scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2021 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Expression Patterns ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Altered Expression ◽  
Solid Agar ◽  
Genes Encoding ◽  
Chemotaxis Proteins ◽  
Flagellar Proteins ◽  
Semi Solid

Abstract RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.

scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2020 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Aromatic Compounds ◽  
Differential Expression Analysis ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Bacterial Degradation ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Chlorinated Aromatic Compounds ◽  
Semi Solid

Abstract Background Aromatic compounds derived from human activities are often released into the environment. Many of them, especially halogenated aromatics, are persistent in nature and pose threats to organisms. Therefore, the microbial degradation of these compounds has been studied intensively. Our laboratory has studied the expression of genes in Cupriavidus necator NH9 involved in the degradation of 3-chlorobenzoate (3-CB), a model compound for studies on bacterial degradation of chlorinated aromatic compounds. In this study aimed at exploring how this bacterium has adapted to the utilization of chlorinated aromatic compounds, we performed RNA-seq analysis of NH9 cells cultured with 3-CB, benzoate (BA), or citric acid. The purpose of these analyses was to identify differentially expressed genes encoding products with various biological functions involved in the degradation of 3-CB and BA. Results Differential expression analysis confirmed strong induction of genes encoding enzymes in degradation pathways of 3-CB and BA (benABCD, cbnABCD, catA, catB, catDC, pcaIJF, and boxABCD). Genes involved in the degradation of 3-hydroxybenzoate and anthranilate were upregulated by 3-CB but not by BA, suggesting that transcriptional regulators of these degradative genes recognized 3-CB (or its intermediate metabolite) as an inducer. Four genes encoding MFS transporters were specifically induced by 3-CB or BA, and one cluster of genes encoding components of the ABC transporter system was significantly induced by 3-CB. Stress response genes encoding chaperones, proteases, the phosphate transporter PstBACS, and superoxide oxidase were upregulated in response to 3-CB and/or BA. Gene Ontology enrichment analysis revealed that genes encoding dioxygenases were upregulated by both 3-CB and BA. Intriguingly, the “cell motility,” “signal transduction,” and “chemotaxis” terms were significantly upregulated by BA compared with 3-CB. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to BA than to 3-CB. Conclusions Our results showed that the chemotaxis behavior of NH9 differs between 3-CB and BA. We inferred that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike its analogous aromatic compound BA, in nature.

scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2020 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Aromatic Compounds ◽  
Differential Expression Analysis ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Major Facilitator Superfamily ◽  
Bacterial Degradation ◽  
Genes Encoding ◽  
Chlorinated Aromatic Compounds ◽  
Major Facilitator

Abstract BackgroundAromatic compounds derived from human activities are often released into the environment. Many of them, especially halogenated aromatics, are persistent in nature and pose threats to organisms. Therefore, the microbial degradation of these compounds has been studied intensively. Our laboratory has studied the expression of genes in Cupriavidus necator NH9 involved in the degradation of 3-chlorobenzoate (3-CB), a model compound for studies on bacterial degradation of chlorinated aromatic compounds. In this study aimed at exploring how this bacterium has adapted to the utilization of chlorinated aromatic compounds, we performed RNA-seq analysis of NH9 cells cultured with 3-CB, benzoate (BA), or citric acid (CA). The purpose of these analyses was to identify differentially expressed genes encoding products with various biological functions involved in the degradation of 3-CB and BA.ResultsDifferential expression analysis confirmed strong induction of genes encoding enzymes in degradation pathways of 3-CB and BA, including benABCD (more than 256-fold compared with CA) encoding benzoate 1,2-dioxygenase involved in initial hydroxylation of both 3-CB and BA, and cbnABCD (more than 200-fold compared with BA and CA) encoding enzymes of chlorocatechol ortho-cleavage pathway. Four genes encoding major facilitator superfamily transporters were specifically induced by 3-CB or BA, and one cluster of genes encoding components of the ATP-binding cassette transporter system was significantly induced by 3-CB. Stress response genes encoding chaperones, proteases, the phosphate transporter PstBACS, and superoxide oxidase were upregulated in response to 3-CB and/or BA. Gene Ontology enrichment analysis revealed that genes encoding dioxygenases were upregulated by both 3-CB and BA. Intriguingly, the “cell motility,” “signal transduction,” and “chemotaxis” terms were significantly upregulated by BA compared with 3-CB. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to BA than to 3-CB.ConclusionsOur results showed that the chemotaxis behavior of NH9 differs between 3-CB and BA. We inferred that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike its analogous aromatic compound BA, in nature.

