Probiotic-derived silver nanoparticles target mTOR/MMP-9/BCL-2/dependent AMPK activation for hepatic cancer treatment

Medical Oncology, Journal Year: 2024, Volume and Issue: 41(5)

Published: April 4, 2024

Language: Английский

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A treasure trove of 1034 actinomycete genomes

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(13), P. 7487 - 7503

Published: June 22, 2024

Abstract Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera 389 species, including 244 likely novel species. All filamentous isolates class Actinomycetia NBC culture collection. The largest genus is Streptomyces with 886 742 We use this data to show that analysis can bring biological understanding not previously derived more fragmented less systematic datasets. document central structured location core genes distal specialized metabolite duplicate linear chromosome, analyze content length terminal inverted repeats which characteristic for Streptomyces. then diversity trans-AT polyketide synthase clusters, encodes machinery a biotechnologically highly interesting compound class. These insights have both ecological biotechnological implications in importance high quality genomic resources complex role synteny plays biology.

Language: Английский

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Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(6), P. 1636 - 1646

Published: March 3, 2022

Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in oceans. Gene content variation among picocyanobacterial populations separate ocean basins often mirrors selective pressures imposed by region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across global ocean, we show that capacity for siderophore-mediated iron uptake is widespread low-light adapted deep chlorophyll maximum layers of iron-depleted regions oligotrophic Pacific S. Atlantic oceans: siderophore consumers were absent N. (higher new flux) but constituted up to half all genomes metagenomes (lower flux). Picocyanobacterial consumers, like many other bacteria this trait, also lack biosynthesis genes indicating they scavenge exogenous siderophores seawater. Statistical modeling suggests endemic remote where atmospheric fluxes smallest, especially at primary nitrite layers. We argue these two common oceanographic features could be a symptom wider community stress, consistent prior hypotheses. Our results provide clear example as force driving evolution marine picocyanobacteria.

Language: Английский

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The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: June 26, 2023

Abstract Background Phosphonates are the main components in global phosphorus redox cycle. Little is known about phosphonate metabolism freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria often dominant primary producers freshwaters; yet, only a few strains cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere defined as microenvironment which extensive phytoplankton and heterotrophic bacteria interactions occur. It demonstrated that may recruit phycospheric based on their own needs. Therefore, establishment community rich phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially waters with scarce phosphorus. We characterized distribution field Microcystis bloom samples laboratory “phycospheres” by qPCR metagenomic analyses. role proliferation was determined through coculturing an axenic aeruginosa strain metatranscriptomic analysis using aggregate . Results Abundant carry C-P lyase clusters were identified plankton from Lakes Dianchi Taihu during periods. Metagenomic 162 non-axenic (consortia cultures containing bacteria) showed 20% (128/647) high-quality bins eighty these consortia intact clusters, abundance ranging up to nearly 13%. Phycospheric bacterial catabolism genes expressed continually across seasons, sixteen samples. Coculturing experiments revealed did not catabolize methylphosphonate when axenic, they sustained growth cocultured phosphonate-utilizing medium sole source Conclusions recruitment hedge against scarcity facilitating availability. Cyanobacterial contributors aquatic mineralization, thereby growth, even maintenance, phosphate-deficient waters.

Language: Английский

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Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(5), P. 720 - 732

Published: Feb. 25, 2023

Abstract The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning genome evolution in ocean, especially for abundant ubiquitous marine picocyanobacteria Prochlorococcus Synechococcus. Here, by combining metagenome analyses Tara Oceans dataset with comparative genomics, including phyletic patterns genomic context individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving different niches possess distinct gene repertoires. We also identify clusters adjacent display specific distribution field (eCAGs) are thus potentially involved same metabolic pathway may have a key role adaptation. Several eCAGs likely uptake or incorporation complex organic forms nutrients, such as guanidine, cyanate, cyanide, pyrimidine, phosphonates, which might be either directly used cells, example biosynthesis proteins DNA, degraded inorganic nitrogen and/or phosphorus forms. highlight enrichment polysaccharide capsule Synechococcus populations both nitrogen- phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting complexes they encode too energy-consuming latter areas. In contrast, Fe-depleted specifically an alternative respiratory terminal oxidase, reduction Fe(III) Fe(II). Altogether, this study insights into how phytoplankton populate oceanic ecosystems, is relevant understanding their capacity respond ongoing climate change.

