An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics.

We used the Exploris 240 mass spectrometer for non-targeted metabolomics on Saccharomyces cerevisiae strain BY4741 and tested AcquireX software for increasing the number of detectable compounds and Compound Discoverer 3.3 software for identifying compounds by MS spectral library matching. AcquireX increased the number of potentially identifiable compounds by 50% through six iterations of MS acquisition.

Indole Alkaloid Production by the Halo Blight Bacterium Treated with the Phytoalexin Genistein.

When pv. , the bacterium that causes halo blight, induces hypersensitive immunity in common bean leaves, salicylic acid and phytoalexins accumulate at the site of infection. Both salicylic acid and the phytoalexin resveratrol exert antibiotic activities and toxicities in vitro, adversely disrupting the pv.

Disruptive Effects of Resveratrol on a Bacterial Pathogen of Beans.

Upon inoculation, common beans immune to pv race 5 (R5) accumulate resveratrol, a phytoalexin. How resveratrol acts upon on this bacterium is not known, although in animal pathogenic bacteria resveratrol reduces ATPase (ATP = adenosine triphosphate) activity, cellular motility, quorum sensing, and biofilm formation. In this study, mass spectrometry was used to monitor the effects of resveratrol on R5.

The Detriment of Salicylic Acid to the pv. Proteome.

Salicylic acid (SA), a natural product, is the major hormonal regulator of the plant immune system. SA also has antibacterial activity that is not completely elucidated. To gain a better understanding of this, pv.

Salicylic Acid and Phytoalexin Induction by a Bacterium that Causes Halo Blight in Beans.

pv. is a bacterium that causes halo blight in beans. Different varieties of beans have hypersensitive resistance to specific races of .

Bacterial Immobilization and Toxicity Induced by a Bean Plant Immune System.

pv. causes halo blight disease in the common bean . The bacterium invades the leaf apoplast and uses a type III secretion system to inject effector proteins into a bean cell to interfere with the bean immune system.

Proteomic Identification and Meta-Analysis in RNA-Seq de novo Assemblies.

While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity "genes" varied considerably among them.

Genomic Resources for pv. Races 5 and 8.

pv. causes halo blight disease on . Using a long-read DNA sequencing platform, we assembled the genome sequences for pv.

The Proteomics of Resistance to Halo Blight in Common Bean.

Halo blight disease of beans is caused by a gram-negative bacterium, pv. . The disease is prevalent in South America and Africa and causes crop loss for indigent people who rely on beans as a primary source of daily nutrition.

Benzothiadiazole Conditions the Bean Proteome for Immunity to Bean Rust.

The common bean rust fungus reduces harvests of the dry, edible common bean. Natural resistance genes in the plant can provide protection until a fungal strain that breaks resistance emerges. In this study, we demonstrate that benzo(1,2,3)thiadiazole-7-carbothioic acid -methyl ester (BTH) sprayed on susceptible beans induces resistance to common bean rust.

Blistering1 Modulates Virulence Via Vesicle-mediated Protein Secretion.

The blue mold fungus, is a postharvest apple pathogen that contributes to food waste by rotting fruit and by producing harmful mycotoxins ( patulin). To identify genes controlling pathogen virulence, a random T-DNA insertional library was created from wild-type strain R19. One transformant, T625, had reduced virulence in apples, blistered mycelial hyphae, and a T-DNA insertion that abolished transcription of the single copy locus in which it was inserted.

Quantitative Proteomics Reveals a Role for SERINE/ARGININE-Rich 45 in Regulating RNA Metabolism and Modulating Transcriptional Suppression the ASAP Complex in .

Pre-mRNA alternative splicing is a conserved mechanism for eukaryotic cells to leverage existing genetic resources to create a diverse pool of protein products. It is regulated in coordination with other events in RNA metabolism such as transcription, polyadenylation, RNA transport, and nonsense-mediated decay protein networks. SERINE/ARGININE-RICH 45 (SR45) is thought to be a neutral splicing regulator.

Quantitative Proteomic Analysis of Staphylococcus aureus Treated With Punicalagin, a Natural Antibiotic From Pomegranate That Disrupts Iron Homeostasis and Induces SOS.

Staphylococcus aureus, a bacterial, food-borne pathogen of humans, can contaminate raw fruits and vegetables. While physical and chemical methods are available to control S. aureus, scientists are searching for inhibitory phytochemicals from plants.

A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii.

Rhizobia colonize legumes and reduce N to NH in root nodules. The current model is that symbiotic rhizobia bacteroids avoid assimilating this NH. Instead, host legume cells form glutamine from NH, and the nitrogen is returned to the bacteroid as dicarboxylates, peptides, and amino acids.

Protection Against Common Bean Rust Conferred by a Gene-Silencing Method.

Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry.

