scholarly journals Pangenomics reveals alternative environmental lifestyles among chlamydiae

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Stephan Köstlbacher ◽  
Astrid Collingro ◽  
Tamara Halter ◽  
Frederik Schulz ◽  
Sean P. Jungbluth ◽  
...  
Keyword(s):  
Core Genome ◽  
Tricarboxylic Acid Cycle ◽  
Atp Synthesis ◽  
Arginine Deiminase ◽  
Intracellular Bacteria ◽  
Large Core ◽  
Environmental Distribution ◽  
Pyruvate Fermentation ◽  
Anaerobic Energy ◽  
Reductive Tricarboxylic Acid Cycle

AbstractChlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

scholarly journals Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period

2018 ◽  
Author(s):  
Angus Angermeyer ◽  
Moon Moon Das ◽  
Durg Vijai Singh ◽  
Kimberley D. Seed
Keyword(s):  
Vibrio Cholerae ◽  
Bay Of Bengal ◽  
Core Genome ◽  
Coastal Areas ◽  
Lytic Bacteriophage ◽  
Large Core ◽  
Accessory Genome ◽  
El Tor ◽  
Endemic Cholera ◽  
Over Time

AbstractThe Vibrio cholerae biotype ‘El Tor’ is responsible for all current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal and are hypothesized to originate from the coastal areas near the Bay of Bengal where the lytic bacteriophage ICP1 specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stool since 2001. However, little is known about its genomic differences between ICP1 strains collected over time. Here we elucidate the pan-genome and phylogeny of ICP1 strains by aligning, annotating and analyzing the genomes of 19 distinct isolates collected between 2001 and 2012. Our results reveal that ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes as well as a CRISPR-Cas system, which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of this V. cholerae-associated bacteriophages.

scholarly journals The effect of glucagon treatment and starvation of virgin and lactating rats on the rates of oxidation of octanoyl-l-carnitine and octanoate by isolated liver mitochondria

1980 ◽  
Vol 190 (2) ◽  
pp. 293-300 ◽  
Author(s):  
Victor A. Zammit
Keyword(s):  
Fatty Acids ◽  
Tricarboxylic Acid Cycle ◽  
Atp Synthesis ◽  
Liver Mitochondria ◽  
Oxidation Rates ◽  
Consumption Rates ◽  
Mitochondrial Oxidation ◽  
Elevated Rate ◽  
Isolated Liver ◽  
Chain Fatty Acids

1. Oxygen-consumption rates owing to oxidation of octanoate or octanoylcarnitine by isolated mitochondria from livers of fed, starved and glucagon-treated virgin or 12-day-lactating animals were measured under State-3 and State-4 conditions, in the presence or absence of l-malate and inhibitors of tricarboxylic acid-cycle activity (malonate and fluorocitrate). 2. Mitochondria from fed lactating animals had a slightly lower rate of octanoylcarnitine oxidation than did those of fed virgin animals, whereas the rates of octanoate oxidation were unaffected. 3. Starvation of virgin animals for 24h or 48h resulted in a large (70–100%) increase in mitochondrial octanoylcarnitine oxidation; rates of octanoate oxidation were either unaffected (24 and 48h starvation in the absence of malonate and fluorocitrate) or diminished by 30% (48h starvation in the presence of inhibitors). In lactating animals, 24h starvation resulted in a smaller increase in the rate of octanoylcarnitine oxidation than that obtained for mitochondria from virgin rats. 4. Glucagon treatment (by intra-abdominal injection) of fed virgin and lactating rats increased the rate of mitochondrial oxidation of both octanoylcarnitine and octanoate. Injection of glucagon into 48h-starved virgin rats did not increase further the already elevated rate of octanoylcarnitine oxidation, but reversed the inhibition of octanoate β-oxidation observed for these mitochondria in the presence of malonate and fluorocitrate. 5. It is suggested that glucagon activates octanoylcarnitine oxidation by increasing the activity of the carnitine/acylcarnitine transport system [Parvin & Pande (1979) J. Biol. Chem.254, 5423–5429] and that the increase in octanoate oxidation by mitochondria from glucagon-treated animals is caused by the increased rate of ATP synthesis in these mitochondria. 6. The results are discussed in relation to the increased capacity of the liver to oxidize long-chain fatty acids and carnitine esters of medium-chain fatty acids under conditions characterized by increased ketogenesis.

scholarly journals The Role of Ketone Bodies in Improving Neurological Function and Efficiency

Health Scope ◽  
2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Deepanshu Naithani ◽  
Santosh Kumar Karn
Keyword(s):  
Cancer Cells ◽  
Single Molecule ◽  
Energy Production ◽  
Ketone Bodies ◽  
Tricarboxylic Acid Cycle ◽  
Energy Levels ◽  
Atp Synthesis ◽  
Water Soluble ◽  
Atp Production ◽  
Small Water