scholarly journals Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

2020 ◽  
Author(s):  
Ryota Moriuchi ◽  
Hideo Dohra ◽  
Yu Kanesaki ◽  
Naoto Ogawa
Keyword(s):  
Aromatic Compounds ◽  
Differential Expression Analysis ◽  
Agar Plate ◽  
Enrichment Analysis ◽  
Cupriavidus Necator ◽  
Major Facilitator Superfamily ◽  
Bacterial Degradation ◽  
Genes Encoding ◽  
Chlorinated Aromatic Compounds ◽  
Major Facilitator

Abstract Background Aromatic compounds derived from human activities are often released into the environment. Many of them, especially halogenated aromatics, are persistent in nature and pose threats to organisms. Therefore, the microbial degradation of these compounds has been studied intensively. Our laboratory has studied the expression of genes in Cupriavidus necator NH9 involved in the degradation of 3-chlorobenzoate (3-CB), a model compound for studies on bacterial degradation of chlorinated aromatic compounds. In this study aimed at exploring how this bacterium has adapted to the utilization of chlorinated aromatic compounds, we performed RNA-seq analysis of NH9 cells cultured with 3-CB, benzoate (BA), or citric acid (CA). The purpose of these analyses was to identify differentially expressed genes encoding products with various biological functions involved in the degradation of 3-CB and BA. Results Differential expression analysis confirmed strong induction of genes encoding enzymes in degradation pathways of 3-CB and BA, including benABCD (more than 256-fold compared with CA) encoding benzoate 1,2-dioxygenase involved in initial hydroxylation of both 3-CB and BA, and cbnABCD (more than 200-fold compared with BA and CA) encoding enzymes of chlorocatechol ortho -cleavage pathway. Four genes encoding major facilitator superfamily transporters were specifically induced by 3-CB or BA, and one cluster of genes encoding components of the ATP-binding cassette transporter system was significantly induced by 3-CB. Stress response genes encoding chaperones, proteases, the phosphate transporter PstBACS, and superoxide oxidase were upregulated in response to 3-CB and/or BA. Gene Ontology enrichment analysis revealed that genes encoding dioxygenases were upregulated by both 3-CB and BA. Intriguingly, the “cell motility,” “signal transduction,” and “chemotaxis” terms were significantly upregulated by BA compared with 3-CB. Consistent with this, in semi-solid agar plate assays, NH9 cells showed stronger chemotaxis to BA than to 3-CB. Conclusions Our results showed that the chemotaxis behavior of NH9 differs between 3-CB and BA. We inferred that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike its analogous aromatic compound BA, in nature.

scholarly journals Macromolecule biosynthesis: a key function of sleep

2007 ◽  
Vol 31 (3) ◽  
pp. 441-457 ◽  
Author(s):  
Miroslaw Mackiewicz ◽  
Keith R. Shockley ◽  
Micah A. Romer ◽  
Raymond J. Galante ◽  
John E. Zimmerman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Sleep Deprivation ◽  
Expression Patterns ◽  
State Level ◽  
Altered Expression ◽  
Mouse Cerebral Cortex ◽  
Genes Encoding ◽  
Function Of Sleep ◽  
Cellular Components

