Lignocellulose degradation mechanisms across the Tree of Life

Cragg, Simon M.; Beckham, Gregg T.; Bruce, Neil C.; Bugg, Timothy D. H.; Distel, Daniel L.; Dupree, Paul; Etxabe, Amaia Green; Goodell, Barry; Jellison, Jody; McGeehan, J.E.; McQueen‐Mason, Simon J.; Schnorr, Kirk; Walton, Paul H.; Watts, Joy E. M.; Zimmer, Martin

doi:10.1016/j.cbpa.2015.10.018

Cited by 515 publications

(382 citation statements)

References 74 publications

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“…The expression of genes encoding diverse lignocellulose-degrading enzymes is affected by fungi, substrates, culture conditions, etc. (Cragg et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

Zhang

Wang

et al. 2017

BioResources

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The Trametes versicolor genome is predicted to encode many enzymes that effectively degrade lignin, making it a potentially useful tool for biopulping. However, the wood degradation mechanism of T. versicolor is not clear. To identify the enzymes that contribute to lignocellulose degradation, changes in the T. versicolor transcriptome during growth on poplar wood, relative to growth on glucose medium, were evaluated. Eight hundred and fifty-three genes were differentially expressed, with 360 genes up-regulated and 493 genes were down-regulated on poplar wood. Notably, most genes involved in lignin degradation were upregulated, including eight lignin peroxidase (LiP) genes. Genes encoding cellulose and hemicellulose degrading-enzymes were mostly downregulated, including six endo-β-1,4-glucanase genes and three cellobiohydrolase I genes. These results characterized transcriptomic changes related to lignocellulose degradation. This information could be used to develop T. versicolor as a tool to improve the efficiency of lignin degradation or to provide a theoretical foundation for a new paper pulp manufacturing process.

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“…The expression of genes encoding diverse lignocellulose-degrading enzymes is affected by fungi, substrates, culture conditions, etc. (Cragg et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

Zhang

Wang

et al. 2017

BioResources

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“…Decomposition of the primary component, cellulose, is catalyzed by glycoside hydrolase (GH) enzymes, which are found ubiquitously in nature (2); therefore, improved catalytic efficiency of cellulose decomposition enzymes would help biomass to compete with non-renewable carbon sources. This motivates molecular-level studies into GH enzymatic mechanisms, as such understanding has previously proven invaluable in efforts to engineer variants with increased activities (3)(4)(5).…”

Section: Introductionmentioning

confidence: 99%

Advantages of a distant cellulase catalytic base

Burgin

Ståhlberg

Mayes

2018

Journal of Biological Chemistry

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The inverting glycoside hydrolase Trichoderma reesei (Hypocrea jecorina) Cel6A is a promising candidate for protein engineering for more economical production of biofuels. Until recently, its catalytic mechanism had been uncertain: the best candidate residue to serve as a catalytic base, D175, is further from the glycosidic cleavage site than in other glycoside hydrolase enzymes. Recent unbiased transition path sampling simulations revealed the hydrolytic mechanism for this more distant base, employing a water wire; however, it is not clear why the enzyme employs a more distant catalytic base, a highly-conserved feature among homologs across different kingdoms. In this work, we describe molecular dynamics simulations designed to uncover how a base with a longer side chain, as in a D175E mutant, affects procession and active site alignment in the Michaelis complex. We show that the hydrogen bond network is tuned to the shorter aspartate side chain, and that a longer glutamate side chain inhibits procession as well as being less likely to adopt a catalytically productive conformation. Furthermore, we draw comparisons between the active site in TrCel6A and another inverting, processive cellulase to deduce the contribution of the wire water to the overall enzyme function, revealing that the more distant catalytic base enhances product release. Our results can inform efforts in the study and design of enzymes by demonstrating how counterintuitive sacrifices in chemical reactivity can have worthwhile benefits for other steps in the catalytic cycle.In order to tap into the deep reservoir of renewable energy represented by fuels derived from plant matter, an economical means of converting lignocellulose is required (1). Decomposition of the primary component, cellulose, is catalyzed by glycoside hydrolase (GH) enzymes, which are found ubiquitously in nature (2); therefore, improved catalytic efficiency of cellulose decomposition enzymes would help biomass to compete with non-renewable carbon sources. This motivates molecular-level studies into GH enzymatic mechanisms, as such understanding has previously proven invaluable in efforts to engineer variants with increased activities (3)(4)(5).A particularly important GH enzyme is Trichoderma reesei Cel6A (TrCel6A), which plays a key synergistic role in industrial enzyme cocktails for cellulose digestion. This enzyme is a cellobiohydrolase of GH family 6, which cleave β-1,4 glycosidic bonds processively along cellulose chains, from the non-reducing towards the reducing end, to release the glucose dimer cellobiose as the main product (6). This processive mode of action is believed to be key to their efficiency on highly crystalline cellulose. Glycoside hydrolase family 6 (GH6) enzymes exhibit a range of activity on a continuum between cellobiohydrolase processive activity and endoglucanase activity, characterized by cleavage of internal bonds (7)(8)(9)(10) Advantages of a Distant Cellulase Catalytic Basegenerally exhibit higher catalytic rate constants, only show app...

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“…It is composed of cellulose, hemicellulose and pectin (recently reviewed in [8]). Hemicellulose can further be divided into three principal classes of polymers: xylan, mannan and xyloglucan [10].…”

Section: Introductionmentioning

confidence: 99%

D-galactose catabolism inPenicillium chrysogenum: Expression analysis of the structural genes of the Leloir pathway

Jónás

Fekete

Németh

et al. 2016

Acta Biologica Hungarica

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In this study, we analyzed the expression of the structural genes encoding the five enzymes comprising the Leloir pathway of D-galactose catabolism in the industrial cell factory Penicillium chrysogenum on various carbon sources. The genome of P. chrysogenum contains a putative galactokinase gene at the annotated locus Pc13g10140, the product of which shows strong structural similarity to yeast galactokinase that was expressed on lactose and D-galactose only. The expression profile of the galactose-1-phosphate uridylyl transferase gene at annotated locus Pc15g00140 was essentially similar to that of galactokinase. This is in contrast to the results from other fungi such as Aspergillus nidulans, Trichoderma reesei and A. niger, where the ortholog galactokinase and galactose-1-phosphate uridylyl transferase genes were constitutively expressed. As for the UDP-galactose-4-epimerase encoding gene, five candidates were identified. We could not detect Pc16g12790, Pc21g12170 and Pc20g06140 expression on any of the carbon sources tested, while for the other two loci (Pc21g10370 and Pc18g01080) transcripts were clearly observed under all tested conditions. Like the 4-epimerase specified at locus Pc21g10370, the other two structural Leloir pathway genes -UDP-glucose pyrophosphorylase (Pc21g12790) and phosphoglucomutase (Pc18g01390) -were expressed constitutively at high levels as can be expected from their indispensable function in fungal cell wall formation.

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Lignocellulose degradation mechanisms across the Tree of Life

Cited by 515 publications

References 74 publications

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

Advantages of a distant cellulase catalytic base

D-galactose catabolism inPenicillium chrysogenum: Expression analysis of the structural genes of the Leloir pathway

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