Pyridoxal-dependent Decarboxylase Research Articles

Effects of Light on the Fruiting Body Color and Differentially Expressed Genes in Flammulina velutipes.

Light plays vital roles in fungal growth, development, reproduction, and pigmentation. In Flammulina velutipes, the color of the fruiting body exhibits distinct changes in response to light; however, the underlying molecular mechanisms remain unknown. Therefore, in this study, we aimed to analyze the F. velutipes transcriptome under red, green, and blue light-emitting diode (LED) lights to identify the key genes affecting the light response and fruiting body color in this fungus. Additionally, we conducted protein-protein interaction (PPI) network analysis of the previously reported fruiting body color-related gene, Fvpal1, to identify the hub genes. Phenotypic analysis revealed that fruiting bodies exposed to green and blue lights were darker than those untreated or exposed to red light, with the color intensifying more after 48 h of exposure to blue light compared to that after 24 h of exposure. Differentially expressed gene (DEG) analyses of all light treatments for 24 h revealed that the numbers of DEGs were 17, 74, and 257 under red, green, and blue lights, respectively. Subsequently, functional enrichment analysis was conducted of the DEGs identified under green and blue lights, which influenced the color of F. velutipes. In total, 103 of 168 downregulated DEGs under blue and green lights were included in the enrichment analysis. Among the DEGs enriched under both green and blue light treatments, four genes were related to monooxygenases, with three genes annotated as cytochrome P450s that are crucial for various metabolic processes in fungi. PPI network analysis of Fvpal1 revealed associations with 11 genes, among which the expression of one gene, pyridoxal-dependent decarboxylase, was upregulated in F. velutipes exposed to blue light. These findings contribute to our understanding of the molecular mechanisms involved in the fruiting body color changes in response to light and offer potential molecular markers for further exploration of light-mediated regulatory pathways.

Characterization of an Arginine Decarboxylase from Streptococcus pneumoniae by Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry.

Polyamines are polycations derived from amino acids that play an important role in proliferation and growth in almost all living cells. In Streptococcus pneumoniae (the pneumococcus), modulation of polyamine metabolism not only plays an important regulatory role in central metabolism, but also impacts virulence factors such as the capsule and stress responses that affect survival in the host. However, functional annotation of enzymes from the polyamine biosynthesis pathways in the pneumococcus is based predominantly on computational prediction. In this study, we cloned SP_0166, predicted to be a pyridoxal-dependent decarboxylase, from the Orn/Lys/Arg family pathway in S. pneumoniae TIGR4 and expressed and purified the recombinant protein. We performed biochemical characterization of the recombinant SP_0166 and confirmed the substrate specificity. For polyamine analysis, we developed a simultaneous quantitative method using hydrophilic interaction liquid chromatography (HILIC)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) without derivatization. SP_0166 has apparent Km, kcat, and kcat/Km values of 11.3 mM, 715,053 min-1, and 63,218 min-1 mM-1, respectively, with arginine as a substrate at pH 7.5. We carried out inhibition studies of SP_0166 enzymatic activity with arginine as a substrate using chemical inhibitors DFMO and DFMA. DFMO is an irreversible inhibitor of ornithine decarboxylase activity, while DFMA inhibits arginine decarboxylase activity. Our findings confirm that SP_0166 is inhibited by DFMA and DFMO, impacting agmatine production. The use of arginine as a substrate revealed that the synthesis of putrescine by agmatinase and N-carbamoylputrescine by agmatine deiminase were both affected and inhibited by DFMA. This study provides experimental validation that SP_0166 is an arginine decarboxylase in pneumococci.

Genome-wide analysis of high-risk primary brain cancer pedigrees identifies PDXDC1 as a candidate brain cancer predisposition gene.

There is evidence for an inherited contribution to primary brain cancer. Linkage analysis of high-risk brain cancer pedigrees has identified candidate regions of interest in which brain cancer predisposition genes are likely to reside. Genome-wide linkage analysis was performed in a unique set of 11 informative, extended, high-risk primary brain cancer pedigrees identified in a population genealogy database, which include from 2 to 6 sampled, related primary brain cancer cases. Access to formalin-fixed paraffin embedded tissue samples archived in a biorepository allowed analysis of extended pedigrees. Individual high-risk pedigrees were singly informative for linkage at multiple regions. Suggestive evidence for linkage was observed on chromosomes 2, 3, 14, and 16. The chromosome 16 region in particular contains a promising candidate gene, pyridoxal-dependent decarboxylase domain-containing 1 (PDXDC1), with prior evidence for involvement with glioblastoma from other previously reported experimental settings, and contains the lead single nucleotide polymorphism (rs3198697) from the linkage analysis of the chromosome 16 region. Pedigrees with a statistical excess of primary brain cancers have been identified in a unique genealogy resource representing the homogeneous Utah population. Genome-wide linkage analysis of these pedigrees has identified a potential candidate predisposition gene, as well as multiple candidate regions that could harbor predisposition loci, and for which further analysis is suggested.

