Cas9 Nickase-Assisted RNA Repression Enables Stable and Efficient Manipulation of Essential Metabolic Genes in Clostridium cellulolyticum

AbstractThere is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.

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Increased fat oxidation and regulation of metabolic genes with ultraendurance exercise

Acta Physiologica ◽

10.1111/j.1748-1716.2007.01709.x ◽

2007 ◽

Vol 191 (1) ◽

pp. 77-86 ◽

Cited By ~ 16

Author(s):

J. W. Helge ◽

N. J. Rehrer ◽

H. Pilegaard ◽

P. Manning ◽

S. J. E. Lucas ◽

...

Keyword(s):

Fat Oxidation ◽

Metabolic Genes

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Tumor metabolism and associated serum metabolites define prognostic subtypes of Asian hepatocellular carcinoma

Scientific Reports ◽

10.1038/s41598-021-91560-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yotsawat Pomyen ◽

Anuradha Budhu ◽

Jittiporn Chaisaingmongkol ◽

Marshonna Forgues ◽

Hien Dang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Fatty Acid ◽

Fatty Acid Metabolism ◽

Acid Metabolism ◽

Treatment Effectiveness ◽

Data Types ◽

Serum Metabolites ◽

Non Invasive ◽

Metabolic Genes ◽

Tissue Metabolites

AbstractTreatment effectiveness in hepatocellular carcinoma (HCC) depends on early detection and precision-medicine-based patient stratification for targeted therapies. However, the lack of robust biomarkers, particularly a non-invasive diagnostic tool, precludes significant improvement of clinical outcomes for HCC patients. Serum metabolites are one of the best non-invasive means for determining patient prognosis, as they are stable end-products of biochemical processes in human body. In this study, we aimed to identify prognostic serum metabolites in HCC. To determine serum metabolites that were relevant and representative of the tissue status, we performed a two-step correlation analysis to first determine associations between metabolic genes and tissue metabolites, and second, between tissue metabolites and serum metabolites among 49 HCC patients, which were then validated in 408 additional Asian HCC patients with mixed etiologies. We found that certain metabolic genes, tissue metabolites and serum metabolites can independently stratify HCC patients into prognostic subgroups, which are consistent across these different data types and our previous findings. The metabolic subtypes are associated with β-oxidation process in fatty acid metabolism, where patients with worse survival outcome have dysregulated fatty acid metabolism. These serum metabolites may be used as non-invasive biomarkers to define prognostic tumor molecular subtypes for HCC.

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Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species

Journal of Fungi ◽

10.3390/jof7060464 ◽

2021 ◽

Vol 7 (6) ◽

pp. 464

Author(s):

Marina Marcet-Houben ◽

Maria Villarino ◽

Laura Vilanova ◽

Antonieta De Cal ◽

Jan A. L. van Kan ◽

...

Keyword(s):

Brown Rot ◽

Weather Conditions ◽

Genomic Variation ◽

Disease Development ◽

Stone Fruits ◽

Yield Losses ◽

Future Studies ◽

Metabolic Genes ◽

Pome Fruits ◽

Significant Yield

Brown rot, caused by Monilinia spp., is among the most important diseases in stone fruits, and some pome fruits (mainly apples). This disease is responsible for significant yield losses, particularly in stone fruits, when weather conditions favorable for disease development appear. To achieve future sustainable strategies to control brown rot on fruit, one potential approach will be to characterize genomic variation among Monilinia spp. to define, among others, the capacity to infect fruit in this genus. In the present work, we performed genomic and phylogenomic comparisons of five Monilinia species and inferred differences in numbers of secreted proteins, including CAZy proteins and other proteins important for virulence. Duplications specific to Monilinia were sparse and, overall, more genes have been lost than gained. Among Monilinia spp., low variability in the CAZome was observed. Interestingly, we identified several secondary metabolism clusters based on similarity to known clusters, and among them was a cluster with homology to pyriculol that could be responsible for the synthesis of chloromonilicin. Furthermore, we compared sequences of all strains available from NCBI of these species to assess their MAT loci and heterokaryon compatibility systems. Our comparative analyses provide the basis for future studies into understanding how these genomic differences underlie common or differential abilities to interact with the host plant.

