Plant virus community structuring is shaped by habitat heterogeneity and traits for host plant resource utilisation.

Host plants provide resources critical to viruses and the spatial structuring of plant communities affects the niches available for colonisation and disease emergence. However, large gaps remain in the understanding of mechanisms that govern plant-virus disease ecology across heterogeneous plant assemblages. We combine high-throughput sequencing, network, and metacommunity approaches to test whether habitat heterogeneity in plant community composition corresponded with virus resource utilisation traits of transmission mode and host range.

A new halotolerant xylanase from expressed in with catalytic efficiency improved by site-directed mutagenesis.

Daily agro-industrial waste, primarily cellulose, lignin, and hemicellulose, poses a significant environmental challenge. Harnessing lignocellulolytic enzymes, particularly endo-1,4-β-xylanases, for efficient saccharification is a cost-effective strategy, transforming biomass into high-value products. This study focuses on the cloning, expression, site-directed mutagenesis, purification, three-dimensional modeling, and characterization of the recombinant endo-1,4-β-xylanase (XlnA) from in .

Ecological Strategies for Resource Use by Three Bromoviruses in Anthropic and Wild Plant Communities.

Ecological strategies for resource utilisation are important features of pathogens, yet have been overshadowed by stronger interest in genetic mechanisms underlying disease emergence. The purpose of this study is to ask whether host range and transmission traits translate into ecological strategies for host-species utilisation in a heterogeneous ecosystem, and whether host utilisation corresponds to genetic differentiation among three bromoviruses. We combine high-throughput sequencing and population genomics with analyses of species co-occurrence to unravel the ecological strategies of the viruses across four habitat types.

Tobamoviruses Show Broad Host Ranges and Little Genetic Diversity Among Four Habitat Types of a Heterogeneous Ecosystem.

Host ranges of plant viruses are poorly known, as studies have focused on pathogenic viruses in crops and adjacent wild plants. High-throughput sequencing (HTS) avoids the bias toward plant-virus interactions that result in disease. Here we study the host ranges of tobamoviruses, important pathogens of crops, using HTS analyses of an extensive sample of plant communities in four habitats of a heterogeneous ecosystem.

Reversion of a resistance-breaking mutation shows reversion costs and high virus diversity at necrotic local lesions.

An instance of host range evolution relevant to plant virus disease control is resistance breaking. Resistance breaking can be hindered by across-host fitness trade-offs generated by negative effects of resistance-breaking mutations on the virus fitness in susceptible hosts. Different mutations in pepper mild mottle virus (PMMoV) coat protein result in the breaking in pepper plants of the resistance determined by the L resistance allele.

Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, , crops, and adjacent wild communities.

The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon () and wild plants of crop (Crop) and adjacent boundaries (Edge).

Structuring of plant communities across agricultural landscape mosaics: the importance of connectivity and the scale of effect.

Background: Plant communities of fragmented agricultural landscapes, are subject to patch isolation and scale-dependent effects. Variation in configuration, composition, and distance from one another affect biological processes of disturbance, productivity, and the movement ecology of species. However, connectivity and spatial structuring among these diverse communities are rarely considered together in the investigation of biological processes.

Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence.

The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data.

Structure-Based Drug Design of Bisubstrate Inhibitors of Phenylethanolamine -Methyltransferase Possessing Low Nanomolar Affinity at Both Substrate Binding Domains.

The enzyme phenylethanolamine -methyltransferase (PNMT, EC 2.1.1.

Genetic variability of watermelon mosaic virus isolates infecting cucurbit crops in Italy.

Watermelon mosaic virus (WMV; genus Potyvirus, family Potyviridae) is responsible for serious cucurbit yield losses worldwide. Different WMV genetic groups have been characterized so far. Among these, the "classical" (CL) group has been present in the Mediterranean basin for 40 years, whereas the "emergent" (EM) group includes isolates that are associated with more-severe symptoms observed since 2000.

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis.

Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon-carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate.

Evolution of plant-virus interactions: host range and virus emergence.

Changes in host range are central to virus emergence. Host range, together with its evolution, is determined by virus intrinsic factors, such as genetic traits determining its fitness in different hosts. Experimental analyses have shown the relevance in host range evolution of across-host fitness trade-offs.

Coinfection Organizes Epidemiological Networks of Viruses and Hosts and Reveals Hubs of Transmission.

