scholarly journals Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon

2017 ◽  
Author(s):  
Evan P. Starr ◽  
Shengjing Shi ◽  
Steven J. Blazewicz ◽  
Alexander J. Probst ◽  
Donald J. Herman ◽  
...  
Keyword(s):  
Rhizosphere Soil ◽  
De Novo ◽  
Plant Root ◽  
Gradient Centrifugation ◽  
Isotopic Labeling ◽  
Building Blocks ◽  
Carbon Utilization ◽  
Nucleotide Synthesis ◽  
Dna And Rna ◽  
Dna And Rna Synthesis

AbstractBackgroundThe transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowledge gaps related to which soil-associated microorganisms take up plant carbon in the rhizosphere and the fate of that carbon.ResultsWe conducted an experiment in which common wild oats (Avena fatua) were grown in a 13CO2 atmosphere and the rhizosphere and non-rhizosphere soil was sampled for genomic analyses. Density gradient centrifugation of DNA extracted from soil samples enabled distinction of microbes that did and did not incorporate the 13C into their DNA. A 1.45 Mbp genome of a Saccharibacteria (TM7) was identified and, despite the microbial complexity of rhizosphere soil, curated to completion. The genome lacks many biosynthetic pathways, including genes required to synthesize DNA de novo. Rather, it requires externally-derived nucleotides for DNA and RNA synthesis. Given this, we conclude that rhizosphere-associated Saccharibacteria recycle DNA from bacteria that live off plant exudates and/or phage that acquired 13C because they preyed upon these bacteria and/or directly from the labelled plant DNA. Isotopic labeling indicates that the population was replicating during the six-week period of plant growth. Interestingly, the genome is ~30% larger than other complete Saccharibacteria genomes from non-soil environments, largely due to more genes for complex carbon utilization and amino acid metabolism. Given the ability to degrade cellulose, hemicellulose, pectin, starch and 1,3-β-glucan, we predict that this Saccharibacteria generates energy by fermentation of soil necromass and plant root exudates to acetate or lactate. The genome encodes a linear electron transport chain featuring a terminal oxidase, suggesting that this Saccharibacteria may respire aerobically. The genome encodes a hydrolase that could breakdown salicylic acid, a plant defense signaling molecule, and genes to make a variety of isoprenoids, including the plant hormone zeatin.ConclusionsRhizosphere Saccharibacteria likely depend on other bacteria for basic cellular building blocks. We propose that isotopically labeled CO2 is incorporated into plant-derived carbon and then into the DNA of rhizosphere organisms capable of nucleotide synthesis, and the nucleotides are recycled into Saccharibacterial genomes.

scholarly journals Targeting viral genome synthesis as broad-spectrum approach against RNA virus infections

2020 ◽  
Vol 28 ◽  
pp. 204020662097678
Author(s):  
Johanna Huchting
Keyword(s):  
Broad Spectrum ◽  
Viral Genome ◽  
De Novo ◽  
Rna Viruses ◽  
Rna Virus ◽  
Antiviral Drug ◽  
Building Blocks ◽  
Structural Features ◽  
Pathogen Transmission ◽  
Nucleotide Synthesis

Zoonotic spillover, i.e. pathogen transmission from animal to human, has repeatedly introduced RNA viruses into the human population. In some cases, where these viruses were then efficiently transmitted between humans, they caused large disease outbreaks such as the 1918 flu pandemic or, more recently, outbreaks of Ebola and Coronavirus disease. These examples demonstrate that RNA viruses pose an immense burden on individual and public health with outbreaks threatening the economy and social cohesion within and across borders. And while emerging RNA viruses are introduced more frequently as human activities increasingly disrupt wild-life eco-systems, therapeutic or preventative medicines satisfying the “one drug-multiple bugs”-aim are unavailable. As one central aspect of preparedness efforts, this review digs into the development of broadly acting antivirals via targeting viral genome synthesis with host- or virus-directed drugs centering around nucleotides, the genomes’ universal building blocks. Following the first strategy, selected examples of host de novo nucleotide synthesis inhibitors are presented that ultimately interfere with viral nucleic acid synthesis, with ribavirin being the most prominent and widely used example. For directly targeting the viral polymerase, nucleoside and nucleotide analogues (NNAs) have long been at the core of antiviral drug development and this review illustrates different molecular strategies by which NNAs inhibit viral infection. Highlighting well-known as well as recent, clinically promising compounds, structural features and mechanistic details that may confer broad-spectrum activity are discussed. The final part addresses limitations of NNAs for clinical development such as low efficacy or mitochondrial toxicity and illustrates strategies to overcome these.

scholarly journals Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

2020 ◽  
Author(s):  
Evan P. Starr ◽  
Shengjing Shi ◽  
Steven J. Blazewicz ◽  
Benjamin J. Koch ◽  
Alexander J. Probst ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Plant Growth ◽  
Rhizosphere Soil ◽  
Plant Root ◽  
Gradient Centrifugation ◽  
Strong Interactions ◽  
Plant Signaling ◽  
Plant Growth Promoting ◽  
Metagenomic Study ◽  
Plant Pathogenicity

