Global Proteomics of Extremophilic Fungi: Mission Accomplished?

Tesei, Donatella; Sterflinger, Katja; Marzban, Gorji

doi:10.1007/978-3-030-19030-9_12

Cited by 6 publications

(10 citation statements)

References 201 publications

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“…[ 288 ]—that can be used individually or combined. Protein extraction from purified vesicles is achieved solely via biochemical interventions with e.g., chaotrope-based homogenization buffers or precipitation [ 24 ] ( Figure 4 B). As the thorough isolation of pure fractions and the integrity of the sample are both crucial, further purification steps in HPLC can be performed to aid the removal of non-exosomal material prior to protein extraction [ 289 ].…”

Section: Proteomics Advances In Ascomycotamentioning

confidence: 99%

“…In case of proteins associated with cell wall polysaccharides, hydrolytic enzymes and chemicals are often additionally required [ 316 ]. Based on the nature of the protein linkage to the wall—i.e., alkali sensitive linkage (ASL)-, GPI-linkage, chitin-bound proteins—different types of commercially available enzymes like e.g., β-glucanases and chitinases or alkali and acids can be applied [ 24 ]. Acids are often used to promote protein deglycosilation prior to downstream separation techniques.…”

Section: Proteomics Advances In Ascomycotamentioning

confidence: 99%

“…Proteomics additionally involves the study of protein posttranslational modifications and protein networks. While initially focusing prevalently on the investigation of the whole-cell proteome, with advancements in the techniques, subfields of proteomics such as secretomics, subcellular, membrane and vesicle proteomics have developed and gained a crucial role in the elucidation of protein biological functions [ 24 ]. Proteomic measurements are accomplished through a combination of highly sensitive instrumentation and powerful computational methods to produce high throughput qualitative and quantitative data.…”

Section: Introductionmentioning

confidence: 99%

“…Given the opportunistic and pathogenic nature of several species, proteomic analyses have been performed to further understand the biological basis of the infectious process [ 37 ] and to comprehend the mechanism required for the biologic control [ 38 ]. The biotechnological potential of fungal enzymes for the biosynthesis of products of significance has also driven an intense activity of proteomics research, more recently extended to the investigation of species from the extremes of life [ 24 , 39 ]. Several species possess excellent ability for protein production which provides one of the important aspects for identifying the protein function [ 40 ].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Muggia

Ametrano

Sterflinger

et al. 2020

Life

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Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

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Section: Proteomics Advances In Ascomycotamentioning

confidence: 99%

Section: Proteomics Advances In Ascomycotamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Muggia

Ametrano

Sterflinger

et al. 2020

Life

Self Cite

View full text Add to dashboard Cite

show abstract

“…For example, the application of proteomics and gene-recombinant protein modification technologies helps to improve the characteristics of enzymes, such as thermal stability, higher activity, specificity, pH, solvent tolerance, etc. (Antikainen and Martin, 2005;Tesei et al, 2019). The information provided by genomics, proteomics, and transcriptome technologies can be used to identify new targets and metabolic engineering for the production of strains in the biorefinery industry.…”

Section: Recent Advancements In Extremozymes Discovery With Multi-omimentioning

confidence: 99%

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

Zhu

Adebisi

Ahmad

et al. 2020

Front. Bioeng. Biotechnol.

104

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The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.

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