Metabolomic Profiles of the Creeping Wood Sorrel Oxalis corniculata in Radioactively Contaminated Fields in Fukushima: Dose-Dependent Changes in Key Metabolites

The biological impacts of the Fukushima nuclear accident, in 2011, on wildlife have been studied in many organisms, including the pale grass blue butterfly and its host plant, the creeping wood sorrel Oxalis corniculata. Here, we performed an LC–MS-based metabolomic analysis on leaves of this plant collected in 2018 from radioactively contaminated and control localities in Fukushima, Miyagi, and Niigata prefectures, Japan. Using 7967 peaks detected by LC–MS analysis, clustering analyses showed that nine Fukushima samples and one Miyagi sample were clustered together, irrespective of radiation dose, while two Fukushima (Iitate) and two Niigata samples were not in this cluster. However, 93 peaks were significantly different (FDR < 0.05) among the three dose-dependent groups based on background, low, and high radiation dose rates. Among them, seven upregulated and 15 downregulated peaks had single annotations, and their peak intensity values were positively and negatively correlated with ground radiation dose rates, respectively. Upregulated peaks were annotated as kudinoside D (saponin), andrachcinidine (alkaloid), pyridoxal phosphate (stress-related activated vitamin B6), and four microbe-related bioactive compounds, including antibiotics. Additionally, two peaks were singularly annotated and significantly upregulated (K1R1H1; peptide) or downregulated (DHAP(10:0); decanoyl dihydroxyacetone phosphate) most at the low dose rates. Therefore, this plant likely responded to radioactive pollution in Fukushima by upregulating and downregulating key metabolites. Furthermore, plant-associated endophytic microbes may also have responded to pollution, suggesting their contributions to the stress response of the plant.

yggS Encoding Pyridoxal 5′-Phosphate Binding Protein Is Required for Acidovorax citrulli Virulence

Bacterial fruit blotch, caused by seed-borne pathogen Acidovorax citrulli, poses a serious threat to the production of cucurbits globally. Although the disease can cause substantial economic losses, limited information is available about the molecular mechanisms of virulence. This study identified that, a random transposon insertion mutant impaired in the ability to elicit a hypersensitive response on tobacco. The disrupted gene in this mutant was determined to be Aave_0638, which is predicted to encode a YggS family pyridoxal phosphate-dependent enzyme. YggS is a highly conserved protein among multiple organisms, and is responsible for maintaining the homeostasis of pyridoxal 5′-phosphate and amino acids in cells. yggS deletion mutant of A. citrulli strain XjL12 displayed attenuated virulence, delayed hypersensitive response, less tolerance to H2O2 and pyridoxine, increased sensitivity to antibiotic β-chloro-D-alanine, and reduced swimming. In addition, RNA-Seq analysis demonstrated that yggS was involved in regulating the expression of certain pathogenicity-associated genes related to secretion, motility, quorum sensing and oxidative stress response. Importantly, YggS significantly affected type III secretion system and its effectors in vitro. Collectively, our results suggest that YggS is indispensable for A.citrulli virulence and expands the role of YggS in the biological processes.

Dissection of Maize Drought Tolerance at the Flowering Stage Using Ge-Nome-Wide Association Study

Drought is one of the most critical environmental factors constraining corn production especially when it occurs during flowering, resulting in serious yield losses. In this study, anthesis to silk interval (ASI), plant height (PH), and ear biomass at the silking date (EBM) of 279 inbred lines were evaluated under water-stress (WS) and well-water (WW) field conditions for three consecutive years. Averagely, ASI was extended by 25.96%, ear biomass was decreased by 17.54%, and the PH was reduced by 12.47% under drought stress conditions. Genome wide association studies (GWAS) were carried out using phenotypic values under WS, WW and drought-tolerance index (WS-WW or WS/WW) applying mixed linear model controlling both population structure and relative kinship. Totally, 71, 159, and 21 SNPs were significantly (P < 10-5) associated with ASI, ear biomass, and PH, respectively. Candidate genes encoding ARABIDILLO 1 protein, glycoprotein, Tic22-like and Zinc finger family protein for ASI, and 26S proteasome non-ATPase regulatory subunit-9 for EBM, were identified under both WW and WS conditions. Pyridoxal phosphate transferase was associated with EBM under drought stress treatment in consecutive two years. Furthermore, most candidate genes were evidenced to be drought responsive in the association panel. Meanwhile, the favourable/drought tolerance haplotypes were identified based on haplotype analysis. These findings provide insights into the genetic basis of drought tolerance at the flowering stage especially for the female inflorescence development and will facilitate high drought tolerant maize breeding.

