Applying biochemical and structural characterization of hydroxycinnamate catabolic enzymes from soil metagenome for lignin valorization strategies

Gonçalves, Thiago Augusto; Sodré, Victoria; Silva, Stephanie Nemesio da; Vilela, Nathália; Tomazetto, Geizecler; Araújo, Juscemácia N.; Muniz, J.R.C.; Fill, Taícia Pacheco; Damásio, André; Garcia, Wânius; Squina, Fábio M.

doi:10.1007/s00253-022-11885-3

Cited by 5 publications

(1 citation statement)

References 60 publications

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“…The biocatalytic conversion of ferulic acid can be useful for the production of desired chemicals [ 46 , 54 , 55 ]. Ferulic acid is usually converted to vanillin by FCS and FCHL with ATP consumption in two steps [ 56 , 57 ]: (i) CoA-thioesterification of ferulic acid by FCS, and (ii) hydration of feruloyl-CoA by FCHL.…”

Section: Discussionmentioning

confidence: 99%

Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production

Vilela

Tomazetto

Gonçalves

et al. 2023

Biotechnol Biofuels

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Background Lignin is an attractive alternative for producing biobased chemicals. It is the second major component of the plant cell wall and is an abundant natural source of aromatic compounds. Lignin degradation using microbial oxidative enzymes that depolymerize lignin and catabolize aromatic compounds into central metabolic intermediates is a promising strategy for lignin valorization. However, the intrinsic heterogeneity and recalcitrance of lignin severely hinder its biocatalytic conversion. In this context, examining microbial degradation systems can provide a fundamental understanding of the pathways and enzymes that are useful for lignin conversion into biotechnologically relevant compounds. Results Lignin-degrading catabolism of a novel Rhodosporidium fluviale strain LM-2 was characterized using multi-omic strategies. This strain was previously isolated from a ligninolytic microbial consortium and presents a set of enzymes related to lignin depolymerization and aromatic compound catabolism. Furthermore, two catabolic routes for producing 4-vinyl guaiacol and vanillin were identified in R. fluviale LM-2. Conclusions The multi-omic analysis of R. fluviale LM-2, the first for this species, elucidated a repertoire of genes, transcripts, and secreted proteins involved in lignin degradation. This study expands the understanding of ligninolytic metabolism in a non-conventional yeast, which has the potential for future genetic manipulation. Moreover, this work unveiled critical pathways and enzymes that can be exported to other systems, including model organisms, for lignin valorization.

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Section: Discussionmentioning

confidence: 99%

Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production

Vilela

Tomazetto

Gonçalves

et al. 2023

Biotechnol Biofuels

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Sustainable biosynthetic pathways to value-added bioproducts from hydroxycinnamic acids

Tramontina

Ciancaglini

Román

et al. 2023

Appl Microbiol Biotechnol

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Precision enzyme discovery through targeted mining of metagenomic data

Ariaeenejad,

Gharechahi,

Foroozandeh Shahraki

et al. 2024

Nat. Prod. Bioprospect.

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Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.

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Applying biochemical and structural characterization of hydroxycinnamate catabolic enzymes from soil metagenome for lignin valorization strategies

Cited by 5 publications

References 60 publications

Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production

Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production

Sustainable biosynthetic pathways to value-added bioproducts from hydroxycinnamic acids

Precision enzyme discovery through targeted mining of metagenomic data

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