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Transcriptome analysis of Escherichia coli K1 after therapy with hesperidin conjugated with silver nanoparticles

BMC Microbiology ◽

10.1186/s12866-021-02097-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Abdulkader Masri ◽

Naveed Ahmed Khan ◽

Muhammad Zarul Hanifah Md Zoqratt ◽

Qasim Ayub ◽

Ayaz Anwar ◽

...

Keyword(s):

Escherichia Coli ◽

Silver Nanoparticles ◽

Minimum Inhibitory Concentration ◽

Inhibitory Concentration ◽

Neonatal Meningitis ◽

E Coli ◽

Drug Candidates ◽

Metabolic Genes ◽

Genetic Mechanisms ◽

Cell Stress Response

Abstract Backgrounds Escherichia coli K1 causes neonatal meningitis. Transcriptome studies are indispensable to comprehend the pathology and biology of these bacteria. Recently, we showed that nanoparticles loaded with Hesperidin are potential novel antibacterial agents against E. coli K1. Here, bacteria were treated with and without Hesperidin conjugated with silver nanoparticles, and silver alone, and 50% minimum inhibitory concentration was determined. Differential gene expression analysis using RNA-seq, was performed using Degust software and a set of genes involved in cell stress response and metabolism were selected for the study. Results 50% minimum inhibitory concentration with silver-conjugated Hesperidin was achieved with 0.5 μg/ml of Hesperidin conjugated with silver nanoparticles at 1 h. Differential genetic analysis revealed the expression of 122 genes (≥ 2-log FC, P< 0.01) in both E. coli K1 treated with Hesperidin conjugated silver nanoparticles and E. coli K1 treated with silver alone, compared to untreated E. coli K1. Of note, the expression levels of cation efflux genes (cusA and copA) and translocation of ions, across the membrane genes (rsxB) were found to increase 2.6, 3.1, and 3.3- log FC, respectively. Significant regulation was observed for metabolic genes and several genes involved in the coordination of flagella. Conclusions The antibacterial mechanism of nanoparticles maybe due to disruption of the cell membrane, oxidative stress, and metabolism in E. coli K1. Further studies will lead to a better understanding of the genetic mechanisms underlying treatment with nanoparticles and identification of much needed novel antimicrobial drug candidates.

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Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues

Metabolites ◽

10.3390/metabo11040240 ◽

2021 ◽

Vol 11 (4) ◽

pp. 240

Author(s):

Alison Woodward ◽

Alina Pandele ◽

Salah Abdelrazig ◽

Catherine A. Ortori ◽

Iqbal Khan ◽

...

Keyword(s):

Metabolic Pathways ◽

Extraction Method ◽

Limit Of Detection ◽

Rna Extraction ◽

Extraction Process ◽

Extraction Methods ◽

Serum Starvation ◽

Extraction Techniques ◽

Metabolic Genes ◽

Dual Extraction

The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.

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The catalytic domain of endoglucanase A from Clostridium cellulolyticum: effects of arginine 79 and histidine 122 mutations on catalysis.

Journal of Bacteriology ◽

10.1128/jb.174.14.4677-4682.1992 ◽

1992 ◽

Vol 174 (14) ◽

pp. 4677-4682 ◽

Cited By ~ 27

Author(s):

A Belaich ◽

H P Fierobe ◽

D Baty ◽

B Busetta ◽

C Bagnara-Tardif ◽

...

Keyword(s):

Catalytic Domain ◽

Clostridium Cellulolyticum

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Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation

Biotechnology for Biofuels ◽

10.1186/1754-6834-7-25 ◽

2014 ◽

Vol 7 (1) ◽

pp. 25 ◽

Cited By ~ 19

Author(s):

Yongchao Li ◽

Tao Xu ◽

Timothy J Tschaplinski ◽

Nancy L Engle ◽

Yunfeng Yang ◽

...

Keyword(s):

Clostridium Cellulolyticum

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