Genome mining of fungal lipid-degrading enzymes for industrial applications

Vorapreeda, Tayvich; Thammarongtham, Chinae; Cheevadhanarak, Supapon; Laoteng, Kobkul

doi:10.1099/mic.0.000127

Cited by 15 publications

(9 citation statements)

References 108 publications

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“…Isolation and screening of microorganisms have been applied as a strategy to obtain strains able to produce industrially-relevant enzymes. Considering the increased number of available genomes, new rational approaches, such as genome mining, provide an attractive alternative to labor-intense screenings [ 1 , 2 ]. This is also an interesting alternative to target the prospection of enzymes in fungi deposited in culture collections.…”

Section: Introductionmentioning

confidence: 99%

Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability

et al. 2018

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BackgroundPeptidases (EC 3.4) consist of a large group of hydrolytic enzymes that catalyze the hydrolysis of proteins accounting for approximately 65% of the total worldwide enzyme production. Peptidases from thermophilic fungi have adaptations to high temperature that makes them adequate for biotechnological application. In the present study, we profiled the genomes of heat-tolerant fungi and phylogenetically related mesophilic species for genes encoding for peptidases and their putative adaptations for thermostability.ResultsWe generated an extensive catalogue of these enzymes ranging from 241 to 820 peptidase genes in the genomes of 23 fungi. Thermophilic species presented the smallest number of peptidases encoding genes in relation to mesophilic species, and the peptidases families with a greater number of genes were the most affected. We observed differences in peptidases in thermophilic species in comparison to mesophilic counterparts, at (i) the genome level: a great reduction in the number of peptidases encoding genes that harbored a higher number of copies; (ii) in the primary protein structure: shifts in proportion of single or groups of amino acids; and (iii) in the three-dimensional structure: reduction in the number of internal cavities. Similar results were reported for extremely thermophilic proteins, but here we show for the first time that several changes also occurred on the moderate thermophilic enzymes of fungi. In regards to the amino acids composition, peptidases from thermophilic species in relation to the mesophilic ones, contained a larger proportion of Ala, Glu, Gly, Pro, Arg and Val residues and a lower number of Cys, His, Ile, Lys, Met, Asn, Gln, Ser, Thr and Trp residues (P < 0.05). Moreover, we observed an increase in the proportion of hydrophobic and charged amino acids and a decrease in polar amino acids.ConclusionsAlthough thermophilic fungi present less genes encoding for peptidases, these have adaptations that could play a role in thermal resistance from genome to protein structure level.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4549-5) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability

et al. 2018

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“…In addition to the common consensus signature motifs (GxSxG and GDSL), several studies have reported a set of specific consensus motifs using alignment of similar homologous sequences. For example, the GxxR motif (GxxR), the GTK motif and the unidentified motif (SLLTxxTPH) are though to play a role in substrate selectivity in the steryl ester hydrolase family, the triacylglycerol lipase family and the acylglycerol lipase family, respectively (Vorapreeda et al 2015). These motifs provide specific biological benefits relevant to the function of the c Fig.…”

Section: Homology-based Mining Of Lipase Genesmentioning

confidence: 99%

“…Therefore, integrative analysis of amino acid sequence similarity with information relevant to conserved structural domains was introduced to classify lipid-degrading enzymes in eukaryotic microorganisms. Based on this strategy, the fungal lipid-degrading enzymes were recently classified into seven families, which have led to improved functional prediction and categorization of fungal enzymes (Vorapreeda et al 2015). The functional conserved domains of the interesting proteins may be identified simply by comparing the amino acid sequences against conserved protein family databases, such as Pfam (Finn et al 2016) and CDD (Marchler-Bauer et al 2015).…”

Section: Homology-based Mining Of Lipase Genesmentioning

confidence: 99%

“…Lipid-degrading enzymes associated with eukaryotic microorganisms (yeast and fungi) are more complicated than bacterial enzymes because of their structural sequences, which may contain more than a single domain, such as triacylglycerol lipases and steryl ester hydrolase (Vorapreeda et al 2015). Therefore, integrative analysis of amino acid sequence similarity with information relevant to conserved structural domains was introduced to classify lipid-degrading enzymes in eukaryotic microorganisms.…”

Section: Homology-based Mining Of Lipase Genesmentioning

confidence: 99%

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Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

Vorapreeda

Thammarongtham

Laoteng

2016

World J Microbiol Biotechnol

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Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.

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“…Asia, in particular China, has focused on economically important fungi in many genome projects. The landscape of Asian genomic and functional genomic projects have concentrated on areas, such as plant and human pathogenic fungi [21], fungal-host interactions [77,78], fungi as biocontrol agents [79], fungi as food [80] and medicinal fungi [20,81]. Asian large scale sequencing bodies, such as Beijing Genomics Institute (China), Macrogen (Korea), Chun Lab (Korea), Softbank (Japan), Temasek (Singapore), Prenetics (Hong Kong), Xcode (India) and Genomico (Iran), have also been collaborating with large scale fungal genomic projects.…”

Section: Genomicsmentioning

confidence: 99%

The rise of mycology in Asia

Hyde¹,

Chethana²,

Jayawardena³

et al. 2020

ScienceAsia

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Mycology was a well-studied discipline in Australia and New Zealand, Europe, South Africa and the USA. In Asia (with the exception of Japan) and South America, the fungi were generally poorly known and studied, except for the result of forays from some American and European mycologists. However, in the last 20 years, the situation has changed. With the development of Asian economies, the funding for science research and development has greatly increased. Mycological research has also diversified in many fields. Many studies have focused on applied aspects and new journals and websites have been established as a platform for Asian mycologists to publish their research. This paper will briefly review the history of the study of fungi in Asia and then discuss how it advanced during the last two decades. It will examine the current situation using case studies in plant pathogens, terrestrial saprobes, aquatic fungi, evolution studies, genomics and applied mycology and biotechnology. Finally, it will suggest research that is needed in the future.

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Genome mining of fungal lipid-degrading enzymes for industrial applications

Cited by 15 publications

References 108 publications

Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability

Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

The rise of mycology in Asia

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