Biology subjects

Murali, R.

Publications and source records attributed to Murali, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Modelling Anaerobic Co-Digestion with Agricultural Feedstock: Model Validation and Cross-Reactor Verification

As the United Kingdom (UK) targets net-zero emissions by 2050, anaerobic digestion (AD) has become a cornerstone of renewable energy infrastructure. However, mathematical models, such as the Anaerobic Digestion Model No. 1 (ADM1), often struggle with high-solids agricultural feedstocks because they rely on Chemical Oxygen Demand (COD), a metric that introduces significant experimental error. To overcome this, this study applies an established mass-based ADM1 framework tailored for the co-digestion of maize silage and cow manure sourced from a UK AD site. This study uses a parallel reactor framework, using two identical laboratory-scale reactors to physically replicate the dynamic conditions of the full-scale site. A Global Sensitivity Analysis was first conducted, identifying biomass decay and carbohydrate breakdown rates as the most influential factors affecting system stability and model accuracy. The model was calibrated using data from the first reactor and then tested against an independent second reactor subjected to significant organic loading stress. Results show high predictive capabilities, with the model achieving a R2 of 0.81 for biogas production during calibration. The model maintained high predictive accuracy during the validation test of the second physical twin, achieving an R2 of 0.85, proving that the framework is robust and not overfitted to a single dataset. While predicting rapid fluctuations in pH and alkalinity remains challenging, the mass-based approach effectively forecasts gas yields and process stability. This methodology provides a reliable foundation for robust process modelling, offering a scalable tool for the UK biogas sector to optimise AD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/721061v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@92c7e2org.highwire.dtl.DTLVardef@80d723org.highwire.dtl.DTLVardef@ac3d24org.highwire.dtl.DTLVardef@1e21a51_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Anaerobic methane oxidation by ANME-2a at two molar chloride in Orca Basin

Anaerobic methane oxidation, typically mediated by consortia of archaea and bacteria, is a key process in the global methane cycle, but little is known about its upper salinity limits. We characterized the microbial methane cycle in the anoxic, hypersaline Orca Basin using metagenomics, metatranscriptomics, fluorescence in situ hybridization, and geochemical measurements at sub-meter resolution. In the brine, we detected transcriptional activity of the halophilic methylotrophic methanogen Methanohalophilus, consistent with a biological source for Orca Basin methane. In the particle-rich halocline ([~]2 M Cl-; [~]2235 meters depth), high mcrA transcription by a novel ANME-2a species was co-located with a positive shift in {delta}13C-CH4 indicative of anaerobic oxidation of methane. ANME-2a also transcribed genes for biosynthesis of the osmolyte N({varepsilon})-acetyl-{beta}-L-lysine, supporting adaptation for hypersaline conditions. At the same depth, consortia of sarcina-like archaea, likely ANME-2a, were observed in association with vibrioid and filamentous bacteria, potentially members of a halotolerant genus in the order Desulfobulbales (family SURF-16, which includes the previously identified ANME partner Seep-DBB) that were active at the same depth. At and above the oxic-anoxic interface, aerobic methane oxidation appears to be mediated by three genera of uncultivated Methylococcales bacteria. Our results double the upper salinity range of ANME-2a to [~]2 M Cl- and reveal the key microbial players in the methane bio-filter between the Orca Basin brine and overlying seawater.

microbiology↗

bioRxiv2025

Cycling of sulfur redox intermediates drives microbial activity in the sulfate-methane transition zone of cold methane seeps

Microbial sulfate reduction is a cornerstone of marine sediment biogeochemistry, driving carbon remineralization and fueling the anaerobic oxidation of methane (AOM). Yet in zones of high methane flux, sulfate limitations may constrain the sulfate-reducing bacteria (SRB) and anaerobic methanotrophic archaea (ANME) that typically perform AOM. Although often overlooked, sulfur redox intermediates are readily utilized by diverse microorganisms, potentially driving AOM in sulfate-limited zones. To resolve the microbial mechanisms underlying cryptic sulfur cycling in such sediments, Monterey Canyon cold methane seeps were investigated through an integrated geochemical, isotopic, and metatranscriptomic approach. High-resolution electrochemical measurements confirmed intense sulfide production in seep sites, and long-term anoxic incubations were conducted with sediment from the SMTZ amended with elemental sulfur, thiosulfate, or sulfate as the sole sulfur source, with or without methane. Over 650 days, sulfide accumulation was greatest in elemental sulfur treatments, followed by thiosulfate and sulfate; in all cases methane addition enhanced sulfide production. Isotopic measurements showed modest S-isotope fractionation indicating that the large fractionations typical of slow sulfate reduction were muted by additional sulfur transformations. In elemental sulfur treatments, isotopic and geochemical patterns suggested that disproportionation was unlikely. Metatranscriptomes revealed broad expression of sox genes and abundant dsr/apr across treatments, along with thiosulfate-linked phs upregulation. While ANME-2c and SEEP-SRB2 activity increased with methane, transcriptomic and isotopic data together highlighted the roles of Desulfocapsaceae, Desulfobulbaceae, and Sulfurovaceae lineages in mediating sulfur transformations. Taken together, these results demonstrate how cryptic sulfur cycling may sustain microbial communities in sulfate-depleted deep-sea sediments and contribute to AOM.