: Neurological coordination is essential for performing biological and mechanical activities achieved by the cooperation of biomolecules such as carbohydrates, lipids, and proteins. It plays an important role in energy production, which can be fascinatingly improved by ketone bodies. Ketone bodies are small, water-soluble lipid molecules by shifting the glycolytic phase KBs directly enters into the tricarboxylic acid cycle for ATP synthesis. It leads to the production of much more energy levels than a single molecule of glucose. Therefore, it could have a profound effect on neuro-metabolism as well as bioenergetics of ATP production. These neuro-enhancement properties are useful for epilepsy, Alzheimer's, and several neurocognitive disorders treatment. Interestingly, the cancer cells cannot use it for efficiently energy production results in decreasing cancer cells viability. This review summarized ketone bodies generation, related imperative effects on normal cells, and more importantly its application in various neurological disorders treatment by rising neuronal functions.

scholarly journals Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Tomonari Sumi ◽  
Kouji Harada
Keyword(s):  
Carbon Metabolism ◽  
Carbon Fixation ◽  
Citrate Synthase ◽  
Tricarboxylic Acid Cycle ◽  
Necessary Condition ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Biomass Components ◽  
Kinetics Of ◽  
Reductive Tricarboxylic Acid Cycle

AbstractThe origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood–Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.

scholarly journals Comparison of two African rice species through a new pan-genomic approach on massive data

2018 ◽  
Author(s):  
Cécile Monat ◽  
Christine Tranchant-Dubreuil ◽  
Stefan Engelen ◽  
Karine Labadie ◽  
Emmanuel Paradis ◽  
...  
Keyword(s):  
Core Genome ◽  
Oryza Glaberrima ◽  
Large Core ◽  
African Rice ◽  
Asian Rice ◽  
External Reference ◽  
Genomic Approach ◽  
Cultivated Species ◽  
Group Species ◽  
High Depth

AbstractPangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii, and mapped them on the external reference from Asian rice O. sativa. We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.

scholarly journals Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and “Candidatus Thiothrix anitrata” sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation

2021 ◽  
Vol 12 ◽  
Author(s):  
Nikolai V. Ravin ◽  
Tatyana S. Rudenko ◽  
Dmitry D. Smolyakov ◽  
Alexey V. Beletsky ◽  
Andrey L. Rakitin ◽  
...  
Keyword(s):  
Core Genome ◽  
Carbon Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Sulfur Metabolism ◽  
Sulfide Oxidation ◽  
Calvin Cycle ◽  
Sulfur Oxidation ◽  
Rrna Gene ◽  
Reduced Sulfur Compounds ◽  
Hybridization Data

Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.

scholarly journals Hormone-Independent Mouse Mammary Adenocarcinomas with Different Metastatic Potential Exhibit Different Metabolic Signatures

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1242
Author(s):  
Daniela Bispo ◽  
Victoria Fabris ◽  
Caroline A. Lamb ◽  
Claudia Lanari ◽  
Luisa A. Helguero ◽  
...  
Keyword(s):  
Acid Metabolism ◽  
Tricarboxylic Acid Cycle ◽  
Metastatic Breast ◽  
Atp Synthesis ◽  
Metastatic Potential ◽  
Polar Compounds ◽  
Phospholipid Metabolism ◽  
Nucleotide Metabolism ◽  
Nmr Metabolomics ◽  
Metabolic Signatures

The metabolic characteristics of metastatic and non-metastatic breast carcinomas remain poorly studied. In this work, untargeted Nuclear Magnetic Resonance (NMR) metabolomics was used to compare two medroxyprogesterone acetate (MPA)-induced mammary carcinomas lines with different metastatic abilities. Different metabolic signatures distinguished the non-metastatic (59-2-HI) and the metastatic (C7-2-HI) lines, with glucose, amino acid metabolism, nucleotide metabolism and lipid metabolism as the major affected pathways. Non-metastatic tumours appeared to be characterised by: (a) reduced glycolysis and tricarboxylic acid cycle (TCA) activities, possibly resulting in slower NADH biosynthesis and reduced mitochondrial transport chain activity and ATP synthesis; (b) glutamate accumulation possibly related to reduced glutathione activity and reduced mTORC1 activity; and (c) a clear shift to lower phosphoscholine/glycerophosphocholine ratios and sphingomyelin levels. Within each tumour line, metabolic profiles also differed significantly between tumours (i.e., mice). Metastatic tumours exhibited marked inter-tumour changes in polar compounds, some suggesting different glycolytic capacities. Such tumours also showed larger intra-tumour variations in metabolites involved in nucleotide and cholesterol/fatty acid metabolism, in tandem with less changes in TCA and phospholipid metabolism, compared to non-metastatic tumours. This study shows the valuable contribution of untargeted NMR metabolomics to characterise tumour metabolism, thus opening enticing opportunities to find metabolic markers related to metastatic ability in endocrine breast cancer.

Sign in / Sign up

Export Citation Format

Share Document