DDC plays vital roles in the wing spot formation, egg production, and chorion tanning in the brown planthopper.

The gene dopa decarboxylase (Nlddc) of the brown planthopper (BPH, Nilaparvata lugens) was identified in the genome and transcriptome of the insect. The open reading frame of Nlddc is 1,434 bp in length and, it has the potential to encode a protein of 477 amino acid with a conserved pyridoxal-dependent decarboxylase domain and a typical motif, NFNPHKW. Real-time quantification polymerase chain reaction analyses revealed that this gene was highly expressed in the integument and brain, and transcript level peaked in the late stages of egg period and each nymph instar with periodicity. RNA interference results revealed that Nlddc played essential roles in pigment synthesis, formation of wing spot, egg production, and tanning of the chorion. A rapid accumulation of Nlddc transcripts was detected, and it coincided with the injection of the hormone 20-hydroxyecdysone (20E), suggesting that Nlddc transcription was regulated by 20E.

Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse

Current antipsychotic medications used to treat schizophrenia all target the dopamine D2 receptor. Although these drugs have serious side effects and limited efficacy, no novel molecular targets for schizophrenia treatment have been successfully translated into new medications. To identify novel potential treatment targets for schizophrenia, we searched for previously unknown molecular modulators of acoustic prepulse inhibition (PPI), a schizophrenia endophenotype, in the mouse. We examined six inbred mouse strains that have a range of PPI, and used microarrays to determine which mRNA levels correlated with PPI across these mouse strains. We examined several brain regions involved in PPI and schizophrenia: hippocampus, striatum, and brainstem, found a number of transcripts that showed good correlation with PPI level, and confirmed this with real-time quantitative PCR. We then selected one candidate gene for further study, Pdxdc1 (pyridoxal-dependent decarboxylase domain containing 1), because it is a putative enzyme that could metabolize catecholamine neurotransmitters, and thus might be a feasible target for new medications. We determined that Pdxdc1 mRNA and protein are both strongly expressed in the hippocampus and levels of Pdxdc1 are inversely correlated with PPI across the six mouse strains. Using shRNA packaged in a lentiviral vector, we suppressed Pdxdc1 protein levels in the hippocampus and increased PPI by 70%. Our results suggest that Pdxdc1 may regulate PPI and could be a good target for further investigation as a potential treatment for schizophrenia.

Abstract P099: A Methylome- and Transcriptome-Wide Study of Dietary Fructose Intake in Humans

Background: Animal model studies reported robust associations between fructose intake, a known determinant of metabolic health across species, and DNA methylation/ gene expression patterns. To date, these associations have not been comprehensively investigated in humans. Methods: Using DNA methylation data on ~470,000 cytosine-phosphate-guanine (CpG) sites in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, n=991) quantified in CD4+ T-cells, we have interrogated the cross-sectional relationships between fructose intake (ascertained using a validated food frequency questionnaire) and epigenome-wide methylation. We fit linear mixed models adjusted for age, sex, study site, technical covariates (fixed effects) and family relatedness (random effect). We have supplemented the methylation analyses with a transcriptome-wide scan on 98 unrelated GOLDN participants with available RNASeq data in whole blood. For the RNASeq data analysis, we used negative binomial models of read counts as a function of fructose intake, adjusted for age, sex, study site, technical covariates (including differential white blood cell counts). Results and Conclusions: The top loci differentially methylated with respect to fructose intake mapped to SNED1 (regression coefficient +/- SE= 0.002 +/- 0.0005, P=5x10-6) and FARSB (regression coefficient +/- SE= 0.002 +/- 0.0004, P=5x10-6) on chromosome 2. SNED1 is an insulin responsive transcription factor that has previously been shown to be downregulated in the setting of metabolic syndrome. FARSB encodes an aminoacyl-tRNA synethetase implicated in cell growth. Additionally, two genes reached transcriptome-wide significance in the RNASeq analysis: MTATP8P1 (P=1x10-7) and PDXDC1 (P=6x10-7). Sequence variation in PDXDC1 (pyridoxal-dependent decarboxylase isoform) has previously been linked to lipid metabolism, while MTATP8P1 is a pseudogene for a mitochondrially encoded ATP synthase. Upon future replication and functional validation, our preliminary findings offer promising insights into the link between fructose intake and metabolic health.