ecology↗

bioRxiv2025

Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia

Efficient energy metabolism is essential for microorganisms living on the thermodynamic edge. Consortia of anaerobic methane-oxidizing archaea (ANME-2) and sulphate-reducing bacteria (SRB) represent globally relevant syntrophic associations capable of growing with minimal amounts of free energy and can persist when methane becomes limiting. Their potential for physiological plasticity, including the use of electron donors beyond methane is poorly understood. Carbon monoxide (CO) has been reported in seep environments and represents a thermodynamically favourable alternative electron donor due to its low reduction potential. We demonstrate that environmental ANME-SRB consortia can oxidize CO in the absence of methane, in anoxic microcosm experiments using a combination of stable isotope geochemical tracers, metatranscriptomics, and single cell activity measurements (FISH-nanoSIMS). The oxidation of CO was coupled with sulphate-reduction by syntrophic consortia, and, in the absence of sulphate, through CO2 reduction to methane by ANME-2. Under these conditions, the production of methane was one ninth the rate of methanotrophy coupled to sulphate-reduction. Paired single cell FISH-nanoSIMS analysis of anabolic activity indicates that CO respiration appears to support cell maintenance rather than active growth, consistent with the observed down-regulation of energy generating complexes in ANME (e.g., mtr, rnf, etc.). The versatile capability of CO oxidation by anaerobic methanotrophic consortia broadens our understanding of carbon cycling in methane seeps and highlights potential mechanisms of resilience by methanotrophic archaea under changing geochemical regimes.

microbiology↗

bioRxiv2025

A paradigm shift of SERPINA3N in neurobehavioral development and brain injury

Murine serine protease inhibitor clade A member 3N (SERPINA3N) and its human ortholog SERPINA3 are dysregulated in neurological disorders. SERPINA3N has been proposed as a protective factor, enhancing neurobehavioral development under homeostasis and mitigating neuronal/glial and vascular damage under neurological conditions. Here, we employed powerful, non-invasive genetic tools to revisit the concept of SERPINA3N in brain development and injury. Brain-specific SERPINA3N overexpression neither alters neuronal or glial development nor improves cognitive ability under homeostasis. In stark contrast, SERPINA3N drives a pro-inflammatory response to brain injury and exacerbates blood-brain barrier dysfunction. Its overexpression promotes neurodegeneration through apoptosis-mediated neuronal loss and disrupts oligodendroglial differentiation and myelination following neonatal brain injury. Collectively, our findings challenge the prevailing paradigm of SERPINA3N in neurodevelopment and injury, revealing that while SERPINA3N is dispensable for neurobehavioral development, it aggravates neural injury and vascular damage under pathological conditions.

neuroscience↗

bioRxiv2025

Viral communities from long-term anaerobic alkane-oxidizing enrichments may promote cell surface adhesion

The anaerobic oxidation of methane and higher C2+ alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. While these processes feed a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral community in long-term sediment-free enrichments of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also found evidence supporting the presence of a viral genus infecting several phyla across both the bacterial and archaeal domains, including one of the sulfate-reducing bacterial partners in the alkane-oxidizing syntrophy. Lastly, we report the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of novel viruses obtained from these enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.