AbstractThe functioning, health, and productivity of soil is intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and non-rhizosphere soil at six and nine weeks of plant growth and extracted DNA that was then separated by density using gradient centrifugation. Thirty-two fractions from each sample were grouped by density, sequenced, assembled, and binned to generate 55 unique microbial genomes that were >70% complete. The complete 18S rRNA sequences of several micro-eukaryotic bacterivores and fungi were enriched in 13C. We generated several circularized bacteriophage (phage) genomes, some of which were the most labelled entities in the rhizosphere. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genomes for traits known to be used in interactions involving bacteria, micro-eukaryotes and plant roots and found that heavily isotopically-labeled bacteria have the ability to modulate plant signaling hormones, possess numerous plant pathogenicity factors, and produce toxins targeting micro-eukaryotes. Overall, 13C stable isotope-informed genome-resolved metagenomics revealed that very active bacteria often have the potential for strong interactions with plants and directly established that phage can be important agents of turnover of plant-derived carbon in soil.

scholarly journals The role of IMP dehydrogenase 2 in Inauhzin-induced ribosomal stress

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Qi Zhang ◽  
Xiang Zhou ◽  
RuiZhi Wu ◽  
Amber Mosley ◽  
Shelya X Zeng ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
De Novo ◽  
Cancer Cell Growth ◽  
Nucleotide Biosynthesis ◽  
Imp Dehydrogenase ◽  
Dna And Rna ◽  
Dna And Rna Synthesis ◽  
P53 Activation ◽  
Ribosomal Stress

The ‘ribosomal stress (RS)-p53 pathway’ is triggered by any stressor or genetic alteration that disrupts ribosomal biogenesis, and mediated by several ribosomal proteins (RPs), such as RPL11 and RPL5, which inhibit MDM2 and activate p53. Inosine monophosphate (IMP) dehydrogenase 2 (IMPDH2) is a rate-limiting enzyme in de novo guanine nucleotide biosynthesis and crucial for maintaining cellular guanine deoxy- and ribonucleotide pools needed for DNA and RNA synthesis. It is highly expressed in many malignancies. We previously showed that inhibition of IMPDH2 leads to p53 activation by causing RS. Surprisingly, our current study reveals that Inauzhin (INZ), a novel non-genotoxic p53 activator by inhibiting SIRT1, can also inhibit cellular IMPDH2 activity, and reduce the levels of cellular GTP and GTP-binding nucleostemin that is essential for rRNA processing. Consequently, INZ induces RS and the RPL11/RPL5-MDM2 interaction, activating p53. These results support the new notion that INZ suppresses cancer cell growth by dually targeting SIRT1 and IMPDH2.

scholarly journals The Dynamic Influence of Olorofim (F901318) on the Cell Morphology and Organization of Living Cells of Aspergillus fumigatus

2020 ◽  
Vol 6 (2) ◽  
pp. 47
Author(s):  
Saskia du Pré ◽  
Mike Birch ◽  
Derek Law ◽  
Nicola Beckmann ◽  
Graham E. M. Sibley ◽  
...  
Keyword(s):  
Cell Wall ◽  
Aspergillus Fumigatus ◽  
De Novo ◽  
Dynamic Structure ◽  
Building Blocks ◽  
Uridine Diphosphate ◽  
Dna And Rna ◽  
Diphosphate Glucose ◽  
Cycle Regulation ◽  
Mitotracker Red

The first characterized antifungal in the orotomide class is olorofim. It targets the de novo pyrimidine biosynthesis pathway by inhibiting dihydroorotate dehydrogenase (DHODH). The pyrimidines uracil, thymine and cytosine are the building blocks of DNA and RNA; thus, inhibition of their synthesis is likely to have multiple effects, including affecting cell cycle regulation and protein synthesis. Additionally, uridine-5′-triphosphate (UTP) is required for the formation of uridine-diphosphate glucose (UDP-glucose), which is an important precursor for several cell wall components. In this study, the dynamic effects of olorofim treatment on the morphology and organization of Aspergillus fumigatus hyphae were analyzed microscopically using confocal live-cell imaging. Treatment with olorofim led to increased chitin content in the cell wall, increased septation, enlargement of vacuoles and inhibition of mitosis. Furthermore, vesicle-like structures, which could not be stained or visualized with a range of membrane- or vacuole-selective dyes, were found in treated hyphae. A colocalization study of DHODH and MitoTracker Red FM confirmed for the first time that A. fumigatus DHODH is localized in the mitochondria. Overall, olorofim treatment was found to significantly influence the dynamic structure and organization of A. fumigatus hyphae.

scholarly journals Inhibition of guanosine monophosphate synthetase (GMPS) blocks glutamine metabolism and prostate cancer growth in vitro and in vivo

