Unlocking the distinctive enzymatic functions of the early plant biomass deconstructive genes in a brown rot fungus by cell-free protein expression.

Saprotrophic fungi that cause brown rot of woody biomass evolved a distinctive mechanism that relies on reactive oxygen species (ROS) to kick-start lignocellulosic polymers' deconstruction. These ROS agents are generated at incipient decay stages through a series of redox relays that shuttle electrons from fungus's central metabolism to extracellular Fenton chemistry. A list of genes has been suggested encoding the enzyme catalysts of the redox processes involved in ROS's function. However, navigating the functions of the encoded enzymes has been challenging due to the lack of a rapid method for protein synthesis. Here, we employed cell-free expression system to synthesize four redox or degradative enzymes, which were identified, by transcriptomic data, as conserved players of the ROS oxidation phase across brown rot fungal species. All four enzymes were successfully expressed and showed activities that enable confident assignment of function, namely, benzoquinone reductase (BQR), ferric reductase, α-L-arabinofuranosidase (ABF), and heme-thiolate peroxidase (HTP). Detailed analysis of their catalytic features within the context of brown rot environments allowed us to interpret their roles during ROS-driven wood decomposition. Specifically, we validated the functions of BQR as the driver redox enzyme of Fenton cycles and reconstructed its interactions with the co-occurring HTP or laccase and ABF. Taken together, this research demonstrated that the cell-free expression platform is adequate for synthesizing functional fungal enzymes and provided an alternative route for the rapid characterization of fungal proteins, escalating our understanding of the distinctive biocatalyst system for plant biomass conversion.IMPORTANCEBrown rot fungi are efficient wood decomposers in nature, and their unique degradative systems harbor untapped catalysts pursued by the biorefinery and bioremediation industries. While the use of "omics" platforms has recently uncovered the key "oxidative-hydrolytic" mechanisms that allow these fungi to attack lignocellulose, individual protein characterization is lagging behind due to the lack of a robust method for rapid synthesis of crucial fungal enzymes. This work delves into the studies of biochemical functions of brown rot enzymes using a rapid, cell-free expression platform, which allowed the successful depictions of enzymes' catalytic features, their interactions with Fenton chemistry, and their roles played during the incipient stage of brown rot when fungus sets off the reactive oxygen species for oxidative degradation. We expect this research could illuminate cell-free protein expression system's use to fulfill the increasing need for functional studies of fungal enzymes, advancing the discoveries of novel biomass-converting catalysts.

Towards an Understanding of Oxidative Damage in an α-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach.

Trichoderma reesei is a "workhorse" fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on α-L-arabinofuranosidase, an enzyme important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render this enzyme inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of the protein when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized protein. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized protein, implying a less favorable reaction pathway. These results reveal the basis for loss of function in this carbohydrate active enzyme (CAZY) in the commercially relevant fungus T. reesei.

Oxidative Damage Control during Decay of Wood by Brown Rot Fungus Using Oxygen Radicals.

Brown rot wood-degrading fungi deploy reactive oxygen species (ROS) to loosen plant cell walls and enable selective polysaccharide extraction. These ROS, including Fenton-generated hydroxyl radicals (HO˙), react with little specificity and risk damaging hyphae and secreted enzymes. Recently, it was shown that brown rot fungi reduce this risk, in part, by differentially expressing genes involved in HO˙ generation ahead of those coding carbohydrate-active enzymes (CAZYs). However, there are notable exceptions to this pattern, and we hypothesized that brown rot fungi would require additional extracellular mechanisms to limit ROS damage. To assess this, we grew Postia placenta directionally on wood wafers to spatially segregate early from later decay stages. Extracellular HO˙ production (avoidance) and quenching (suppression) capacities among the stages were analyzed, along with the ability of secreted CAZYs to maintain activity postoxidation (tolerance). First, we found that H2O2 and Fe2+ concentrations in the extracellular environment were conducive to HO˙ production in early (H2O2:Fe2+ ratio 2:1) but not later (ratio 1:131) stages of decay. Second, we found that ABTS radical cation quenching (antioxidant capacity) was higher in later decay stages, coincident with higher fungal phenolic concentrations. Third, by surveying enzyme activities before/after exposure to Fenton-generated HO˙, we found that CAZYs secreted early, amid HO˙, were more tolerant of oxidative stress than those expressed later and were more tolerant than homologs in the model CAZY producer Trichoderma reesei Collectively, this indicates that P. placenta uses avoidance, suppression, and tolerance mechanisms, extracellularly, to complement intracellular differential expression, enabling this brown rot fungus to use ROS to degrade wood.IMPORTANCE Wood is one of the largest pools of carbon on Earth, and its decomposition is dominated in most systems by fungi. Wood-degrading fungi specialize in extracting sugars bound within lignin, either by removing lignin first (white rot) or by using Fenton-generated reactive oxygen species (ROS) to "loosen" wood cell walls, enabling selective sugar extraction (brown rot). Although white rot lignin-degrading pathways are well characterized, there are many uncertainties in brown rot fungal mechanisms. Our study addressed a key uncertainty in how brown rot fungi deploy ROS without damaging themselves or the enzymes they secrete. In addition to revealing differentially expressed genes to promote ROS generation only in early decay, our study revealed three spatial control mechanisms to avoid/tolerate ROS: (i) constraining Fenton reactant concentrations (H2O2, Fe2+), (ii) quenching ROS via antioxidants, and (iii) secreting ROS-tolerant enzymes. These results not only offer insight into natural decomposition pathways but also generate targets for biotechnological development.