Protective Effects of Aminooxyacetic Acid on Colitis Induced in Mice with Dextran Sulfate Sodium

As a known inhibitor of pyridoxal phosphate-dependent transaminase glutamic-oxaloacetic transaminase 1 (GOT1), aminooxyacetic acid (AOAA) has been pointed out to have potential pharmacological effects in antiepileptic, anticonvulsant, antibacterial, cancer cell proliferation inhibition, and acute myocardial infarction (MI) relief. However, its role in inflammatory bowel disease (IBD) has not been reported. Through the in vivo experiment of dextran sulfate sodium- (DSS-) induced colitis in mice, it was found that AOAA significantly attenuated the symptoms, signs, and pathological changes of colitis. In addition, AOAA treatment prevented gut barrier damages by enhancing the expression of zona occludens- (ZO-) 1, occludin, claudin-1, and E-cadherin and recovering the upregulation of the most abundant intermediate filament protein (vimentin). Moreover, the release of interleukin- (IL-) 1β, IL-6, and tumour necrosis factor- (TNF-) α was suppressed, yet the level of IL-10 was upregulated by AOAA treatment compared to the model group. Furthermore, it was shown that AOAA administration boosted M2-like phenotype and effectively reduced M1 macrophage phenotype in the lamina propria of mouse colonic epithelium. Similarly, the effect of AOAA was verified in vitro. AOAA effectively inhibited the classically activated M1 macrophage phenotype and proinflammatory cytokine (IL-1β, TNF-α, and IL-6) expression induced by lipopolysaccharide (LPS) and promoted M2-like phenotype. Collectively, this study reveals for the first time that short-term treatment of AOAA can significantly alleviate DSS-induced acute colitis by regulating intestinal barrier function and macrophage polarization, which provides a theoretical basis for the potential use of AOAA in the treatment of IBD.

MicroRNA-6498-5p Inhibits Nosema bombycis Proliferation by Downregulating BmPLPP2 in Bombyx mori

As microRNAs (miRNAs) are important expression regulators of coding RNA, it is important to characterize their role in the interaction between hosts and pathogens. To obtain a comprehensive understanding of the miRNA alternation in Bombyx mori (B. mori) infected with Nosema bombycis (N. bombycis), RNA sequencing and stem-loop qPCR were conducted to screen and identify the significantly differentially expressed miRNAs (DEmiRNAs). A total of 17 such miRNAs were identified in response to N. bombycis infection, among which miR6498-5p efficiently inhibited the proliferation of N. bombycis in BmE-SWU1 (BmE) cells by downregulating pyridoxal phosphate phosphatase 2 (BmPLPP2). In addition, a fluorescence in situ hybridization (FISH) assay showed that miR6498-5p was located in the cytoplasm of BmE cells, while it was not found in the schizonts of N. bombycis. Further investigation of the effect of BmPLPP2 on the proliferation of schizonts found that the positive factor BmPLPP2 could facilitate N. bombycis completing its life cycle in cells by overexpression and RNAi of BmPLPP2. Our findings offer multiple new insights into the role of miRNAs in the interaction between hosts and microsporidia.

Comparative Proteomic Analysis for a Putative Pyridoxal Phosphate-Dependent Aminotransferase Required for Virulence in Acidovorax citrulli

Acidovorax citrulli (Ac) is the causative agent of bacterial fruit blotch disease in watermelon. Since resistant cultivars have not yet been developed, the virulence factors/mechanisms of Ac need to be characterized. This study reports the functions of a putative pyridoxal phosphate-dependent aminotransferase (PpdaAc) that transfers amino groups to its substrates and uses pyridoxal phosphate as a coenzyme. It was observed that a ppdaAc knockout mutant had a significantly reduced virulence in watermelon when introduced via germinated-seed inoculation as well as leaf infiltration. Comparative proteomic analysis predicted the cellular mechanisms related to PpdaAc. Apart from causing virulence, the PpdaAc may have significant roles in energy production, cell membrane, motility, chemotaxis, post-translational modifications, and iron-related mechanisms. Therefore, it is postulated that PpdaAc may possess pleiotropic effects. These results provide new insights into the functions of a previously unidentified PpdaAc in Ac.

