The marine nitrogen cycle: new developments and global change

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(7), P. 401 - 414

Published: Feb. 7, 2022

Language: Английский

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DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change

Journal of Experimental Botany, Journal Year: 2023, Volume and Issue: 74(14), P. 4259 - 4276

Published: April 26, 2023

Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms environmental changes. However, how might act cooperatively gene transcription mediate long-term adaptive responses marine microalgae global change is virtually unknown. Here we performed a transcriptomic analysis, whole-genome bisulfite sequencing, along phenotypic analysis model diatom Phaeodactylum tricornutum adapted for 2 years high CO2 and/or warming conditions. Our results show that methylated islands (peaks methylation) mCHH were positively correlated expression genes in subregion body when populations grown under or its combination ~2 years. We further identified differentially expressed (DEGs), hence metabolic pathways which they function, at transcriptomics level regions (DMRs). Although DEGs DMRs contributed only 18-24% total DEGs, found those acted then regulated key central carbon metabolism, amino acid ribosome biogenesis, terpenoid backbone biosynthesis, degradation misfolded proteins. Taken together, by integrating transcriptomic, epigenetic, our study provides evidence acting contribute adaptation

Language: Английский

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Transcriptome remodeling drives acclimation to iron availability in the marine N ₂ -fixing cyanobacterium Trichodesmium erythraeum IMS101

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

ABSTRACT While enhanced phytoplankton growth as a result of iron (Fe) fertilization has been extensively characterized, our understanding the underlying mechanisms remains incomplete. Here, we show in laboratory setup mimicking Fe field that transcriptome remodeling is primary driver acclimation to availability marine diazotrophic cyanobacterium Trichodesmium erythraeum IMS101. supplementation promoted cell growth, photosynthesis and N 2 fixation, concomitant expression fixation genes. The genes encoding major Fe-binding metalloproteins tightly linked cellular carbon nitrogen metabolism appears be controlled by ferric uptake regulator FurA, which involved regulating homeostasis. This feedback loop reinforced substitutive functionally equivalent or competitive depending on availability, well co-expression multiple stress inducible isiA genes, an adaptive strategy evolved elicit Fe-responsive cascade. study provides genome-wide perspective prominent diazotroph reveals upgraded portfolio indicator can used better assess status environment, predicts scenarios how diazotrophs may affected future ocean. IMPORTANCE scarcity trace metal global oceans great impact growth. productivity molecular remain poorly understood. By subjecting model IMS101 increasing concentrations supplemented Fe, demonstrate it comprehensively remodeled drives mobilization for coordinated reallocation energy resources. Our data provide broad genomic insight into enabling versatility flexibility choice monitoring environment having implications persist

Language: Английский

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Two co‐dominant nitrogen‐fixing cyanobacteria demonstrate distinct acclimation and adaptation responses to cope with ocean warming

Environmental Microbiology Reports, Journal Year: 2022, Volume and Issue: 14(2), P. 203 - 217

Published: Jan. 13, 2022

Summary The globally dominant N 2 ‐fixing cyanobacteria Trichodesmium and Crocosphaera provide vital nitrogen supplies to subtropical tropical oceans, but little is known about how they will be affected by long‐term ocean warming. We tested their thermal responses using experimental evolution methods during years of selection at optimal (28°C), supra‐optimal (32°C) suboptimal (22°C) temperatures. After several hundred generations under selection, changes in growth parameters, as well C fixation rates, suggested that did not adapt the three temperature regimes 2‐year experiment, could instead rapidly reversibly acclimate shifts from 20°C 34°C. In contrast, over same timeframe apparent adaptation was observed , evidenced irreversible phenotypic whole‐genome sequencing variant analysis. Especially stressful warming conditions (34°C), 32°C‐selected cells had an advantage survival cell lines selected 22°C 28°C. distinct strategies plasticity versus these two sympatric diazotrophs are both viable ways maintain fitness despite changes, so help stabilize key cycle functions future scenarios.

Language: Английский

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Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 29, 2022

Background: A high mortality rate makes hepatocellular carcinoma (HCC) one of the most common types cancer globally. 5-methylcytosine (m5C) is an epigenetic modification that contributes to prognosis several cancers, but its relevance HCC remains unknown. We sought determine if m5C-related regulators had any diagnostic or prognostic value in HCC. Methods: M5C regulatory genes were screened and compared between normal tissue from The Cancer Genome Atlas (TCGA)and Gene Expression Omnibus (GEO) databases. Least absolute shrinkage selection operator method (LASSO) univariate Cox regression analysis differentially expressed then performed identify markers. LASSO model was constructed using with values by TCGA expression data. patients stratified based on risk score, clinical characteristics immune correlation for each subgroup, molecular functions different subgroups analyzed both Set Enrichment Analysis (GSEA) Variation (GSVA). evaluated multivariate analyses as well a nomogram. Molecular typing according m5C checkpoint respectively, characterization subgroup. Results: are differently pathological characteristics, mutations these frequent. Based five (NOP2, NSUN2, TET1, YBX1, DNMT3B), we predictive ability. score found be independent indicator. Additionally, scores can also applied indicators. Conclusion: study combined data GEO first time reveal genetic significance HCC, which provides new directions identifying biomarkers developing molecularly targeted therapies

