Metabolic evolution of pyranopterin-dependent biochemistry DOI Creative Commons
Joshua E. Goldford, Ranjani Murali, Joan Selverstone Valentine

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 5, 2023

Abstract Molybdenum (Mo)-dependent biochemistry is essential for many key metabolic pathways. However, theory and geological evidence suggests that its solubility during long intervals with low dioxygen would have limited availability on early Earth. We developed models of evolution found reactions employing tungsten (W)-dependent likely preceded Mo-dependent reactions, where Mo-usage increased dramatically after the production dioxygen. Consistent this finding, we analyzed genomes from over 65,000 phylogenetically diverse microbes metagenomes an environmental dataset, observed dioxygen-utilizing prokaryotes living in aerobic niches are enriched enzymes as compared to anaerobic microbes. As independent evaluation hypothesis, combined protein language models, machine learning, phylogenomic analysis build a classifier W- or Mo-pterin dependence DMSO reductase superfamily, W-pterin-dependent cluster near root tree subset late-evolving aldehyde oxidoreductases (AORs) aerobes predicted rely Mo instead W. Overall, our combination modeling, phenotypic analysis, suggest Mo-pterin-dependent derived biochemistry, drastically rise oxygen.

Язык: Английский

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact? DOI Creative Commons
Armen Y. Mulkidjanian, Daria V. Dibrova, A. Yu. Bychkov

и другие.

Life, Год журнала: 2025, Номер 15(3), С. 399 - 399

Опубликована: Март 4, 2025

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor potassium alkali cofactor, which implies their abundance in the habitats of first organisms. Intriguingly, lunar rocks contain a hundred times less ten than Earth’s crust; Moon is also depleted other moderately volatile elements (MVEs). Current theories impact formation attribute this depletion to MVEs still being gaseous state when hot post-impact disk contracted separated from nascent Moon. then fell out onto juvenile protocrust; zinc, most metal, precipitated last, just after potassium. According our calculations, top layer protocrust must have contained up 1019 kg metallic powerful reductant. venting geothermal fluids through MVE-fallout layer, rich radioactive potassium, both capable reducing carbon dioxide dinitrogen, yielded plethora organic molecules released with vapor. In pools vapor condensate, RNA-like may emerged pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, polymerizable molecules.

Язык: Английский

Процитировано

0
Transcriptome Screening of Hormone-Regulated Genes Related to Fruit Development in Zizyphus jujuba Mill. cv. Goutou Fruits at Different Ripening Stages DOI Open Access

Shuting Luo,

Yusen Zhang, Beibei Shi

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(8), С. 3476 - 3476

Опубликована: Апрель 8, 2025

Zizyphus jujuba Mill. cv. Goutou is an edible and medicinal fruit whose development significantly impacts the metabolism accumulation of nutrients regulated by plant hormones. In this study, metal element triterpene acid content were investigated transcriptomic analyses conducted to evaluate changes in seven ripening stages (Stages I–VII) Z. Goutou. We first analyzed elements found that concentrations Magnesium (Mg), Aluminum (Al), Calcium (Ca), Manganese (Mn), Cuprum (Cu) highest at Stage I; comparison, Zinc (Zn) Ferrum (Fe) IV. Additionally, three acids detected fruits, with contents betulinic oleanolic being VII ursolic I. Subsequently, through Gene Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) annotations, we identified 40, 18, 9, 6, 11 differentially expressed genes involved auxin, abscisic (ABA), ethylene, gibberellic (GA), jasmonic (JA) signaling pathways, respectively. Notably, associated ABA, including ZjABA3, ZjABA4, ZjABA6, ZjABA7, ZjABA10, ZjABA11, ZjABA15-ZjABA19, ZjABA22-ZjABA25, ZjABA27-ZjABA33, downregulated from I VII. Conversely, expression ZjACO ethylene pathway was ZjMYC2-1, a JA gene, induced compared other stages. The ZjGID-1 ZjTF-1, related GA, exhibited levels VI.

Язык: Английский

Процитировано

0
Iron: Life’s primeval transition metal DOI Creative Commons
Jena E. Johnson, Theodore M. Present, Joan Selverstone Valentine

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(38)

Опубликована: Сен. 9, 2024

Modern life requires many different metal ions, which enable diverse biochemical functions. It is commonly assumed that ions’ environmental availabilities controlled the evolution of early life. We argue can only explore chemistry encounters, and fortuitous chemical interactions between ions biological compounds be selected for if they first occur sufficiently frequently. calculated maximal transition ion concentrations in ancient ocean, determining amounts biologically important were orders magnitude lower than ferrous iron. Under such conditions, primitive bioligands would predominantly interact with Fe(II). While other metals certain environments may have provided evolutionary opportunities, capacities Fe(II), Fe–S clusters, or plentiful magnesium calcium could satisfied all functions needed by Primitive organisms used Fe(II) exclusively their requirements.