Using in silico techniques: Isolation and characterization of an insect cuticle-degrading-protease gene from Beauveria bassiana

Cuticle-degrading-proteases (CDPs) secreted by Beauveria spp. are pivotal biocontrol substances, possessing commercial potential for developing bio-pesticides. Therefore, a thoughtful and contemplative understanding and assessment of the structural and functional features of these proteases would markedly assist the development of biogenic pesticides. Computational molecular biology is a new facile alternative approach to the tedious experimental molecular biology; therefore, by using bioinformatics tools, we isolated and characterized an insect CDP gene from Beauveria bassiana 70 s.l. genomic DNA.The CDP gene (1240 bp with GeneBank accession no. KT804651.1) consisted of three introns and four CDS exons, and shared 74–100% sequence identity to the reference CDP genes. Its phylogenetic tree results showed a unique evolution pattern, and the predicted amino acid peptide (PAAP) consisted of 344 amino acid residues with pI, molecular weight, instability index, grand average hydropathicity value and aliphatic index of 7.2, 35.4 kDa, 24.45, −0.149, and 76.63, respectively. The gene possessed 74–89% amino acid sequence similarity to the 12 reference strains. Three motifs (Peptidase_S8 subtilase family) were detected in the PAAP, and the computed 3D structure possessed 79.09% structural identity to alkaline serine proteases. The PAAP had four (three serine proteases and one Pyridoxal-dependent decarboxylase) conserved domains, a disulfide bridge, two calcium binding sites, MY domain, and three predicted active sites in the serine family domains.These results will set the groundwork for further exploitation of proteases and understanding the mechanism of disease caused by cuticle-degrading-serine-proteases from entomopathogenic fungi.

A glutamic acid decarboxylase (CgGAD) highly expressed in hemocytes of Pacific oyster Crassostrea gigas

Glutamic acid decarboxylase (GAD), a rate-limiting enzyme to catalyze the reaction converting the excitatory neurotransmitter glutamate to inhibitory neurotransmitter γ-aminobutyric acid (GABA), not only functions in nervous system, but also plays important roles in immunomodulation in vertebrates. However, GAD has rarely been reported in invertebrates, and never in molluscs. In the present study, one GAD homologue (designed as CgGAD) was identified from Pacific oyster Crassostrea gigas. The full length cDNA of CgGAD was 1689 bp encoding a polypeptide of 562 amino acids containing a conserved pyridoxal-dependent decarboxylase domain. CgGAD mRNA and protein could be detected in ganglion and hemocytes of oysters, and their abundance in hemocytes was unexpectedly much higher than those in ganglion. More importantly, CgGAD was mostly located in those granulocytes without phagocytic capacity in oysters, and could dynamically respond to LPS stimulation. Further, after being transfected into HEK293 cells, CgGAD could promote the production of GABA. Collectively, these findings suggested that CgGAD, as a GABA synthase and molecular marker of GABAergic system, was mainly distributed in hemocytes and ganglion and involved in neuroendocrine-immune regulation network in oysters, which also provided a novel insight to the co-evolution between nervous system and immune system.

Dietary fatty acids modulate associations between genetic variants and circulating fatty acids in plasma and erythrocyte membranes: Meta-analysis of nine studies in the CHARGE consortium.

Tissue concentrations of omega-3 fatty acids may reduce cardiovascular disease risk, and genetic variants are associated with circulating fatty acids concentrations. Whether dietary fatty acids interact with genetic variants to modify circulating omega-3 fatty acids is unclear. We evaluated interactions between genetic variants and fatty acid intakes for circulating alpha-linoleic acid, eicosapentaenoic acid, docosahexaenoic acid, and docosapentaenoic acid. We conducted meta-analyses (N = 11668) evaluating interactions between dietary fatty acids and genetic variants (rs174538 and rs174548 in FADS1 (fatty acid desaturase 1), rs7435 in AGPAT3 (1-acyl-sn-glycerol-3-phosphate), rs4985167 in PDXDC1 (pyridoxal-dependent decarboxylase domain-containing 1), rs780094 in GCKR (glucokinase regulatory protein), and rs3734398 in ELOVL2 (fatty acid elongase 2)). Stratification by measurement compartment (plasma versus erthyrocyte) revealed compartment-specific interactions between FADS1 rs174538 and rs174548 and dietary alpha-linolenic acid and linoleic acid for docosahexaenoic acid and docosapentaenoic acid. Our findings reinforce earlier reports that genetically based differences in circulating fatty acids may be partially due to differences in the conversion of fatty acid precursors. Further, fatty acids measurement compartment may modify gene-diet relationships, and considering compartment may improve the detection of gene-fatty acids interactions for circulating fatty acid outcomes.

