Biology subjects

Varma, S. J.

Publications and source records attributed to Varma, S. J..

5 recordsLinked to original sources

bioRxiv2024

Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance in Candida albicans

BackgroundFungal infections are an increasing concern, particularly among immunocompromised patients and those with comorbidities who require multiple medications. However, the effects of drugs targeting human pathways on fungal cells, and whether they influence antifungal drug responses, are poorly understood. MethodsWe systematically analyzed clinical guidelines to shortlist non-antifungal drugs commonly used in conditions that increase the likelihood of fungal infections. Focusing on the most prevalent fungal pathogen, we then tested how these drugs affected the antifungal response of Candida albicans to two commonly used antifungals, fluconazole and anidulafungin. Drug interactions identified were further assessed using checkerboard and disk diffusion assays. Finally, antifungal treatment efficacy of fluconazole in combination with negatively interacting drugs was evaluated in an in vivo Galleria mellonella model of disseminated C. albicans infection. FindingsOut of 119 drugs frequently co-administered with antifungals in 40 conditions associated with a high risk of fungal infections, 34 compounds affected the antifungal drug response in C. albicans, with most drugs reducing or antagonising antifungal efficacy, several through increasing resistance or tolerance. Notably, fluconazole combinations with carvedilol and loperamide promoted antifungal resistance in both fungal cultures and in Galleria mellonella. InterpretationOur findings suggest that medications frequently taken by patients at risk of fungal infections regularly act on the fungal pathogens and can affect the effectiveness of antifungals. We propose that human drugs acting on fungal pathogens may be an underestimated factor contributing to the evolution of antifungal tolerance and resistance.

microbiology↗

bioRxiv2022

Occurrence and quantities of DNA modifications across the tree of life

Enzymatic DNA modifications like methylcytosine (5mdC), methyladenine (N6mdA), or hydroxymethylcytosine (5hmdC) are key for chromatin function, gene expression regulation, and antiviral defense, but they remain understudied in non-model organisms. We established a mass spectrometric method for the sensitive and accurate quantification of enzymatic DNA modifications, and analyzed 85 bacterial genomes, 19 plant samples, 41 tissues from 12 animal species, 6 yeast species, and two archaeal species. We report no or only very low concentrations of DNA modifications in yeast and insects, but find DNA modifications universal to both bacteria and higher eukaryotes. Specifically for prokaryotes, our dataset indicates that evolutionary relationships and host-pathogen interactions, but not the ecological niche in general, select for a similar degree of DNA modification. In higher eukaryotes, largest concentration differences between tissues are detected for 5hmdC. Our dataset further reveals unique biological cases that warrant attention in the study of DNA modifications. For instance, while our data shows that most species contain just one dominating DNA modification, we detect all dominianting DNA modifications (5mdC, N6mdA, and 5hmdC) to exist in parallel in Raphanus sativus. Other plant species, like onion, sunflower, or the grass big bluestem, can have more than 35% of cytosines methylated. Finally, 5hmdC, so far mostly studied in the vertebrate central nervous system, was identified to reach a concentration of up to 8% of all cytosines in the Oman garra brain, and was also detected in several plants, like Lepidium sativum. The present study underscores the exploitation of biological diversity for studying DNA modifications.

genomics↗

bioRxiv2020

Single amino acid-promoted reactions link a non-enzymatic chemical network to the early evolution of enzymatic pentose phosphate pathway