Evaluation of colorimetric assays for determination of H2O2in planta during fungal wood decomposition.

Hydrogen peroxide (H2O2) plays a critical role in generating oxygen radicals as fungi attack and deconstruct plant cell walls. Its concentrations in planta, however, are often low during decomposition and evade detection by traditional methods. Here, we compared relevant methods and selected the best based on detection limits and selectivity.

DISEÑO Y PRODUCCIÓN DE UNA HERRAMIENTA MOLECULAR PARA EL ESTUDIO DEL N-TERMINAL DE LA NICOTINAMIDA MONONUCLEÓTIDO ADENILIL TRANSFERASA (NMNAT) EN Leishmania braziliensis / DESIGN AND PRODUCTION OF A MOLECULAR TOOL TO STUDY OF N-TERMINAL NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE (NMNAT) IN Leishmania braziliensis / DESIGN E PRODUÇÃO DE UMA FERRAMENTA MOLECULAR PARA O ESTUDO DO TERMINALN DA NICOTINAMIDA CICLASE MONONUCLEÓTIDO TRANSFERASE (NMNAT) EM Leishmania braziliensis

Leishmania braziliensis es un parásito protozoario causante de la mayor parte de casos de leishmaniasis cutánea en al menos quince países del continente americano. La Organización Mundial de la Salud (OMS) ha reportado que cerca de doce millones de personas están infectadas en el mundo y que este número aumenta cada año. Debido al delicado problema de salud pública derivado de la prevalencia de esta enfermedad se hace necesario el estudio del metabolismo de este parásito. En tal sentido se ha estudiado la proteína NMNAT de este parásito, la cual es una enzima central del metabolismo de todos los organismos al estar encargada de la síntesis del NAD+, un importante cofactor en reacciones redox de procesos centrales del metabolismo celular. En la NMNAT de L. braziliensis se ha encontrado una secuencia de 44 aminoácidos en el extremo N-terminal carente de homología con la proteína del hospedero. En este estudio se produjeron anticuerpos IgG específicos contra esta secuencia, utilizando como antígenos péptidos que contuvieran la secuencia mencionada. Los anticuerpos obtenidos mostraron un reconocimiento de la NMNAT recombinante de L. braziliensis mediante ensayo por western blot.

Leishmania braziliensis is a protozoan which is cause of the most of the cutaneous leishmaniasis cases in at least 15 countries from America. World Health Organization (WHO) has reported that around 12 millions of people are infected in the world and this number increase every year. Because of the delicate problem of public health due to the prevalence of this disease, it is necessary the metabolism study in this parasite. In this way has been studied NMNAT protein of the parasite, which is a central enzyme of the metabolism of all organisms, since it is in charge of synthesizing NAD+, an important cofactor in oxidation-reduction reactions of central processes in the cellular metabolism. In The NMNAT of L. has been found a 43 amino acids sequence in the N terminal, which does not have homology with the protein in the human host. In this study were produced IgG antibodies against this sequence, using like antigens peptides that had the mentioned sequence. The produced antibodies recognized the recombinant NMNAT of L. braziliensis through western blot assay.

Leishmania braziliensis é um parasita protozoário que causa a maioria dos casos de leishmaniose cutânea em pelo menos 15 países das Américas. A Organização Mundial de Saúde (OMS) informou que cerca de 12 milhões de pessoas estão infectadas em todo o mundo e esse número aumenta a cada ano. Devido ao delicado problema de saúde pública decorrentes da prevalência desta doença é necessário estudar o metabolismo do parasita. A este respeito temos estudado a proteína NMNAT deste parasita, que é uma enzima central no metabolismo de todos os organismos de estar envolvido na produção de NAD+, um importante cofator em reações redox de processos centrais de celulares metabolismo. No L. braziliensis NMNAT encontrou uma seqüencia de 43 aminoácidos no terminal N homologia com a proteína faltando host. Este estudo produziu anticorpos IgG específicos para esta seqüência, usando como peptídeos de antígeno contendo a seqüência mencionada. Os anticorpos obtidos mostraram um reconhecimento da NMNAT L. braziliensis recombinantes por meio de julgamento por western blot.