Different Cellular Origins and Functions of Extracellular Proteins from Escherichia coli O157:H7 and O104:H4 as Determined by Comparative Proteomic Analysis.

Unlabelled: Extracellular proteins play important roles in bacterial interactions with the environmental matrices. In this study, we examined the extracellular proteins from Escherichia coli O157:H7 and O104:H4 by tandem mass spectrometry. We identified 500 and 859 proteins from the growth media of E.

Doubling down on phosphorylation as a variable peptide modification.

Some mass spectrometrists believe that searching for variable PTMs like phosphorylation of serine or threonine when using database-search algorithms to interpret peptide tandem mass spectra will increase false-positive matching. The basis for this is the premise that the algorithm compares a spectrum to both a nonphosphorylated peptide candidate and a phosphorylated candidate, which is double the number of candidates compared to a search with no possible phosphorylation. Hence, if the search space doubles, false-positive matching could increase accordingly as the algorithm considers more candidates to which false matches could be made.

Putative Rust Fungal Effector Proteins in Infected Bean and Soybean Leaves.

The plant-pathogenic fungi Uromyces appendiculatus and Phakopsora pachyrhizi cause debilitating rust diseases on common bean and soybean. These rust fungi secrete effector proteins that allow them to infect plants, but their effector repertoires are not understood. The discovery of rust fungus effectors may eventually help guide decisions and actions that mitigate crop production loss.

Expression of a synthetic rust fungal virus cDNA in yeast.

Mycoviruses are viruses that infect fungi. Recently, mycovirus-like RNAs were sequenced from the fungus Phakopsora pachyrhizi, the causal agent of soybean rust. One of the RNAs appeared to represent a novel mycovirus and was designated Phakopsora pachyrhizi virus 2383 (PpV2383).

Phosphothreonine 218 is required for the function of SR45.1 in regulating flower petal development in Arabidopsis.

RNA splicing is crucial to the production of mature mRNAs (mRNA). In Arabidopsis thaliana, the protein Arginine/Serine-rich 45 (SR45) acts as an RNA splicing activator and initiates the spliceosome assembly. SR45 is alternatively spliced into 2 isoforms.

Proteomics of nitrogen remobilization in poplar bark.

Seasonal nitrogen (N) cycling in temperate deciduous trees involves the accumulation of bark storage proteins (BSPs) in phloem parenchyma and xylem ray cells. BSPs are anabolized using recycled N during autumn leaf senescence and later become a source of N during spring shoot growth as they are catabolized. Little is known about the catabolic processes involved in remobilization and reutilization of N from BSPs in trees.

Proof by synthesis of Tobacco mosaic virus.

Background: Synthetic biology is a discipline that includes making life forms artificially from chemicals. Here, a DNA molecule was enzymatically synthesized in vitro from DNA templates made from oligonucleotides representing the text of the first Tobacco mosaic virus (TMV) sequence elucidated in 1982. No infectious DNA molecule of that seminal reference sequence exists, so the goal was to synthesize it and then build viral chimeras.

Disruption of Rpp1-mediated soybean rust immunity by virus-induced gene silencing.

Phakopsora pachyrhizi, a fungus that causes rust disease on soybean, has potential to impart significant yield loss and disrupt food security and animal feed production. Rpp1 is a soybean gene that confers immunity to soybean rust, and it is important to understand how it regulates the soybean defense system and to use this knowledge to protect commercial crops. It was previously discovered that some soybean proteins resembling transcription factors accumulate in the nucleus of Rpp1 soybeans.

The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families.

Haustoria of biotrophic rust fungi are responsible for the uptake of nutrients from their hosts and for the production of secreted proteins, known as effectors, which modulate the host immune system. The identification of the transcriptome of haustoria and an understanding of the functions of expressed genes therefore hold essential keys for the elucidation of fungus-plant interactions and the development of novel fungal control strategies. Here, we purified haustoria from infected leaves and used 454 sequencing to examine the haustorial transcriptomes of Phakopsora pachyrhizi and Uromyces appendiculatus, the causal agents of soybean rust and common bean rust, respectively.

Separation anxiety: an analysis of ethylene-induced cleavage of EIN2.

Since the discovery of the CTR1 protein kinase and the endoplasmic reticulum (ER)-localized EIN2 protein nearly 20 y ago, plant biologists have wondered how these proteins respectively serve as negative and positive regulators of ethylene-mediated signal transduction in plants. Now with the publication of four studies, it can be concluded that in the absence of ethylene (ET) in Arabidopsis thaliana, CTR1 phosphorylates EIN2 thereby inactivating ET signal transduction, while in the presence of ET, CTR1 no longer phosphorylates EIN2 and the cytosolic C-terminus of EIN2 is released from the ER to translocate to the nucleus to promote gene transcription. Chen et al.