How metabolic pathways emerged in early evolution remains largely unknown. Recently discovered chemical networks driven by iron and sulfur resemble reaction sequences found within glycolysis, gluconeogenesis, the oxidative and reductive Krebs cycle, the Wood Ljungdahl as well as the S-adenosylmethionine pathways, components of the core cellular metabolic network. These findings suggest that the evolution of central metabolism was primed by environmental chemical reactions, implying that non-enzymatic reaction networks served as a "template" in the evolution of enzymatic activities. We speculated that the turning point for this transition would depend on the catalytic properties of the simplest structural components of proteins, single amino acids. Here, we systematically combine constituents of Fe(II)-driven non-enzymatic reactions resembling glycolysis and pentose phosphate pathway (PPP), with single proteinogenic amino acids. Multiple reaction rates are enhanced by amino acids. In particular, cysteine is able to replace (and/or complement) the metal ion Fe(II) in driving the non-enzymatic formation of the RNA-backbone metabolite ribose 5-phosphate from 6-phosphogluconate, a rate-limiting reaction of the oxidative PPP. In the presence of both Fe(II) and cysteine, a complex is formed, enabling the non-enzymatic reaction to proceed at a wide range of temperatures. At mundane temperatures, this minimal enzyme-like complex achieves a much higher specificity in the formation of ribose 5-phosphate than the Fe(II)-driven reaction at high temperatures. Hence, simple amino acids can accelerate key steps within metal-promoted metabolism-like chemical networks. Our results imply a stepwise scenario, in which environmental chemical networks served as primers in the early evolution of the metabolic network structure. Significance StatementThe evolutionary roots of metabolic pathways are barely understood. Here we show results consistent with a stepwise scenario during the evolution of (enzymatic) metabolism, starting from non-enzymatic chemical networks. By systematic screening of metabolic-like reactivities in vitro, and using high-throughput analytical techniques, we identify an iron/cysteine complex to act as a minimal enzymelike complex, which consists of a metal ion, an amino acid, and a sugar phosphate ligand. Integrated in a metal-driven, non-enzymatic pentose phosphate pathway, it promotes the formation of the RNA-backbone precursor ribose 5-phosphate at ambient temperature.

biochemistry↗

bioRxiv2019

A hydrogen dependent geochemical analogue of primordial carbon and energy metabolism

Hydrogen gas, H2, is generated in alkaline hydrothermal vents from reactions of iron containing minerals with water during a geological process called serpentinization. It has been a source of electrons and energy since there was liquid water on the early Earth, and it fuelled early anaerobic ecosystems in the Earths crust1-3. H2 is the electron donor for the most ancient route of biological CO2 fixation, the acetyl-CoA (or Wood-Ljungdahl) pathway, which unlike any other autotrophic pathway simultaneously supplies three key requirements for life: reduced carbon in the form of acetyl groups, electrons in the form of reduced ferredoxin, and ion gradients for energy conservation in the form of ATP4,5. The pathway is linear, not cyclic, it releases energy rather than requiring energy input, its enzymes are replete with primordial metal cofactors6,7, it traces to the last universal common ancestor8 and abiotic, geochemical organic syntheses resembling segments of the pathway occur in hydrothermal vents today9,10. Laboratory simulations of the acetyl-CoA pathways reactions include the nonenzymatic synthesis of thioesters from CO and methylsulfide11, the synthesis of acetate12 and pyruvate13 from CO2 using native iron or external electrochemical potentials14 as the electron source. However, a full abiotic analogue of the acetyl-CoA pathway from H2 and CO2 as it occurs in life has not been reported to date. Here we show that three hydrothermal minerals -- awaruite (Ni3Fe), magnetite (Fe3O4) and greigite (Fe3S4) -- catalyse the fixation of CO2 with H2 at 100 {degrees}C under alkaline aqueous conditions. The product spectrum includes formate (100 mM), acetate (100 M), pyruvate (10 M), methanol (100 M), and methane. With these simple catalysts, the overall exergonic reaction of the acetyl-CoA pathway is facile, shedding light on both the geochemical origin of microbial metabolism and on the nature of abiotic formate and methane synthesis in modern hydrothermal vents.

evolutionary biology↗

bioRxiv2017

Metals enable a non-enzymatic acetyl CoA pathway

The evolutionary origins of carbon fixation, the biological conversion of CO2 to metabolites, remain unclear. Phylogenetics indicates that the AcCoA pathway, the reductive fixation of CO2 to acetyl and pyruvate, was a key biosynthetic route used by the Last Universal Common Ancestor (LUCA) to build its biochemistry. However, debate exists over whether CO2 fixation is a relatively late invention of pre-LUCA evolution or whether it dates back to prebiotic chemistry. Here we show that zero-valent forms of the transition metals known to act as co-factors in the AcCoA pathway (Fe0, Ni0, Co0) fix CO2 on their surface in a manner closely resembling the biological pathway, producing acetate and pyruvate in near mM concentrations following cleavage from the surface. The reaction is robust over a wide range of temperatures and pressures with acetate and pyruvate constituting the major products in solution at 1 bar of CO2 and 30 {degrees}g;C. The discovered conditions also promote 7 of the 11 steps of the rTCA cycle and amino acid synthesis, providing a stunning direct connection between simple inorganic chemistry and ancient CO2-fixation pathways. The results strongly sup-port the notion that CO2-fixation pathways are an outgrowth of spontaneous geochemistry.

evolutionary biology↗