The function(s) of sleep remains a major unanswered question in biology. We assessed changes in gene expression in the mouse cerebral cortex and hypothalamus following different durations of sleep and periods of sleep deprivation. There were significant differences in gene expression between behavioral states; we identified 3,988 genes in the cerebral cortex and 823 genes in the hypothalamus with altered expression patterns between sleep and sleep deprivation. Changes in the steady-state level of transcripts for various genes are remarkably common during sleep, as 2,090 genes in the cerebral cortex and 409 genes in the hypothalamus were defined as sleep specific and changed (increased or decreased) their expression during sleep. The largest categories of overrepresented genes increasing expression with sleep were those involved in biosynthesis and transport. In both the cerebral cortex and hypothalamus, during sleep there was upregulation of multiple genes encoding various enzymes involved in cholesterol synthesis, as well as proteins for lipid transport. There was also upregulation during sleep of genes involved in synthesis of proteins, heme, and maintenance of vesicle pools, as well as antioxidant enzymes and genes encoding proteins of energy-regulating pathways. We postulate that during sleep there is a rebuilding of multiple key cellular components in preparation for subsequent wakefulness.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2019 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Abstract Backgrounds Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown. Results In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
Lin Fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Backgrounds: Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown.Results: In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Exosomal Aβ-Binding Proteins Identified by “In Silico” Analysis Represent Putative Blood-Derived Biomarker Candidates for Alzheimer´s Disease

2021 ◽  
Vol 22 (8) ◽  
pp. 3933
Author(s):  
Tânia Soares Martins ◽  
Rui Marçalo ◽  
Maria Ferreira ◽  
Margarida Vaz ◽  
Raquel M. Silva ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Enrichment Analysis ◽  
Disease Diagnosis ◽  
Easy Access ◽  
Altered Expression ◽  
Disease Biomarkers ◽  
Go Enrichment

The potential of exosomes as biomarker resources for diagnostics and even for therapeutics has intensified research in the field, including in the context of Alzheimer´s disease (AD). The search for disease biomarkers in peripheral biofluids is advancing mainly due to the easy access it offers. In the study presented here, emphasis was given to the bioinformatic identification of putative exosomal candidates for AD. The exosomal proteomes of cerebrospinal fluid (CSF), serum and plasma, were obtained from three databases (ExoCarta, EVpedia and Vesiclepedia), and complemented with additional exosomal proteins already associated with AD but not found in the databases. The final biofluids’ proteomes were submitted to gene ontology (GO) enrichment analysis and the exosomal Aβ-binding proteins that can constitute putative candidates were identified. Among these candidates, gelsolin, a protein known to be involved in inhibiting Abeta fibril formation, was identified, and it was tested in human samples. The levels of this Aβ-binding protein, with anti-amyloidogenic properties, were assessed in serum-derived exosomes isolated from controls and individuals with dementia, including AD cases, and revealed altered expression patterns. Identification of potential peripheral biomarker candidates for AD may be useful, not only for early disease diagnosis but also in drug trials and to monitor disease progression, allowing for a timely therapeutic intervention, which will positively impact the patient’s quality of life.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Phenotypic Resemblance to Neuropsychiatric Disorder and Altered mRNA Profiles in Cortex and Hippocampus Underlying IL15Rα Knockout

2021 ◽  
Vol 14 ◽  
Author(s):  
Yi He ◽  
Yuxin Yu ◽  
Yanan Li ◽  
Weicheng Duan ◽  
Zuoli Sun ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Control Group ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Altered Expression ◽  
Y Maze

BackgroundPrevious studies of the functions of IL15Rα have been limited to immune activities and skeletal muscle development. Immunological factors have been identified as one of the multiple causes of psychosis, and neurological symptoms have been described in IL15Rα knockout (KO) mice. Seeking to explore possible mechanisms for this in the IL15Rα–/– mouse brain, we analyzed gene expression patterns in the cortex and hippocampus using the RNA-seq technique.MethodsIL15Rα KO mice were generated and littermate wildtype (WT) mice were used as a control group. A Y-maze was used to assess behavior differences between the two groups. The cortex and hippocampus of 3-month-old male mice were prepared and RNA-seq and transcriptome analysis were performed by gene set enrichment analysis (GSEA).ResultsCompared with the WT group, IL15Rα KO animals showed higher speed in the novel arm and more entrance frequency in the old arm in the Y-maze experiment. GSEA indicated that 18 pathways were downregulated and 13 pathways upregulated in both cortex and hippocampus from the GO, KEGG, and Hallmark gene sets. The downregulated pathways formed three clusters: respiratory chain and electron transport, regulation of steroid process, and skeletal muscle development.ConclusionIL15Rα KO mice exhibit altered expression of multiple pathways, which could affect many functions of the brain. Lipid biosynthesis and metabolism in the central nervous system (CNS) should be investigated to provide insights into the effect of IL15Rα on psychosis in this murine model.

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