Identification of Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) responsive miRNAs in banana root

Abstract The fungus, Fusarium oxysporum f. sp. cubense (Foc), is the causal agent of Fusarium wilt disease, which is the most serious disease affecting the whole banana industry. Although extensive studies have characterized many Foc-responsive genes in banana, the molecular mechanisms on microRNA level underlying both banana defense and Foc pathogenesis are not yet fully understood. In this study, we aimed to reveal the role of miRNA during banana-Foc TR4 interactions. Illumina sequencing was used to reveal the changes in small RNAome profiles in roots of Foc TR4-inoculated ‘Tianbaojiao’ banana (Musa acuminata cv. Tianbaojiao) in the early stages (i.e. 5 h, 10 h and 25 h post Foc TR4 inoculation, respectively). The expression of some differentially expressed (DE) miRNAs and their predicted target genes was studied by using quantitative real time PCR (qRT-PCR). Totally, 254 known miRNAs from 31 miRNA families and 28 novel miRNAs were identified. Differential expression analysis identified 84, 77 and 74 DE miRNAs at the three respective Foc TR4 infection time points compared with control healthy banana (CK). GO and KEGG analysis revealed that most of the predicted target genes of DE miRNAs (DET) were implicated in peroxisome, fatty acid metabolism, auxin-activated signaling pathway, sulfur metabolism, lignin metabolism and so on, and many known stress responsive genes were identified to be DETs. Moreover, expected inverse correlations were confirmed between some miRNA and their corresponding target genes by using qRT-PCR analysis. Our study revealed that miRNA play important regulatory roles during the banana-Foc TR4 interaction by regulating peroxidase, fatty acid metabolism, auxin signaling, sulfur metabolism, lignin metabolism related genes and many known stress responsive genes.

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Transcriptome analysis reveals differentially expressed genes for improving survival of dormant Apostichopus japonicus in response to high temperature

10.21203/rs.2.17599/v1 ◽

2019 ◽

Author(s):

Yang Qiuhua ◽

Zhang Xusheng ◽

Lu Zhen ◽

Huang Ruifang ◽

Ngoc Tuan Tran ◽

...

Keyword(s):

Fatty Acid ◽

High Temperature ◽

Fatty Acid Metabolism ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Rna Seq ◽

Sea Cucumbers ◽

Apostichopus Japonicas ◽

Qrt Pcr ◽

Carbohydrate Hydrolysis

Abstract Background: Aestivation is one of the strategies used by sea cucumbers (Apostichopus japonicas) in order to improve survival in response to the high-temperature and droughty conditions. Previous studies have carried out to investigate the immune or physiological alterations at the aestivation stage. However, it lacks information on the relationship between immunity and physiology. Herein, transcriptome sequencing was used to study gene expression during the aestivation stage. The results of this study provide a comprehensive understanding of the molecular mechanisms that protect sea cucumbers from the high-temperature condition, which favors improving survival in cultured sea cucumbers. Results: The transcriptome analysis of dormant (aestivation) and revival sea cucumbers generated 2,368 differentially expressed genes (down-regulation: 927; up-regulation: 1,441) and 39,081 unchanged genes. Basing on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, the down-regulated genes of dormant group were identified to be involved in DNA replication, RNA metabolic process, protein modification and biosynthesis, macromolecule metabolism, and cellular metabolism, which resulted in the inhibition of motility, skeletal development, neural activity, cell proliferation and development of A. japonicas. In contrast, the up-regulated genes were associated with fatty acid metabolism, carbohydrate hydrolysis, and phagocytosis. Protein-protein interaction network analysis further revealed that carbohydrate hydrolysis promoted the phagocytosis activity in the dormant group. Furthermore, the expression pattern of all tested genes in qRT-PCR analysis fitted well with those in RNA-Seq, with the exception of FASNL, which was unchanged in the qRT-PCR but up-regulated in RNA-seq. Conclusions: During the dormant stage, sea cucumbers decreased DNA replication, transcription and translation to achieve a hypometabolic state beneficial for reducing energy consumption. On the contrary, fatty acid metabolism and carbohydrate hydrolysis were increased for energy supply. Moreover, high levels of carbohydrate hydrolysis promoted phagocytosis, which is a crucial innate immune response to infection by pathogens. These results provided new insight into potential molecular mechanisms that enable the sea cucumbers to respond to high temperatures. Keywords: Aestivation, Apostichopus japonicas, hypometabolism, fatty acid metabolism, carbohydrate hydrolysis, phagocytosis