Differential expression of the ornithine decarboxylase gene during carposporogenesis in the thallus of the red seaweed Grateloupia imbricata (Halymeniaceae)

This paper describes the cloning of the ornithine decarboxylase gene from a red seaweed, Grateloupia imbricata (Rhodophyta), the characterization of its expression throughout the reproductive process, and demonstrates how polyamines are involved in seaweed reproduction. In addition, the data indicate that the basal perennial and non-spore-forming thalli behave physiologically and genetically differently from the distal reproductive tissue. The common polyamines putrescine, spermidine and spermine have been associated with carposporogenesis in red seaweeds. Ornithine decarboxylase (ODC, EC 4.1.1.17) produces the diamine putrescine from the non-protein amino acid, ornithine. ODC is predominant in the synthesis of polyamines in G. imbricata. The gene encoding the ornithine decarboxylase in G. imbricata was cloned by genomic polymerase chain reaction (PCR) using degenerate primers against conserved motives, followed by chromosome walking using inverse PCR (iPCR). The encoded protein (GiODC, accession # FJ223132) was very similar to other ODCs, bearing the characteristic conserved domain of pyridoxal-dependent decarboxylases. The expression of the GiODC gene was investigated by real-time PCR and in situ hybridization (ISH), and was observed to vary according to cystocarp differentiation. It was weakly transcribed in apical parts of fertile tissue where the cystocarps are located, while the transcript levels were comparatively high in the basal part. This expression pattern correlated with the levels of free polyamines, which were higher at the basal part.

Partially-supervised protein subclass discovery with simultaneous annotation of functional residues

BackgroundThe study of functional subfamilies of protein domain families and the identification of the residues which determine substrate specificity is an important question in the analysis of protein domains. One way to address this question is the use of clustering methods for protein sequence data and approaches to predict functional residues based on such clusterings. The locations of putative functional residues in known protein structures provide insights into how different substrate specificities are reflected on the protein structure level.ResultsWe have developed an extension of the context-specific independence mixture model clustering framework which allows for the integration of experimental data. As these are usually known only for a few proteins, our algorithm implements a partially-supervised learning approach. We discover domain subfamilies and predict functional residues for four protein domain families: phosphatases, pyridoxal dependent decarboxylases, WW and SH3 domains to demonstrate the usefulness of our approach.ConclusionThe partially-supervised clustering revealed biologically meaningful subfamilies even for highly heterogeneous domains and the predicted functional residues provide insights into the basis of the different substrate specificities.

Trypanosoma brucei bruceiinduces alteration in the head proteome of the tsetse fly vectorGlossina palpalis gambiensis

Parasitic manipulations of host behaviour are known from a wide range of host-parasite associations. However, the understanding of these phenomena is far from complete and detailed investigation of their proximate causes is needed. Many studies report behavioural modifications, such as altered feeding rates in tsetse fly (Glossina) infected with the mature transmissible stage (i.e. metacyclic) of the trypanosomes. Here, bidimensional (2D) gel electrophoresis and mass spectrometry were employed to analyse and compare the head proteome between four Glossina palpalis gambiensis categories (uninfected, refractory, mature infection, immature infection). Twenty-four protein spots specifically present or absent in the head of metacyclic-infected flies were observed. These protein spots were subsequently identified and functionally classified as glycolitic, neurotransmiter synthesis, signalling, molecular chaperone and transcriptional regulation proteins. Our results indicate altered energy metabolism in the head of metacyclic-infected tsetse flies. Some of the proteins identified, such as casein kinase 2 and jun kinase have previously been shown to play critical roles in apoptosis in insect neurones. In addition, we found two pyridoxal-dependent decarboxylases (dopa decarboxylase and alpha methyldopa hypersensitive protein), suggesting a modification of serotonin and/or dopamine in the brain of metacyclic-infected tsetse flies. Our data pave the way for future investigation of the alteration of the glossina central nervous system during infection by trypanosomes.

Prokaryotic and eukaryotic pyridoxal-dependent decarboxylases are homologous

A database search has revealed significant and extensive sequence similarities among prokaryotic and eukaryotic pyridoxal phosphate (PLP)-dependent decarboxylases, including Drosophila glutamic acid decarboxylase (GAD) and bacterial histidine decarboxylase (HDC). Based on these findings, the sequences of seven PLP-dependent decarboxylases from five different organisms have been aligned to derive a consensus sequence for this family of enzymes. In addition, quantitative methods have been employed to calculate the relative evolutionary distances between pairs of the decarboxylases comprising this family. The multiple sequence analysis together with the quantitative results strongly suggest an ancient and common origin for all PLP-dependent decarboxylases. This analysis also indicates that prokaryotic and eukaryotic HDC activities evolved independently. Finally, a sensitive search algorithm (PROFILE) was unable to detect additional members of this decarboxylase family in protein sequence databases.