ecology↗

bioRxiv2025

Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Novel pMMO Diversity

At methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria (ANME-SRB) promote carbonate precipitation and rock formation, acting as methane and carbon sink. While maintenance of active anaerobic oxidation of methane (AOM) within seep carbonates has been documented, the ANME-SRB reactivity to methane exposure remains uncertain. Surface-associated microbes may metabolize AOM-derived sulfide, maintain carbonate anoxia, and contribute to carbonate dissolution and higher trophic levels; however, these microbial communities are poorly described thus far. Here we provide new insights into microbial diversity, metabolic potential, activity, and resiliency within and on Southern Californian methane seep carbonates, by combining 16S rRNA and metagenomic sequencing, laboratory incubations, and BONCAT-FISH. Ca. Methanophaga (ANME-1) dominated the carbonate interiors across different seepage activities, based on sequencing, while the dominant SRB was Ca. Desulfaltia, potentially a new ANME partner. BONCAT-FISH revealed differences in ANME-1 cell activity, suggesting cell dormancy or DNA preservation at less active seep sites. Carbonate incubations from low activity seeps ([≥]24 months) showed an exponential AOM reactivation (44-day doubling time), suggesting seep carbonates remain potential methane sinks over dynamic seepage conditions. The surface-associated communities were distinct from the carbonate interior and other seep habitats, and highly heterogeneous. Surface ANME-SRB biofilms and sulfide-oxidizing bacterial mats were associated with high and intermediate AOM carbonates, potentially influencing carbonate precipitation/dissolution. Carbonate surfaces shared diverse aerobic methanotrophs with invertebrates, potentially serving as pool for animal epibionts. Besides particulate methane monooxygenases from aerobic methanotrophs, we found divergent forms including within a Methylophagaceae (GCA-002733105) MAG suggesting a new function within Methylophagaceae.

ecology↗

bioRxiv2024

Butyrophilin 2A2 promotes T cell immunoregulation by enhancing CD45 phosphatase activity within the immune synapse

B7 costimulatory family member Butyrophilin 2A2 (BTN2A2) is predominantly expressed by antigen presenting cells and regulates T cell immunity, but molecular mechanisms are unclear. Using immunoblots analyzing TCR-initiated signaling intermediaries, co-immunoprecipitation studies, confocal microscopy, structural modeling-guided mutational analyses, and microscale thermophoresis, we demonstrate that BTN2A2 directly interacts with CD45RO, resulting in CD45 retention within the immune synapse during TCR activation. Recombinant BTN2A2 increased murine CD4+Foxp3+ regulatory T cells (Treg) and reduced T helper 17 (Th17) cells in vitro through mechanisms dependent on CD45 phosphatase activity. BTN2A2 treatment reduced clinical expression of two murine autoimmune disease models and increased Treg/Th17 ratios. Analyses of BTN2A2-deficient animals showed exacerbated disease associated with reduced Treg/Th17 ratios. Addition of BTN2A2 to human mixed lymphocyte responses similarly enhanced human Treg and suppressed Th17 cells and was CD45 phosphatase dependent. Together, our studies identify BTN2A2 as a physiological CD45RO ligand that enhances CD45 phosphatase activity in murine and human T cells, providing mechanisms for BTN2A2-mediated amelioration of autoimmunity. SummaryButyrophilin 2A2 ameliorates autoimmunity by binding to CD45RO on activated T cell surfaces leading to dampened TCR signaling which in turn leads to expansion of T regulatory cells and reduction of Th17 differentiation.

immunology↗

bioRxiv2024

CABO-16S : A Combined Archaea, Bacteria, Organelle 16S database for amplicon analysis of prokaryotes and eukaryotes in environmental samples

Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by either the burden of additional sequencing required to obtain both 16S and 18S rRNA sequences or the introduction of multiple biases induced by the use of "universal" primers. Organellar 16S rRNA sequences are automatically amplified and sequenced along with prokaryote 16S rRNA, and may provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. CABO-16S also provides the framework to add curated datasets of specialized sequences for further classification of clades which are not currently included in other databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. Such additions may simplify analysis of communities contributing to the anaerobic oxidation of methane, and highlight the potential benefit of amending existing training sets with curated sequences when studying extreme or unique environments underrepresented in existing databases.

microbiology↗

bioRxiv2024

Retinoid X Receptor Signaling Mediates Cancer Cell Lipid Metabolism in the Leptomeninges

Cancer cells metastatic to the leptomeninges encounter a metabolically-challenging extreme microenvironment. To understand adaptations to this space, we subjected leptomeningeal-metastatic (LeptoM) mouse breast and lung cancers isolated from either the leptomeninges or orthotopic primary sites to ATAC-and RNA-sequencing. When inhabiting the leptomeninges, the LeptoM cells demonstrated transcription downstream of retinoid-X-receptors (RXRs). We found evidence of local retinoic acid (RA) generation in both human leptomeningeal metastasis and mouse models in the form of elevated spinal fluid retinol and expression of RA-generating dehydrogenases within the leptomeningeal microenvironment. Stimulating LeptoM cells with RA induced expression of transcripts encoding de novo fatty acid synthesis pathway enzymes in vitro. In vivo, while deletion of Stra6 did not alter cancer cell leptomeningeal growth, knockout of Rxra/b/g interrupted cancer cell lipid biosynthesis and arrested cancer growth. These observations illustrate a mechanism whereby metastatic cancer cells awake locally-generated developmental cues for metabolically reprograming, suggesting novel therapeutic approaches.