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FC 102PD INDUCED ARTERIOLAR AND PERITONEAL PATHOMECHANISMS ARE PARTIALLY REVERSED AFTER KIDNEY TRANSPLANTATION

Nephrology Dialysis Transplantation ◽

10.1093/ndt/gfab135.001 ◽

2021 ◽

Vol 36 (Supplement_1) ◽

Author(s):

Conghui Zhang ◽

Maria Bartosova ◽

Betti Schaefer ◽

Rebecca Herzog ◽

Rimante Cerkauskiene ◽

...

Keyword(s):

Kidney Transplantation ◽

Fatty Acid ◽

Fatty Acid Metabolism ◽

Fatty Acid Synthase ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Parietal Peritoneum ◽

Gene Set Enrichment Analysis ◽

Biological Processes ◽

Cell Counts

Abstract Background and Aims Due to the unphysiological composition of PD fluids, chronic peritoneal dialysis (PD) induces progressive peritoneal fibrosis, hypervascularization, and vasculopathy. The evolution of the PD membrane and vasculopathy following kidney transplantation (KTx) is largely unknown. Method Arteriolar and peritoneal tissues were obtained from 107 children with chronic kidney disease (CKD5), 72 children on PD (treated with neutral pH PD fluids, with low glucose degradation product content, GDP) and 21 children, who underwent KTx 4-5 weeks after a median 21 months of PD. Specimen underwent standardized digital quantitative histomorphometry. Molecular mechanisms were studied in omental arterioles microdissected from surrounding fat by multi-omics followed by Gene Set Enrichment Analysis (GSEA); key findings were validated in parietal tissues of independent, matched cohorts by quantitative immunohistochemistry (n=15/group). Results Arteriolar transcriptome and proteome GSEA revealed suppression of leucocyte migration and T-cell activation / secretory pathways regulation, of sprouting angiogenesis biological processes and of epithelial proliferation and cell cycle after KTx as compared to PD. Lipid / fatty acid metabolism, autophagy and ATP synthesis pathways were activated. Transcriptome analysis including KTx, PD and CKD5 specifically attributed regulation of arteriolar lipid and fatty acid metabolism to transplantation and comprised 140 transcripts; their regulation was confirmed on the proteome level. Hub gene fatty acid synthase was identified by protein interaction analysis (string-db.org). 15 arteriolar genes activated by PD were inactivated after KTx and included glucose metabolisms and cytoskeleton related transcripts. 24 transcripts and 10 corresponding proteins induced by PD were still active after KTx and associated with biological processes related to TGF-ß signaling, fibrosis and mineral absorption. In line with arteriolar multi-omics findings, peritoneal hypervascularization induced by chronic PD was reversed after Tx to CKD5 level. CD45 positive tissue infiltrating leucocytes count was reduced by 40% and was independently associated with microvessel density in multivariable analysis including PD vintage, daily GDP exposure and recent KTx. Peritoneal lymphatic vessel density, submesothelial thickness, activated fibroblast, fibrin deposit, macrophage and EMT cell counts remained unchanged after KTx compared to PD. Arteriolar lumen to vessel ratios (a marker of vasculopathy) were similar in both groups. Vessel-homeostasis-related proteins in independent, matched cohorts demonstrated increased caspase-3 abundance in peritoneal arterioles after KTx. Arteriolar VEGF-A, thrombospondin, angiopoietin1/2, and hypoxia-inducible factor-1 (HIF-1a) were unchanged, while submesothelial HIF-1a and angiopoietin1/2 were decreased after Tx, favoring vessel maturation. The abundance of the key driver of fibrosis, TGF-ß-effector pSMAD2/3, was unchanged in the peritoneum and arterioles after Tx. Conclusion Our multi-omics analyses of fat covered omental arterioles, not directly exposed to PD fluids, demonstrate inhibition of PD induced immune response and angiogenesis pathways, of glucose metabolism and cytoskeleton regulation to levels similar as seen in children with CKD5. Arteriolar lipid and fatty acid metabolism is selectively altered after KTx. Reversal of low GDP PD induced hypervascularization and inflammation of the parietal peritoneum after KTx, mirror molecular changes in omental arterioles, while profibrotic activity persists after KTx in omental arterioles and in the parietal peritoneum.

