation with normal human cholangiocyte (H69) cells. Exosomes were internalized into H69 cells and had no effects on viability or proliferation of the host cells. Interestingly, the exosomes from KKU-M213 cells only induced migration and invasion of H69 cells. Proteomic analysis of the exosomes from KKU-M213 cells disclosed multiple cancer related proteins that are not present in H69 exosomes. Consistent with the protein profile, treatment with KKU-M213 exosomes induced β-catenin and reduced E-cadherin expressions in H69 cells. Collectively, our results suggest that a direct cell-to-cell transfer of oncogenic proteins via exosomal pathway may be a novel mechanism for CCA progression and metastasis.

Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.

Data for iTRAQ secretomic analysis of Aspergillus fumigatus in response to different carbon sources

Here, we provide data related to the research article entitled “Quantitative proteomics study of Aspergillus fumigatus secretome revealed deamidation of secretory enzymes” by Adav et al. (J. Proteomics (2015) [1]). Aspergillus sp. plays an important role in lignocellulosic biomass recycling. To explore biomass hydrolyzing enzymes of A. fumigatus, we profiled secretome under different carbon sources such as glucose, cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). The data presented here represents the detailed comparative abundances of diverse groups of biomass hydrolyzing enzymes including cellulases, hemicellulases, lignin degrading enzymes, and peptidases and proteases; and their post translational modification like deamidation.