Язык: Английский

Процитировано

3
Mechanism of mitochondrial [2Fe-2S] cluster biosynthesis DOI
Kristian Want, Benoît D’Autréaux

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Год журнала: 2024, Номер 1871(8), С. 119811 - 119811

Опубликована: Авг. 10, 2024

Язык: Английский

Процитировано

2
Identification and pyramiding of iron and zinc homeostasis genes introgressed from non-progenitor Aegilops species to bread wheat DOI

Harneet Kaur,

Vikrant Tyagi, Jitendra Kumar

и другие.

Euphytica, Год журнала: 2024, Номер 220(11)

Опубликована: Окт. 4, 2024

Язык: Английский

Процитировано

2
Investigating Iron-Sulfur Proteins in Infectious Diseases: A Review of Characterization Techniques DOI Creative Commons
Md Kausar Raza, Vivian Robert Jeyachandran, Sania Bashir

и другие.

Inorganics, Год журнала: 2024, Номер 12(1), С. 25 - 25

Опубликована: Янв. 7, 2024

Iron-sulfur [Fe-S] clusters, comprising coordinated iron and sulfur atoms arranged in diverse configurations, play a pivotal role redox reactions various biological processes. Diverse structural variants of clusters exist, each possessing distinct attributes functions. Recent discovery infectious pathogens, such as Mycobacterium tuberculosis, viruses, rotavirus, polyomavirus, hepatitis virus, mimivirus, coronavirus, have sparked interest them being potential therapeutics target. findings associated these cluster proteins playing critical host protein activity. However, for very long time, metalloenzymes containing iron-sulfur been prone to destabilization the presence oxygen, which led delayed understanding compared other non-heme iron-containing proteins. Consequently, working with require specialized equipment, anaerobic chambers maintain cofactor integrity, tools like ultraviolet visible (UV-Vis) spectroscopy, mass spectrometry, X-ray crystallography, nuclear magnetic resonance (NMR), electron paramagnetic (EPR), Mössbauer spectroscopy electrochemical characterization. Many misannotated Zinc-binding when purified aerobically. Moreover, assembly cofactors not fully understood since it is multi-step process. Additionally, disruptions this process linked human diseases. With rapid advancements gloveboxes spectroscopic techniques, characterization cluster-containing that are essential pathogens can open up new avenues diagnostics therapeutics.

Язык: Английский

Процитировано

1
The Cryptic Nature of Fe-S Clusters: A Case Study of the Hepatitis B HBx Oncoprotein DOI Creative Commons

Trent Quist,

Jiahua Chen,

Alex MacNeil

и другие.

Inorganics, Год журнала: 2023, Номер 11(12), С. 475 - 475

Опубликована: Дек. 6, 2023

Fe-S clusters are ubiquitous inorganic cofactors found in proteins across all domains of life, including viruses. Their prevalence stems from their unique redox and structural plasticity that supports functions ranging electron transfer catalysis to stabilization protein structure. Although the ability exchange electrons is often functionally crucial, it can also act as an Achilles heel when these exposed oxidizing conditions, leading degradation. This O2 sensitivity has rendered certain untraceable, particularly nascent isolated under ambient conditions. As a consequence this sensitivity, growing number with roles viral infection have been harbor rather than annotated Zn2+ cofactor. The enigmatic X (HBx) Hepatitis B Virus multifunctional essential for replication development liver disease. HBx defied biochemical characterization over forty years, shown coordinate redox-active cluster represents significant feature establishing its molecular function. present review narrates approaches validate metallocofactor be broadly applied guide uncovering presence non-canonical sequence motifs.

Язык: Английский

Процитировано

2
Diverse YqeK Diadenosine Tetraphosphate Hydrolases Control Biofilm Formation in an Iron-Dependent Manner DOI Open Access
Chie Ueda,

Natalie Chin,

Qianyi Yang

и другие.