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Bacillus subtilis Gene Cluster Involved in Calcium Carbonate Biomineralization

Journal of Bacteriology ◽

10.1128/jb.01450-06 ◽

2006 ◽

Vol 189 (1) ◽

pp. 228-235 ◽

Cited By ~ 101

Author(s):

Chiara Barabesi ◽

Alessandro Galizzi ◽

Giorgio Mastromei ◽

Mila Rossi ◽

Elena Tamburini ◽

...

Keyword(s):

Bacillus Subtilis ◽

Fatty Acid ◽

Calcium Carbonate ◽

Fatty Acid Metabolism ◽

Insertional Mutagenesis ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Precipitation Process ◽

Calcium Carbonate Precipitation ◽

Wide Range

ABSTRACT Calcium carbonate precipitation, a widespread phenomenon among bacteria, has been investigated due to its wide range of scientific and technological implications. Nevertheless, little is known of the molecular mechanisms by which bacteria foster calcium carbonate mineralization. In our laboratory, we are studying calcite formation by Bacillus subtilis, in order to identify genes involved in the biomineralization process. A previous screening of UV mutants and of more than one thousand mutants obtained from the European B. subtilis Functional Analysis project allowed us to isolate strains altered in the precipitation phenotype. Starting from these results, we focused our attention on a cluster of five genes (lcfA, ysiA, ysiB, etfB, and etfA) called the lcfA operon. By insertional mutagenesis, mutant strains carrying each of the five genes were produced. All of them, with the exception of the strain carrying the mutated lcfA operon, were unable to form calcite crystals. By placing transcription under IPTG (isopropyl-β-d-thiogalactopyranoside) control, the last gene, etfA, was identified as essential for the precipitation process. To verify cotranscription in the lcfA operon, reverse transcription-PCR experiments were performed and overlapping retrocotranscripts were found comprising three adjacent genes. The genes have putative functions linked to fatty acid metabolism. A link between calcium precipitation and fatty acid metabolism is suggested.

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Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdominal adipogenesis

10.21203/rs.3.rs-20642/v2 ◽

2020 ◽

Author(s):

Meng Zhang ◽

Yu Han ◽

Yanhui Zhai ◽

Xiangfei Ma ◽

Xinglan An ◽

...

Keyword(s):

Fatty Acid ◽

Fatty Acid Metabolism ◽

Target Genes ◽

Acid Metabolism ◽

Adipogenic Differentiation ◽

Expression Patterns ◽

Fat Deposition ◽

Circular Rnas ◽

Tissue Specific ◽

Functional Roles

Abstract Background: Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, animal development, metabolism, and adipogenesis. In this study, to assess the functional roles of circRNAs in adipogenesis and tissue-specific fat deposition, we comprehensively analyzed the Ribo-Zero RNA-Seq and miRNAs data during chicken intramuscular and abdominal adipogenic differentiation. Results: circRNAs and miRNAs profiles during chicken adipogenic differentiation were found in adipocytes derived from various adipose tissues. It was also discovered that high levels of downregulated miRNAs potentially promote adipogenesis by activating their target genes which are associated with fatty acid metabolism and adipogenic differentiation. Through analysis of the correlation between the expression levels of circRNAs and adipogenic genes, as well as the dynamic expression patterns of circRNAs during adipogenic differentiation, several candidate circRNAs were identified. Moreover, competing endogenous RNA (ceRNAs) networks were constructed during chicken intramuscular and abdominal adipogenesis by combining miRNAs with mRNAs data. Several candidate circRNAs potentially influence adipogenesis by regulating miRNAs via PPAR and fatty acid metabolism-related pathways were identified, such as circLCLAT1, circFNDC3AL, circCLEC19A and circARMH1. Conclusion: In conclusion, our findings reveal that circRNAs and the circRNA-miRNAs-mRNAs-ceRNAs network may play important roles in chicken adipocytes differentiation and tissue-specific fat deposition.

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Exploration the mechanism of doxorubicin-induced Heart failure in Rats by integration of proteomics and metabolomics data

10.21203/rs.3.rs-58887/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Yu Yuan ◽

Simiao Fan ◽

Lexin Shu ◽

Wei Huang ◽

Lijuan Xie ◽

...