An Overview of Bioprocesses Employing Specifically Selected Microbial Catalysts for γ-Aminobutyric Acid Production

Gamma-aminobutyric acid (GABA) is an important chemical compound in the human brain. GABA acts as an inhibitory neurotransmitter by inducing hyperpolarization of cellular membranes. Usually, this pharmaceutically important compound is synthesized using a chemical process, but in this short overview we have only analysed microbial processes, which have been studied for the biosynthesis of this commercially important compound. The content of this article includes the following summarised information: the search for biological processes showed a number of lactic acid bacteria and certain species of fungi, which could be effectively used for the production of GABA. Strains found to possess GABA-producing pathways include Lactobacillus brevis CRL 1942, L. plantarum FNCC 260, Streptococcus salivarius subsp. thermophilus Y2, Bifidobacterium strains, Monascus spp., and Rhizopus spp. Each of these strains required specific growth conditions. However, several factors were common among these strains, such as the use of two main supplements in their fermentation medium—monosodium glutamate and pyridoxal phosphate—and maintaining an acidic pH. Optimization studies of GABA production were comprised of altering the media constituents, modifying growth conditions, types of cultivation system, and genetic manipulation. Some strains increased the production of GABA under anaerobic conditions. Genetic manipulation focused on silencing some genes or overexpression of gadB and gadC. The conclusion, based on the review of information available in published research, is that the targeted manipulation of selected microorganisms, as well as the culture conditions for an optimised bioprocess, should be adopted for an increased production of GABA to meet its increasing demand for food and pharmaceutical applications.

Mechanisms of Neuronal Damage in Acute Hepatic Porphyrias

Porphyrias are a group of congenital and acquired diseases caused by an enzymatic impairment in the biosynthesis of heme. Depending on the specific enzyme involved, different types of porphyrias (i.e., chronic vs. acute, cutaneous vs. neurovisceral, hepatic vs. erythropoietic) are described, with different clinical presentations. Acute hepatic porphyrias (AHPs) are characterized by life-threatening acute neuro-visceral crises (acute porphyric attacks, APAs), featuring a wide range of neuropathic (central, peripheral, autonomic) manifestations. APAs are usually unleashed by external “porphyrinogenic” triggers, which are thought to cause an increased metabolic demand for heme. During APAs, the heme precursors δ-aminolevulinic acid (ALA) and porphobilinogen (PBG) accumulate in the bloodstream and urine. Even though several hypotheses have been developed to explain the protean clinical picture of APAs, the exact mechanism of neuronal damage in AHPs is still a matter of debate. In recent decades, a role has been proposed for oxidative damage caused by ALA, mitochondrial and synaptic ALA toxicity, dysfunction induced by relative heme deficiency on cytochromes and other hemeproteins (i.e., nitric oxide synthases), pyridoxal phosphate functional deficiency, derangements in the metabolic pathways of tryptophan, and other factors. Since the pathway leading to the biosynthesis of heme is inscribed into a complex network of interactions, which also includes some fundamental processes of basal metabolism, a disruption in any of the steps of this pathway is likely to have multiple pathogenic effects. Here, we aim to provide a comprehensive review of the current evidence regarding the mechanisms of neuronal damage in AHPs.

Hydrogel-Based Enzyme and Cofactor Co-Immobilization for Efficient Continuous Transamination in a Microbioreactor

A microbioreactor was developed in which selected amine transaminase was immobilized together with the cofactor pyridoxal phosphate (PLP) to allow efficient continuous transamination. The enzyme and cofactor were retained in a porous copolymeric hydrogel matrix formed in a two-plate microreactor with an immobilization efficiency of over 97%. After 10 days of continuous operation, 92% of the initial productivity was retained and no leaching of PLP or enzyme from the hydrogel was observed. The microbioreactor with co-immobilized cofactor showed similar performance with and without the addition of exogenous PLP, suggesting that the addition of PLP is not required during the process. The space-time yield of the microbioreactor was 19.91 g L−1 h−1, while the highest achieved biocatalyst productivity was 5.4 mg mgenzyme−1 h−1. The immobilized enzyme also showed better stability over a wider pH and temperature range than the free enzyme. Considering the time and cost efficiency of the immobilization process and the possibility of capacity expansion, such a system is of great potential for industrial application.

Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms

Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.