cancer biology↗

bioRxiv2023

ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer

Significance StatementONECUT2 (OC2) is a master transcription factor that alters lineage identity by activating gene networks associated with both neuroendocrine prostate cancer and prostate adenocarcinoma. A small molecule inhibitor of OC2 represses the lineage plasticity program activated by enzalutamide, suggesting OC2 inhibition as a novel therapeutic strategy to prevent emergence of treatment-resistant variants. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/560025v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@13278a4org.highwire.dtl.DTLVardef@8e82aeorg.highwire.dtl.DTLVardef@25a115org.highwire.dtl.DTLVardef@728eb4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractC_FLOATNO C_FIG Androgen receptor-(AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that the HOX/CUT transcription factor ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 targets include the glucocorticoid receptor and the NE splicing factor SRRM4, among others. OC2 regulates gene expression by promoter binding, enhancement of chromatin accessibility, and formation of novel super-enhancers. OC2 also activates glucuronidation genes that irreversibly disable androgen, thereby evoking phenotypic heterogeneity indirectly by hormone depletion. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC. Our findings support enhanced efforts to therapeutically target this protein as a means of suppressing treatment-resistant disease.

cancer biology↗

bioRxiv2023

Metabolic evolution of pyranopterin-dependent biochemistry

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

evolutionary biology↗

bioRxiv2023

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

Most of lifes diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) [~]2.33 billion years ago (Ga, (Poulton et al. 2021)), in which oxygenic photosynthesis and tectonism (Eguchi, Seales, and Dasgupta 2019) transformed Earths biosphere from dominantly anaerobic to aerobic. Here, we combine machine learning and phylogenetic reconciliation to infer ancestral transitions to aerobic lifestyles during bacterial evolution. Linking these transitions to the GOE provides new constraints to infer the timetree of Bacteria. We find that extant bacterial phyla are truly ancient, having radiated in the Archaean and the Proterozoic: the oldest include Bacillota (Firmicutes), which radiated 3.1-3.7 Ga, Cyanobacteria (3.3-3.5 Ga) and Patescibacteria (3-3.5 Ga). We show that most bacterial phyla were ancestrally anaerobic and that most transitions to an aerobic lifestyle post-dated the GOE. Our analyses trace oxygen production and consumption back to Cyanobacteria. From that starting point, horizontal transfer seeded aerobic lifestyles across bacterial diversity over hundreds of millions of years. Our analyses demonstrate that the diversification of aerobes proceeded in two waves corresponding to the GOE and to a second sustained rise in atmospheric O2 at the dawn of the Palezoic (Krause et al. 2022).

evolutionary biology↗

bioRxiv2023

The homeodomain drives favorable DNA binding energetics of prostate cancer target ONECUT2

The ONECUT transcription factors feature a CUT and a homeodomain, evolutionarily conserved elements that bind DNA cooperatively, but the process remains mechanistically enigmatic. Using an integrative DNA binding analysis of ONECUT2, a driver of aggressive prostate cancer, we show that the homeodomain energetically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. Further, evolutionarily conserved base-interactions in both the CUT and homeodomain are necessary for the favorable thermodynamics. We have identified a novel arginine pair unique to the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions in general, including by this arginine pair, are critical for optimal DNA binding and transcription in a prostate cancer model. These findings provide fundamental insights into DNA binding by CUT-homeodomain proteins with potential therapeutic implications. One-Sentence SummaryBase-specific interactions regulate homeodomain-mediated stabilization of DNA binding by the ONECUT2 transcription factor.