Keyword(s):

Heart Failure ◽

Fatty Acid ◽

Fatty Acid Metabolism ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Systemic Disease ◽

Cardiac Metabolism ◽

Glutathione Metabolism ◽

High Morbidity ◽

Metabolomics Data

Abstract Background Heart failure is currently a worldwide systemic disease with high morbidity and mortality and is very common. At present, many studies have shown that heart failure is associated with obesity, hypertension and diabetes, but it is still unable to prevent the disease from progressing. Here, we elucidate the molecular mechanisms of doxorubicin–induced harmful effects on rat cardiac metabolism and function from a new perspective, using metabonomics and Proteomics analysis data. Methods The aim of this study was to use metabonomic and proteomic techniques to systematically elucidate the molecular mechanisms of doxorubicin (DOX)–induced heart failure (HF) in rat. In this study, we aimed to systematically elucidate the molecular action of Dox on rats heart and the reasons for DOX–induced the HF mechanism through the metabonomics tandem mass tag (TMT)–based quantitative proteomics approach. Rats were gavaged with DOX (3 mg/kg) for 6 weeks and the plasma metabonomics, cardiac tissue proteomics, histopathology and related proteins expression levels. Results A total of 278 proteins and 21 metabolites were significantly altered in rats following DOX treatments. The responsive proteins and metabolites were predominantly involved in Fatty acid metabolism, Glycolysis, glycerophospholipid metabolism, TCA cycle, Glutathione metabolism, Myocardial contraction. Conclusions The present study indicates the PTP1B inhibits the expression of HIF-1α by inhibiting the phosphorylation of IRS, leading to disorders of fatty acid metabolism and glycolysis, which together with the decrease of Nrf2, SOD, Cytc and AK4 proteins lead to oxidative stress, suggesting the PTP1B may serve as a potential target in the treatment of heart failure.

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Sterol and fatty acid metabolism in Fusarium oxysporum.

Agricultural and Biological Chemistry ◽

10.1271/bbb1961.41.1233 ◽

1977 ◽

Vol 41 (7) ◽

pp. 1233-1238 ◽

Cited By ~ 4

Author(s):

C. MADHOSINGH

Keyword(s):

Fatty Acid ◽

Fusarium Oxysporum ◽

Fatty Acid Metabolism ◽

Acid Metabolism

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Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis

PeerJ ◽

10.7717/peerj.11339 ◽

2021 ◽

Vol 9 ◽

pp. e11339

Author(s):

Yinan Wang ◽

Mengke Wang ◽

Min Li ◽

Te Zhao ◽

Lin Zhou

Keyword(s):

Fatty Acid ◽

Protein Kinase ◽

Fatty Acid Metabolism ◽

Acid Metabolism ◽

Phytophthora Capsici ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Expression Level ◽

Pcr Analysis ◽

Qrt Pcr

Background Phytophthora capsici Leonian (P. capsici) can cause wilting and roots rotting on pepper and other cash crops. The new fungicide cinnamaldehyde (CA) has high activity against this pathogen. However, its potential mechanism is still unknown. Methods In order to gain insights into the mechanism, isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics was used to analyze P. capsici treated with CA. The iTRAQ results were evaluated by parallel reaction monitoring (PRM) analysis and quantitative real-time PCR (qRT-PCR) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to speculate the biochemical pathways that the agent may act on. Results The results showed that 1502 differentially expressed proteins were identified, annotated and classified into 209 different terms (like metabolic process, cellular process, single-organism process) based on Gene Ontology (GO) functional enrichment analysis and nine different pathways (glyoxylate and dicarboxylate metabolism, fatty acid metabolism and so on) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This study suggested that CA disordered fatty acid metabolism, polysaccharide metabolism and leucine metabolism. Based on PRM analysis, five proteins including CAMK/CAMK1 protein kinase, glucan 1,3-beta-glucosidase, 1,3-beta-glucanosyltransferase, methylcrotonoyl-CoA carboxylase subunit alpha and isovaleryl-CoA dehydrogenase were down-regulated in P. capsici treated with CA. Furthermore, the qRT-PCR analysis showed that the gene expression level of the interested proteins was consistent with the protein expression level, except for CAMK/CAMK1 protein kinase, acetyl-CoA carboxylase and fatty acid synthase subunit alpha. Conclusions CA destroyed the metabolic homoeostasisof P. capsici, which led to cell death. This is the first proteomic analysis of P. capsici treated with CA, which may provide an important information for exploring the mechanism of the fungicide CA against P. capsici.