2020 ◽  
Author(s):  
Qian Wang ◽  
Yi F. Guan ◽  
Sarah E. Hancock ◽  
Kanu Wahi ◽  
Michelle van Geldermalsen ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cell Growth ◽  
Cancer Cells ◽  
De Novo ◽  
Building Blocks ◽  
Guanosine Monophosphate ◽  
Glutamine Metabolism ◽  
Metabolic Effects ◽  
Nucleotide Synthesis ◽  
Purine Salvage Pathways

AbstractCancer cells increase their uptake of nutrients and metabolize them to provide the necessary building blocks for new cancer cells. Glutamine is a critical nutrient in cancer, however its contribution to purine metabolism in prostate cancer has not previously been determined. Guanosine monophosphate synthetase (GMPS) acts in the de novo purine biosynthesis pathway, utilizing a glutamine amide to synthesize the guanine nucleotide and replenish the purine pool in proliferative cancer cells. This study demonstrates that GMPS mRNA expression correlates with Gleason score in prostate cancer samples, while high GMPS expression was associated with decreased rates of overall and disease/progression-free survival. Pharmacological inhibition or knockdown of GMPS significantly decreased cell growth in both LNCaP and PC-3 prostate cancer cells. GMPS knockdown was rescued by addition of extracellular guanosine to the media, suggesting a direct effect on nucleotide synthesis. We utilized 15N-(amide)-glutamine and U-13C5-glutamine metabolomics to dissect the pathways involved, and intriguingly, despite similar growth inhibition by GMPS knockdown, we show unique metabolic effects across each cell line. PC-3 cells showed a build-up of purine precursors, as well as activation of purine salvage pathways highlighted by significant increases in guanine, adenosine, inosine and cytosine. Both cell lines exhibited increased levels of pyrimidines and prioritized TCA cycle in distinct ways to produce increased aspartate, another important purine precursor. Using a PC-3 xenograft mouse model, tumor growth was also significantly decreased after GMPS knockdown. These data further highlight the importance of glutamine metabolism for prostate cancer cell growth and provide support for GMPS as a new therapeutic target in prostate cancer.

scholarly journals Antimicrobial Activity and Mode of Action of Celastrol, a Nortriterpen Quinone Isolated from Natural Sources

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 591
Author(s):  
Nayely Padilla-Montaño ◽  
Leandro de León Guerra ◽  
Laila Moujir
Keyword(s):  
Antimicrobial Activity ◽  
Cytoplasmic Membrane ◽  
Bactericidal Effect ◽  
Inoculum Size ◽  
Bacterial Populations ◽  
Gram Positive Bacteria ◽  
Dna And Rna ◽  
Dna And Rna Synthesis ◽  
Natural Derivative ◽  
Interesting Alternative

Species of the Celastraceae family are traditionally consumed in different world regions for their stimulating properties. Celastrol, a triterpene methylene quinone isolated from plants of celastraceas, specifically activates satiety centers in the brain that play an important role in controlling body weight. In this work, the antimicrobial activity and mechanism of action of celastrol and a natural derivative, pristimerin, were investigated in Bacillus subtilis. Celastrol showed a higher antimicrobial activity compared with pristimerin, being active against Gram-positive bacteria with minimum inhibitory concentrations (MICs) that ranged between 0.16 and 2.5 µg/mL. Killing curves displayed a bactericidal effect that was dependent on the inoculum size. Monitoring of macromolecular synthesis in bacterial populations treated with these compounds revealed inhibition in the incorporation of all radiolabeled precursors, but not simultaneously. Celastrol at 3 µg/mL and pristimerin at 10 µg/mL affected DNA and RNA synthesis first, followed by protein synthesis, although the inhibitory action on the uptake of radiolabeled precursors was more dramatic with celastrol. This compound also caused cytoplasmic membrane disruption observed by potassium leakage and formation of mesosome-like structures. The inhibition of oxygen consumption of whole and disrupted cells after treatments with both quinones indicates damage in the cellular structure, suggesting the cytoplasmic membrane as a potential target. These findings indicate that celastrol could be considered as an interesting alternative to control outbreaks caused by spore-forming bacteria.

scholarly journals Cellular pyrimidine imbalance triggers mitochondrial DNA–dependent innate immunity

2021 ◽  
Author(s):  
Hans-Georg Sprenger ◽  
Thomas MacVicar ◽  
Amir Bahat ◽  
Kai Uwe Fiedler ◽  
Steffen Hermans ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Cultured Cells ◽  
De Novo ◽  
Metabolic Response ◽  
Interferon Response ◽  
Type I ◽  
Nucleotide Synthesis ◽  
Pyrimidine Synthesis ◽  
Pyrimidine Nucleotide ◽  
De Novo Pyrimidine Synthesis

AbstractCytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP–AMP synthase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS–STING–TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflammation in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS–STING–TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.

De Novo Synthesis of l-Colitose and l-Rhodinose Building Blocks

2011 ◽  
Vol 77 (2) ◽  
pp. 870-877 ◽  
Author(s):  
Oliviana Calin ◽  
Rajan Pragani ◽  
Peter H. Seeberger
Keyword(s):  
De Novo ◽  
Building Blocks ◽  
De Novo Synthesis
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