biophysics↗

bioRxiv2023

Cancer cells co-evolve with retrotransposons to mitigate viral mimicry

Overexpression of repetitive elements is an emerging hallmark of human cancers1. Diverse repeats can mimic viruses by replicating within the cancer genome through retrotransposition, or presenting pathogen-associated molecular patterns (PAMPs) to the pattern recognition receptors (PRRs) of the innate immune system2-5. Yet, how specific repeats affect tumor evolution and shape the tumor immune microenvironment (TME) in a pro- or anti-tumorigenic manner remains poorly defined. Here, we integrate whole genome and total transcriptome data from a unique autopsy cohort of multiregional samples collected in pancreatic ductal adenocarcinoma (PDAC) patients, into a comprehensive evolutionary analysis. We find that more recently evolved Short Interspersed Nuclear Elements (SINE), a family of retrotransposable repeats, are more likely to form immunostimulatory double-strand RNAs (dsRNAs). Consequently, younger SINEs are strongly co-regulated with RIG-I like receptor associated type-I interferon genes but anti-correlated with pro-tumorigenic macrophage infiltration. We discover that immunostimulatory SINE expression in tumors is regulated by either Long Interspersed Nuclear Elements 1 (LINE1/L1) mobility or ADAR1 activity in a TP53 mutation dependent manner. Moreover, L1 retrotransposition activity tracks with tumor evolution and is associated with TP53 mutation status. Altogether, our results suggest pancreatic tumors actively evolve to modulate immunogenic SINE stress and induce pro-tumorigenic inflammation. Our integrative, evolutionary analysis therefore illustrates, for the first time, how dark matter genomic repeats enable tumors to co-evolve with the TME by actively regulating viral mimicry to their selective advantage.

cancer biology↗

bioRxiv2022

Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we explore the metabolic adaptation of four syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a and Seep-SRB1g) from a phylogenomics perspective, tracing the evolution of conserved proteins in the syntrophic SRB clades, and comparing the genomes of syntrophic SRB to their nearest evolutionary neighbors in the phylum Desulfobacterota. We note several examples of gain, loss or biochemical adaptation of proteins within pathways involved in extracellular electron transfer, electron transport chain, nutrient sharing, biofilm formation and cell adhesion. We demonstrate that the metabolic adaptations in each of these syntrophic clades are unique, suggesting that they have independently evolved, converging to a syntrophic partnership with ANME. Within the clades we also investigated the specialization of different syntrophic SRB species to partnerships with different ANME clades, using metagenomic sequences obtained from ANME and SRB partners in individual consortia after fluorescent-sorting of cell aggregates from anaerobic sediments. In one instance of metabolic adaptation to different partnerships, we show that Seep-SRB1a partners of ANME-2c appear to lack nutritional auxotrophies, while the related Seep-SRB1a partners of a different methanotrophic archaeal lineage, ANME-2a, are missing the cobalamin synthesis pathway, suggesting that the Seep-SRB1a partners of ANME-2a may have a nutritional dependence on its partner. Together, our paired genomic analysis of AOM consortia highlights the specific adaptation and diversification of syntrophic SRB clades linked to their associated ANME lineages.

microbiology↗

bioRxiv2022

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Somatic mutations in cancer genes have been ubiquitously detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, mutated and wildtype cells are morphologically and phenotypically similar, limiting the ability to link genotypes with cellular phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing the mutation with transcriptomes and methylomes in stem and progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations resulted in myeloid over lymphoid bias, and in expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate. We observed dysregulated expression of lineage and leukemia stem cell markers. DNMT3A R882 led to preferential hypomethylation of polycomb repressive complex 2 targets and a specific sequence motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A R882 mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics pave the road to defining the downstream consequences of mutations that drive human clonal mosaicism.

cancer biology↗

bioRxiv2021

Diversity and evolution of nitric oxide reduction

Nitrogen is an essential element for life, with the availability of fixed nitrogen limiting productivity in many ecosystems. The return of oxidized nitrogen species to the atmospheric N2 pool is predominately catalyzed by microbial denitrification (NO3- [->] NO2- [->] NO [->] N2O [->] N2)1. Incomplete denitrification can produce N2O as a terminal product, leading to an increase in atmospheric N2O, a potent greenhouse and ozone-depleting gas2. The production of N2O is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) superfamily3. Here we use phylogenomics to identify a number of previously uncharacterized HCO families and propose that many of them (eNOR, sNOR, gNOR, and nNOR) perform nitric oxide reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple nitric oxide reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from Rhodothermus marinus, verifying that it performs nitric oxide reduction both in vitro and in vivo. These newly identified NORs exhibit broad phylogenetic and environmental distributions, expanding the diversity of microbes that can perform denitrification. Phylogenetic analyses of the HCO superfamily demonstrate that nitric oxide reductases evolved multiple times independently from oxygen reductases, suggesting that complete denitrification evolved after aerobic respiration.

biochemistry↗