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Cellular pathways during spawning induction in the starlet sea anemone Nematostella vectensis

10.1101/2021.03.16.435650 ◽

2021 ◽

Author(s):

Shelly Reuven ◽

Mieka Rinsky ◽

Vera Brekhman ◽

Assaf Malik ◽

Oren Levy ◽

...

Keyword(s):

Fatty Acid ◽

Sexual Reproduction ◽

Fatty Acid Metabolism ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Light Exposure ◽

Model Organism ◽

Sea Anemone ◽

Nematostella Vectensis ◽

Minor Effect

AbstractIn cnidarians, long-term ecological success relies on sexual reproduction. The sea anemone Nematostella vectensis, which has emerged as an important model organism for developmental studies, can be induced for spawning by temperature elevation and light exposure. To uncover molecular mechanisms and pathways underlying spawning, we characterized the transcriptome of Nematostella females before and during spawning induction. We identified an array of processes involving numerous receptors, circadian clock components, cytoskeleton, and extracellular transcripts that are upregulated upon spawning induction. Concurrently, processes related to the cell cycle, fatty acid metabolism, and other housekeeping functions are downregulated. Real-time qPCR revealed that light exposure has a minor effect on expression levels of most examined transcripts, implying that temperature change is a stronger inducer for spawning in Nematostella. Our findings reveal the mechanisms that may enable the mesenteries to serve as a gonad-like tissue for the developing oocytes and expand our understanding of sexual reproduction in cnidarians.Summary statementAnalysis of transcriptional changes during spawning induction in Nematostella vectensis, revealed upregulation of processes related to signal perception and cytoskeleton rearrangement and downregulation of fatty acid metabolism and housekeeping processes.

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Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds

Animals ◽

10.3390/ani11113169 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3169

Author(s):

Xinhua Hou ◽

Ligang Wang ◽

Fuping Zhao ◽

Xin Liu ◽

Hongmei Gao ◽

...

Keyword(s):

Skeletal Muscle ◽

Fatty Acid ◽

Fatty Acid Metabolism ◽

Muscle Development ◽

Target Genes ◽

Acid Metabolism ◽

Differentially Expressed ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Pig Breeds

RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.

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Analysis of Serum Biochemical Indexes, Egg Quality, and Liver Transcriptome in Laying Hens Fed Diets Supplemented with Gynostemma pentaphyllum Powder

Genes ◽

10.3390/genes12121942 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1942

Author(s):

Tao Li ◽

Shuya Zhang ◽

Jiqiao Zhang ◽

Yiping Song ◽

Xiuyu Bao ◽

...

Keyword(s):

Fatty Acid ◽

Fatty Acid Metabolism ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Egg Quality ◽

Cholesterol Concentration ◽

Feed Additive ◽

Control Group ◽

Gynostemma Pentaphyllum ◽

Ppar Pathway

Gynostemma pentaphyllum (GP), known as “southern ginseng”, can reduce the blood pressure and blood lipid levels. In this study, 300 layer chicks of one day old were divided randomly into three groups (control group (base diet), high addition group (base diet with 1% GP), and low addition group (base diet with 0.5% GP)). After 29 weeks, the growth performance, egg quality, and serum index were determined. Additionally, liver mRNA was identified using RNA-seq to investigate the molecular mechanisms. The results indicated that the serum total cholesterol and triglycerides decreased significantly in the GP addition group. The addition of GP increased the egg weight, Haugh unit and redness (a*) of the egg yolk color, and reduced the yolk cholesterol concentration. Moreover, 95 differentially expressed genes (DEGs) were screened between the control and GP addition group. GO and the KEGG analysis showed that the PPAR pathway was significantly enriched. Five fatty acid metabolism-related genes (FABP3, CYP7A1, ANKRD22, SCD1, and PCK1) were validated by qRT-PCR analysis, which confirmed the tendency of the expression. These DEGs in the PPAR pathway may be the key factors of GP affecting fatty acid metabolism. These results may provide a theoretical basis for further research and new insights into GP as a feed additive.

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