The Role of Arbuscular Mycorrhiza Fungi in the Decomposition of Fresh Residue and Soil Organic Carbon : A Mini-Review

Arbuscular mycorrhizal fungi (AMF) are widespread in terrestrial ecosystems. In addition to their contributions to plant nutrient uptake, AMF also provide many ecological functions including regulation of soil C dynamics. However, both stimulating and retarding soil organic decomposition by AMF have been observed. Here we discuss the possible reasons for such a contradiction. Arbuscular mycorrhizal fungi contribute to soil aggregation mainly through hyphal enmeshment, saprotrophic suppression, and production of glomalin-related soil proteins, while AMF can also stimulate organic decomposition through promoting degradative enzymes, modifying root production and activity, and/or through regulating the microbial community in the mycorrhizosphere and hyphosphere. The role of AMF in C decomposition is strongly dependent on the quality and quantity of different soil C pools. Arbuscular mycorrhizal fungi can stimulate fresh residue decomposition initially through stimulating the decomposition of fresh residues (particularly those having high C/N ratio), whereas for older or decomposed soil organic C, AMF tend to suppress decomposition by promoting soil aggregation. Under elevated CO2 (eCO(2)), AMF show additive effects on residue decomposition, priming effects, and changes in soil a regation. Despite organic decomposition rates differing in the short term and long term following litter experiments, our discussion highlights the role of AMF in organic C dynamics. We hypothesize that AMF would benefit soil C gain in the long term and thereby predict that disturbances that impacts negatively on AMF, such as tillage, residue burning, fertilization, and fungicide application, would lead to soil C decline particularly under eCO(2).Peer reviewe

A Convenient, Rapid, Sensitive, and Reliable Spectrophotometric Assay for Adenylate Kinase Activity

Enzymatic activity assays are essential and critical for the study of enzyme kinetics. Adenylate kinase (Adk) plays a fundamental role in cellular energy and nucleotide homeostasis. To date, assays based on different principles have been used for the determination of Adk activity. Here, we show a spectrophotometric analysis technique to determine Adk activity with bromothymol blue as a pH indicator. We analyzed the effects of substrates and the pH indicator on the assay using orthogonal design and then established the most optimal assay for Adk activity. Subsequently, we evaluated the thermostability of Adk and the inhibitory effect of KCl on Adk activity with this assay. Our results show that this assay is simple, rapid, and precise. It shows great potential as an alternative to the conventional Adk activity assay. Our results also suggest that orthogonal design is an effective approach, which is very suitable for the optimization of complex enzyme reaction conditions

In Situ Synthesis of Silver Nanoparticles on the Polyelectrolyte-Coated Sericin/PVA Film for Enhanced Antibacterial Application

To develop silk sericin (SS) as a potential antibacterial biomaterial, a novel composite of polyelectrolyte multilayers (PEMs) coated sericin/poly(vinyl alcohol) (SS/PVA) film modified with silver nanoparticles (AgNPs) has been developed using a layer-by-layer assembly technique and ultraviolet-assisted AgNPs synthesis method. Ag ions were enriched by PEMs via the electrostatic attraction between Ag ions and PEMs, and then reduced to AgNPs in situ with the assistance of ultraviolet irradiation. PEMs facilitated the high-density growth of AgNPs and protected the synthesized AgNPs due to the formation of a 3D matrix, and thus endowed SS/PVA film with highly effective and durable antibacterial activity. Scanning electron microscopy, energy dispersive spectroscopy, X-ray diffractometry, Fourier transfer infrared spectroscopy, water contact angle, mechanical property and thermogravimetric analysis were applied to characterize SS/PVA, PEMs-SS/PVA and AgNPs-PEMs-SS/PVA films, respectively. AgNPs-PEMs-SS/PVA film has exhibited good mechanical performance, hydrophilicity, water absorption capability as well as excellent and durable antibacterial activity against Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and good stability and degradability. This study has developed a simple method to design and prepare AgNPs-PEMs-SS/PVA film for potential antibacterial application

Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase.