Language: Английский

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Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 2, 2023

Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During process serpentinization, water circulates through systems crust where oxidizes Fe (II) ultramafic minerals generate (III) H 2 . Molecular hydrogen can, turn, serve as a freely diffusible source electrons reduction CO organic compounds, provided that suitable are present. Using naturally synthesized during serpentinization reduces formate, acetate, pyruvate, methane. These compounds represent backbone microbial carbon energy metabolism acetogens methanogens, strictly anaerobic chemolithoautotrophs use acetyl-CoA pathway fixation inhabit serpentinizing environments today. reduced carbon, nitrogen — newer findings suggest phosphorous were likely conducive origins process. In addition, gives rise inorganic microcompartments proton gradients right polarity sufficient magnitude support chemiosmotic ATP synthesis by rotor-stator synthase. This would help explain why principle harnessing more conserved (older) than machinery ion via pumping coupled exergonic chemical reactions, which case methanogens involve -dependent reduction. Serpentinizing exist terrestrial deep ocean environments. On early Earth they probably abundant There evidence once occurred on Mars still occurring Saturn’s icy moon Enceladus, providing perspective disequilibrium other worlds.

Language: Английский

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Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 2, 2024

Abstract Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations the Precambrian ocean, during life’s origin and early evolution, vary over several orders magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on Earth remains unknown. Here, we reconstruct phylogenomic record life find that transporting genes ( pnas ) evolved Paleoarchean (ca. 3.6-3.2 Ga) are consistent with above modern levels > 3 µM). The first gene optimized for low pstS ; <1 µM) appeared around same time or Mesoarchean depending reconstruction method. Most enzymatic pathways metabolising emerged expanded across tree later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising hypophosphite-oxidising pathways. CP-lyases particularly abundant dissolved below 0.1 µM. Our results thus indicate at least local regions declining through Archean, possibly linked phosphate-scavenging Fe(III), which limited productivity. However, did not become widely used until after Paleoproterozoic Great Oxidation Event (2.3 Ga), expansion biosphere time.

Language: Английский

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Aerobic methane production by phytoplankton as an important methane source of aquatic ecosystems: Reconsidering the global methane budget

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 907, P. 167864 - 167864

Published: Oct. 20, 2023

Language: Английский

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The Microbial Degradation of Natural and Anthropogenic Phosphonates

Molecules, Journal Year: 2023, Volume and Issue: 28(19), P. 6863 - 6863

Published: Sept. 29, 2023

Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They environmentally ubiquitous: some of them produced by microorganisms invertebrates, whereas others derive from anthropogenic activities. Because their stability potential toxicity, man-made phosphonates pose pollution problems, many studies have tried identify biocompatible systems for elimination. On the other hand, resource living in environments where availability phosphate limited; thus, bacteria particular evolved uptake catabolize phosphonates. Such can be either selective narrow subset or show broader specificity. The role, distribution, evolution microbial genes enzymes dedicated phosphonate degradation, as well regulation, been subjects substantial studies. At least three enzyme identified so far, schematically distinguished based on mechanism C-P bond ultimately cleaved-i.e., through hydrolytic, radical, oxidative reaction. This review summarizes our current understanding molecular pathways that serve phosphonates, regulatory mechanisms govern activity.

Language: Английский

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A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions – Identifying knowledge gaps

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 355, P. 120453 - 120453

Published: March 1, 2024

Language: Английский

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