Catalysts, Год журнала: 2024, Номер 14(9), С. 652 - 652

Опубликована: Сен. 23, 2024

YqeK is a bacterial HD-domain metalloprotein that hydrolyzes the putative second messenger diadenosine tetraphosphate (Ap4A). Elevated Ap4A levels are primarily observed upon exposure of bacteria to factors such as heat or oxidative stress and cause pleiotropic effects, including antibiotic sensitivity disrupted biofilm formation. thus plays central role in physiology metabolism, its hydrolysis by intimately linked ability these microbes cope with stress. Although reported hydrolyze under aerobic conditions, all four existing crystal structures reveal an active site consists diiron center, portraying cryptic chemical nature for metallocofactor. This study examines two proteins from ecologically diverse parent organisms: obligate anaerobe Clostridium acetobutylicum facultative aerobe Bacillus halodurans. Both enzymes utilize Fe-based cofactors catalysis, while ambient Bh more efficiently compared Ca YqeK. redox-dependent activity difference stems following molecular mechanisms: incorporation mixed-metal, bimetallic cofactors, which metal redox inert (i.e., Fe–Zn) upshift Fe–Fe cofactor reduction potentials. In addition, three strictly conserved, positively charged residues vicinal critical tuning hydrolysis. conclusion, Fe-dependent phosphohydrolase appears have evolved permit different environmental niches (aerobic vs. anaerobic) expanding configuration O2 tolerance.

Язык: Английский

Процитировано

0
Micronutrient availability alters Candida albicans growth and farnesol accumulation: implications for studies using RPMI-1640 DOI Creative Commons
Cory H. T. Boone, Daniel J. Gutzmann, Jaxon J. Kramer

и другие.

Microbiology Spectrum, Год журнала: 2024, Номер 12(11)

Опубликована: Сен. 24, 2024

ABSTRACT Science is challenging because we do not know what know. Commercial chemicals are often marketed with >99% purity, but 0.5–1% impurity can impact results and cloud data interpretation. We recently developed an assay for farnesol aromatic fusel alcohols from Candida albicans . During proof-of-concept experiments using RPMI-1640 growth media, the buffering compound was switched MOPS obtained Acros Organics to Sigma-Aldrich, both labeled 99% + purity. observed a twofold decrease in growth, along three- fivefold increase production per cell upon switch. ICP-MS showed that trace Mn(II) present absent Sigma MOPS. Optimal achieved by addition of Mn(II), Zn(II), Fe(II). established upper lower limits Fe(II), Cu(II), allowed similar then assessed 16 different mineral combinations base media. The show increased when Zn(II) abundant, further Fe(II) abundant. Finally, antifungal susceptibility testing displayed no significant difference between RPMI/MOPS without supplementation. Supplemental most needed while supplemental alcohols. To avoid these artifacts due metal contamination, now use modified RPMI supplemented 1 mg/ L IMPORTANCE dimorphic fungus major opportunistic pathogen humans. chemically defined medium commonly used C. identified over 32,000 publications keywords Additionally, Antifungal Susceptibility Testing (AFST) protocols United States (CLSI) Europe (EUCAST) utilize as media assess drug efficacy against clinical fungal isolates. contains many nutrients added metals. found characteristics were dependent on which buffer chosen contamination levels Zn(II). Added secretion other signaling molecules.

Язык: Английский

Процитировано

0
Metabolic evolution of pyranopterin-dependent biochemistry DOI Creative Commons
Joshua E. Goldford, Ranjani Murali, Joan Selverstone Valentine

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 5, 2023

Abstract Molybdenum (Mo)-dependent biochemistry is essential for many key metabolic pathways. However, theory and geological evidence suggests that its solubility during long intervals with low dioxygen would have limited availability on early Earth. We developed models of evolution found reactions employing tungsten (W)-dependent likely preceded Mo-dependent reactions, where Mo-usage increased dramatically after the production dioxygen. Consistent this finding, we analyzed genomes from over 65,000 phylogenetically diverse microbes metagenomes an environmental dataset, observed dioxygen-utilizing prokaryotes living in aerobic niches are enriched enzymes as compared to anaerobic microbes. As independent evaluation hypothesis, combined protein language models, machine learning, phylogenomic analysis build a classifier W- or Mo-pterin dependence DMSO reductase superfamily, W-pterin-dependent cluster near root tree subset late-evolving aldehyde oxidoreductases (AORs) aerobes predicted rely Mo instead W. Overall, our combination modeling, phenotypic analysis, suggest Mo-pterin-dependent derived biochemistry, drastically rise oxygen.

Язык: Английский

Процитировано

1