The isonitrile moiety is found in marine sponges and some microbes, where it plays a role in processes such as virulence and metal acquisition. Until recently only one route was known for isonitrile biosynthesis, a condensation reaction that brings together a nitrogen atom of l-Trp/l-Tyr with a carbon atom from ribulose-5-phosphate. With the discovery of ScoE, a mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase from Streptomyces coeruleorubidus, a second route was identified. ScoE forms isonitrile from a glycine adduct, with both the nitrogen and carbon atoms coming from the same glycyl moiety. This reaction is part of the nonribosomal biosynthetic pathway of isonitrile lipopeptides. Here, we present structural, biochemical, and computational investigations of the mechanism of isonitrile formation by ScoE, an unprecedented reaction in the mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase superfamily. The stoichiometry of this enzymatic reaction is measured, and multiple high-resolution (1.45-1.96 Å resolution) crystal structures of Fe(II)-bound ScoE are presented, providing insight into the binding of substrate, (R)-3-((carboxylmethyl)amino)butanoic acid (CABA), cosubstrate α-ketoglutarate, and an Fe(IV)=O mimic oxovanadium. Comparison to a previously published crystal structure of ScoE suggests that ScoE has an "inducible" α-ketoglutarate binding site, in which two residues arginine-157 and histidine-299 move by approximately 10 Å from the surface of the protein into the active site to create a transient α-ketoglutarate binding pocket. Together, data from structural analyses, site-directed mutagenesis, and computation provide insight into the mode of α-ketoglutarate binding, the mechanism of isonitrile formation, and how the structure of ScoE has been adapted to perform this unusual chemical reaction

Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase

The isonitrile moiety is found in marine sponges and some microbes, where it plays a role in processes such as virulence and metal acquisition. Until recently only one route was known for isonitrile biosynthesis, a condensation reaction that brings together a nitrogen atom of L-Trp/L-Tyr with a carbon atom from ribulose-5-phosphate. With the discovery of ScoE, a mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase from Streptomyces coeruleorubidus, a second route was identified. ScoE forms isonitrile from a glycine adduct, with both the nitrogen and carbon atoms coming from the same glycyl moiety. This reaction is part of the nonribosomal biosynthetic pathway of isonitrile lipopeptides. Here, we present structural, biochemical, and computational investigations of the mechanism of isonitrile formation by ScoE, an unprecedented reaction in the mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase superfamily. The stoichiometry of this enzymatic reaction is measured, and multiple high-resolution (1.45–1.96 Å resolution) crystal structures of Fe(II)-bound ScoE are presented, providing insight into the binding of substrate, (R)-3-((carboxylmethyl)amino)butanoic acid (CABA), cosubstrate α-ketoglutarate, and an Fe(IV)=O mimic oxovanadium. Comparison to a previously published crystal structure of ScoE suggests that ScoE has an “inducible” α-ketoglutarate binding site, in which two residues arginine-157 and histidine-299 move by approximately 10 Å from the surface of the protein into the active site to create a transient α-ketoglutarate binding pocket. Together, data from structural analyses, site-directed mutagenesis, and computation provide insight into the mode of α-ketoglutarate binding, the mechanism of isonitrile formation, and how the structure of ScoE has been adapted to perform this unusual chemical reaction

Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase.

The isonitrile moiety is found in marine sponges and some microbes, where it plays a role in processes such as virulence and metal acquisition. Until recently only one route was known for isonitrile biosynthesis, a condensation reaction that brings together a nitrogen atom of l-Trp/l-Tyr with a carbon atom from ribulose-5-phosphate. With the discovery of ScoE, a mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase from Streptomyces coeruleorubidus, a second route was identified. ScoE forms isonitrile from a glycine adduct, with both the nitrogen and carbon atoms coming from the same glycyl moiety. This reaction is part of the nonribosomal biosynthetic pathway of isonitrile lipopeptides. Here, we present structural, biochemical, and computational investigations of the mechanism of isonitrile formation by ScoE, an unprecedented reaction in the mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase superfamily. The stoichiometry of this enzymatic reaction is measured, and multiple high-resolution (1.45-1.96 Å resolution) crystal structures of Fe(II)-bound ScoE are presented, providing insight into the binding of substrate, (R)-3-((carboxylmethyl)amino)butanoic acid (CABA), cosubstrate α-ketoglutarate, and an Fe(IV)=O mimic oxovanadium. Comparison to a previously published crystal structure of ScoE suggests that ScoE has an "inducible" α-ketoglutarate binding site, in which two residues arginine-157 and histidine-299 move by approximately 10 Å from the surface of the protein into the active site to create a transient α-ketoglutarate binding pocket. Together, data from structural analyses, site-directed mutagenesis, and computation provide insight into the mode of α-ketoglutarate binding, the mechanism of isonitrile formation, and how the structure of ScoE has been adapted to perform this unusual chemical reaction