Multiple virus infections affect the competence of host plants to transmit disease. The effects of coinfection on transmission are expected to produce ecologically complex pathogen and host-pathogen interactions. However, the prediction of disease risk will rely on untangling nonrandom from random patterns of infection to identify underlying processes that drive these interactions.

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism.

Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data.

Ecological Complexity in Plant Virus Host Range Evolution.

The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution.

Scale dependencies and generalism in host use shape virus prevalence.

Processes that generate the distribution of pathogens and their interactions with hosts are not insensitive to changes in spatial scale. Spatial scales and species traits are often selected intentionally, based on practical considerations, ignoring biases that the scale and type of observation may introduce. Specifically, these biases might change the interpretation of disease-diversity relationships that are reported as either 'dilution' or 'amplification' effects.

Phosphonodifluoropyruvate is a mechanism-based inhibitor of phosphonopyruvate decarboxylase from Bacteroides fragilis.

Bacteroides fragilis, a human pathogen, helps in the formation of intra-abdominal abscesses and is involved in 90% of anaerobic peritoneal infections. Phosphonopyruvate decarboxylase (PnPDC), a thiamin diphosphate (ThDP)-dependent enzyme, plays a key role in the formation of 2-aminoethylphosphonate, a component of the cell wall of B. fragilis.

Environmental heterogeneity and the evolution of plant-virus interactions: Viruses in wild pepper populations.

Understanding host-pathogen interactions requires analyses to address the multiplicity of scales in heterogeneous landscapes. Anthropogenic influence on plant communities, especially cultivation, is a major cause of environmental heterogeneity. We have approached the analysis of how environmental heterogeneity determines plant-virus interactions by studying virus infection in a wild plant currently undergoing incipient domestication, the wild pepper or chiltepin, across its geographical range in Mexico.

Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily.

Benzaldehyde dehydrogenase from Pseudomonas putida (PpBADH) belongs to the Class 3 aldehyde dehydrogenase (ALDH) family. The Class 3 ALDHs are unusual in that they are generally dimeric (rather than tetrameric), relatively non-specific and utilize both NAD+ and NADP+. To date, X-ray structures of three Class 3 ALDHs have been determined, of which only two have cofactor bound, both in the NAD+ form.

Specificity and mechanism of mandelamide hydrolase catalysis.

The best-studied amidase signature (AS) enzyme is probably fatty acid amide hydrolase (FAAH). Closely related to FAAH is mandelamide hydrolase (MAH), whose substrate specificity and mechanism of catalysis are described in this paper. First, we developed a convenient chromogenic substrate, 4-nitrophenylacetamide, for MAH.

The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes.

Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate. It is the penultimate enzyme in both the mandelate pathway and the d-phenylglycine degradation pathway. The ThDP-dependent Enzyme Engineering Database (TEED) now lists more than 800 sequences annotated as BFDCs, including one from Mycobacterium smegmatis (MsBFDC).

Extended reaction scope of thiamine diphosphate dependent cyclohexane-1,2-dione hydrolase: from C-C bond cleavage to C-C bond ligation.

ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the CC bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the CC bond formation, while the ability for CC bond cleavage is still intact.

Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer.

The X-ray structure of benzoylformate decarboxylase (BFDC) from Pseudomonas putida ATCC 12633 shows it to be a tetramer. This was believed to be typical of all thiamin diphosphate-dependent decarboxylases until recently when the structure of KdcA, a branched-chain 2-keto acid decarboxylase from Lactococcus lactis, showed it to be a homodimer. This lent credence to earlier unfolding experiments on pyruvate decarboxylase from Saccharomyces cerevisiae that indicated that it might be active as a dimer.

Identification of charge transfer transitions related to thiamin-bound intermediates on enzymes provides a plethora of signatures useful in mechanistic studies.

Identification of enzyme-bound intermediates via their spectroscopic signatures, which then allows direct monitoring of the kinetic fate of these intermediates, poses a continuing challenge. As an electrophilic covalent catalyst, the thiamin diphosphate (ThDP) coenzyme forms a number of noncovalent and covalent intermediates along its reaction pathways, and multiple UV-vis and circular dichroism (CD) bands have been identified at Rutgers pertinent to several among them. These electronic transitions fall into two classes: those for which the conjugated system provides a reasonable guide to the observed λmax and others in which there is no corresponding conjugated system and the observed CD bands are best ascribed to charge transfer (CT) transitions.