Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi

Filho, Jaire Alves Ferreira; Rosolen, Rafaela Rossi; Almeida, Déborah Aires; Azevedo, Paulo; Motta, Maria Lorenza Leal; Aono, Alexandre Hild; Santos, Clelton A.; Horta, Maria Augusta Crivelente; Souza, Anete Pereira de

doi:10.1007/s13205-021-03032-y

Cited by 4 publications

(3 citation statements)

References 224 publications

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“…Co-expression network analysis is a biologically driven data analysis technique that has been used extensively to extract modules and genes that function in certain biological pathways. Many genes playing vital roles in multiple biological processes or molecular functions have been successfully identified using this methodology ( Filho et al, 2021 ; Zainal-Abidin et al, 2022 ). In the present study, two modules that were closely related to the F. oxysporum infection process in all pathogen-host systems were identified and their hub genes were validated.…”

Section: Discussionmentioning

confidence: 99%

Meta-analysis of fungal plant pathogen Fusarium oxysporum infection-related gene profiles using transcriptome datasets

Cai

Liu

et al. 2022

Front. Microbiol.

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Fusarium oxysporum is a serious soil-borne fungal pathogen that affects the production of many economically important crops worldwide. Recent reports suggest that this fungus is becoming the dominant species in soil and could become the main infectious fungus in the future. However, the infection mechanisms employed by F. oxysporum are poorly understood. In the present study, using a network meta-analysis technique and public transcriptome datasets for different F. oxysporum and plant interactions, we aimed to explore the common molecular infection strategy used by this fungus and to identify vital genes involved in this process. Principle component analysis showed that all the fungal culture samples from different datasets were clustered together, and were clearly separated from the infection samples, suggesting the feasibility of an integrated analysis of heterogeneous datasets. A total of 335 common differentially expressed genes (DEGs) were identified among these samples, of which 262 were upregulated and 73 were downregulated significantly across the datasets. The most enriched functional categories of the common DEGs were carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Nine co-expression modules were identified, and two modules, the turquoise module and the blue module, correlated positively and negatively with all the infection processes, respectively. Co-expression networks were constructed for these two modules and hub genes were identified and validated. Our results comprise a cross fungal-host interaction resource, highlighting the use of a network biology approach to gain molecular insights.

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Section: Discussionmentioning

confidence: 99%

Meta-analysis of fungal plant pathogen Fusarium oxysporum infection-related gene profiles using transcriptome datasets

Cai

Liu

et al. 2022

Front. Microbiol.

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“…Filamentous fungi are important for the biotechnological production of industrial enzymes and chemical products ( 4 – 6 ). Thus, studies on either transcriptional regulation or protein secretion are critical for characterizing and constructing complex expression systems involving filamentous fungi ( 63 , 64 ). Lignocellulolytic enzyme production in saprophytic filamentous fungi is controlled at the transcriptional level via the activities of regulators, such as CreA/CRE-1 ( 23 , 28 , 29 ), CLR-1/A, CLR-2/B ( 25 – 27 ), and XYR-1/XLR-1/XInR ( 24 , 31 – 33 ), or at the posttranslational level through the HAC-1 mediated UPR signaling pathway ( 17 , 18 , 47 ).…”

Section: Discussionmentioning

confidence: 99%

MtTRC-1, a Novel Transcription Factor, Regulates Cellulase Production via Directly Modulating the Genes Expression of the Mthac-1 and Mtcbh-1 in Myceliophthora thermophila

Liu

et al. 2022

Appl Environ Microbiol

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In the present study, we characterized a novel regulator MtTRC-1 in M. thermophila , which regulated cellulase production through direct transcriptional regulation of the Mthac-1 and Mtcbh-1 genes. Our data demonstrated that MtHAC-1 is a key factor for the cellulase secretion capacity of M. thermophila .

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“…Many concepts for developing industrial products that can be built to optimize the degrading environment have been pointed out by researchers [ 158 ]. This diversity of concepts for improving degradation rates can be seen in significant patent disclosures [ 159 , 160 ].…”

Section: Design For Degradationmentioning

confidence: 99%

A Review on the Modification of Cellulose and Its Applications

et al. 2022

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The latest advancements in cellulose and its derivatives are the subject of this study. We summarize the characteristics, modifications, applications, and properties of cellulose. Here, we discuss new breakthroughs in modified cellulose that allow for enhanced control. In addition to standard approaches, improvements in different techniques employed for cellulose and its derivatives are the subject of this review. The various strategies for synthetic polymers are also discussed. The recent advancements in polymer production allow for more precise control, and make it possible to make functional celluloses with better physical qualities. For sustainability and environmental preservation, the development of cellulose green processing is the most abundant renewable substance in nature. The discovery of cellulose disintegration opens up new possibilities for sustainable techniques. Based on the review of recent scientific literature, we believe that additional chemical units of cellulose solubility should be used. This evaluation will evaluate the sustainability of biomass and processing the greenness for the long term. It appears not only crucial to dissolution, but also to the greenness of any process.

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Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi

Cited by 4 publications

References 224 publications

Meta-analysis of fungal plant pathogen Fusarium oxysporum infection-related gene profiles using transcriptome datasets

Meta-analysis of fungal plant pathogen Fusarium oxysporum infection-related gene profiles using transcriptome datasets

MtTRC-1, a Novel Transcription Factor, Regulates Cellulase Production via Directly Modulating the Genes Expression of the Mthac-1 and Mtcbh-1 in Myceliophthora thermophila

A Review on the Modification of Cellulose and Its Applications

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