Language: Английский

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Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacteriumSynechococcus

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(47)

Published: Nov. 16, 2023

The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, it remains unclear if such strain-level microdiversity will affect fitness persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains the ubiquitous picocyanobacterium Synechococcus isolated from Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed at cool warm temperatures had subdivided initial population into thermotypes with pronounced differences maximum growth temperatures. Curiously, genomes all isolates were almost identical (average nucleotide identities >99.99%, >99% genome aligning) no gene content or single variants associated either temperature phenotypes. Despite very high level genomic similarity, sequenced epigenomes for two showed methylation on genes photosynthesis. These corresponded to measured photophysiology, suggesting potential pathway future mechanistic research microdiversity. Our study demonstrates that present-day can harbor cryptic but environmentally relevant which may increase their resilience rising

Language: Английский

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Bacterial Epigenomics: Coming of Age

mSystems, Journal Year: 2021, Volume and Issue: 6(4)

Published: Aug. 17, 2021

Epigenetic DNA methylation in bacteria has been traditionally studied the context of antiparasitic defense and as part innate immune discrimination between self nonself DNA. However, sequencing advances that allow genome-wide analysis at single-base resolution are nowadays expanding have propelled a modern epigenomic revolution our understanding extent, evolution, physiological significance methylation.

Language: Английский

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Advances in RNA Epigenetic Modifications in Hepatocellular Carcinoma and Potential Targeted Intervention Strategies

Frontiers in Cell and Developmental Biology, Journal Year: 2021, Volume and Issue: 9

Published: Oct. 29, 2021

The current interventions for hepatocellular carcinoma (HCC) are not satisfactory, and more precise targets promising strategies need to be explored. Recent research has demonstrated the non-negligible roles of RNA epigenetic modifications such as N6-methyladenosine (m6A) 5-methylcytosine (m5C) in various cancers, including HCC. However, specific targeting mechanisms well elucidated. In this review, we focus on occurrence detailed physiopathological multiple diverse RNAs closely related HCC process. particular, highlight fresh insights into impact these posttranscriptional whole progression Furthermore, analyzed possibilities significance regulators potential therapeutic treatment, which provides foundation exploring targeted intervention strategies. This review will propel identification novel that can translated clinical applications treatment.

Language: Английский

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Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(9), P. e3002792 - e3002792

Published: Sept. 20, 2024

Adaptation is usually explained by beneficial genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, mutation analysis alone not sufficient fully explain adaptive processes, several studies report existence of nongenetic (or epigenetic) inheritance can enable adaptation new environments. In present work, we tested hypothesis role DNA methylation, a form epigenetic modification, plant pathogen Ralstonia pseudosolanacearum host during experimental evolution. Using SMRT-seq technology, analyzed methylomes 31 experimentally evolved clones obtained after serial passages on 5 different species 300 generations. Comparison with methylome ancestral clone revealed list 50 differential methylated sites (DMSs) at GTWWAC motif. Gene expression 39 genes targeted these DMSs limited correlation between methylation corresponding genes. Only 1 gene showed correlation, RSp0338 encoding EpsR regulator protein. The MSRE-qPCR used as an alternative approach for analysis, also found 2 upstream RSp0338. site-directed mutagenesis, demonstrated contribution adaptation. As appeared very early evolution, hypothesize such fast changes allow rapid stem environment. addition, change remains stable least 100 generations outside thus contribute long-term plant. To our knowledge, this first study showing direct link bacterial variation

Language: Английский

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Adaptive Strategies and Evolutionary Responses of Microbial Organisms to Changing Oceans

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: June 16, 2022

Environmental variability is an intrinsic characteristic of nature. Variability in factors such as temperature, UV, salinity, and nutrient availability can influence structural functional properties marine microbial organisms. This has profound implications for biochemical cycles the ecosystem services provided by oceans. In this review we discuss some most relevant mechanisms underpinning adaptive strategies organisms variable dynamic We assess extent to which magnitude rate environmental change plastic phenotypic adjustments evolutionary trajectories populations. understanding fundamental developing better predictions regarding dynamics at ecological time-scales response climate change.

Language: Английский

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