Biology subjects

Chadwick, G.

Publications and source records attributed to Chadwick, G..

6 recordsLinked to original sources

bioRxiv2025

Identification of radical SAM enzymes responsible for the methylation and desaturation of archaeal lipids and an AttH hydratase mediating hydroxy-GDGT biosynthesis

Lipid biosynthesis in archaea is highly dependent upon radical (S)-adenosyl methionine (rSAM) enzymes. The formation of their membrane-spanning lipids, known as glycerol dibiphytanyl glycerol tetraethers (GDGTs), is catalyzed by the rSAM tetraether synthase and the subsequent cyclization of their lipid tails is performed by the B12-binding rSAM (B12-rSAM) GDGT ring synthase. Further, GDGT tails are cross-linked by the rSAM GMGT synthase and then methylated by the B12-rSAM GMGT methylase. Here, utilizing three archaeal model organisms - Sulfolobus acidocaldarius, Thermococcus kodakarensis, and Methanosarcina acetivorans - we expand this repertoire of rSAM enzymes further, identifying two B12-rSAM GDGT methylases and a novel B12-rSAM GDGT desaturase. We also extend beyond the rSAM enzyme superfamily, identifying an AttH-like hydratase mediating hydroxy-GDGT (OH-GDGT) biosynthesis. Specifically, we identify two GDGT methylases in S. acidocaldarius and Thermococcus aggregans which possess different substrate specificities. While GDGT methylation is generally low in archaea, we observe high levels of lipid methylation in response to penicillin G and hexanoic acid amphiphile exposure, suggesting a role for lipid methylation in response to membrane-destabilizing chemical agents. Utilizing heterologous expression in M. acetivorans and T. kodakarensis, we uncover a novel B12-rSAM enzyme from Candidatus Bathyarchaeota B1_G15 with unusual tetraether desaturase (Ted) activity that seemingly reverses previous saturation by geranylgeranyl reductase, anaerobically forming double bonds in the inert hydrocarbon tails of a GDGT. Finally, we show that a non-rSAM AttH-like hydratase, genomically associated with Ted, is a hydroxy-GDGT synthase (Hgs), putatively hydrating the double bond(s) introduced by Ted to form OH-GDGTs. These results highlight the value of exploring the rSAM enzyme landscape of archaea - revealing diverse and novel rSAM enzyme activities amongst homologous proteins that invoke new paradigms such as reversibility in the archaeal lipid biosynthesis pathway.

microbiology↗

bioRxiv2025

The Ambiguous Genetic Code of Methanogenic Archaea that Grow on Methylamines

Natural genetic code expansion is a phenomenon wherein an additional amino acid is encoded by a stop codon. These non-standard amino acids are beneficial as they facilitate novel biochemical reactions. However, code expansion leads to ambiguity at the recoded stop codon, which can either be read through or terminated. Pyrrolysine (Pyl) is encoded by the amber codon (TAG/UAG) and is widespread in archaea, where it is required for methylamine-mediated methanogenesis, an environmentally important metabolism. Mechanisms to conditionally suppress the amber stop codon for Pyl installation during protein synthesis have not been identified. Using the model methanogen, Methanosarcina acetivorans, we demonstrate that Pyl-encoding archaea maintain an ambiguous genetic code wherein UAG encodes dual meaning as stop and Pyl. Our data suggest that expression of Pyl biosynthesis and incorporation genes is tuned to the cellular demand for Pyl, which allows these archaea to navigate ambiguous stop decoding in response to environmental cues.

microbiology↗

bioRxiv2022

Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring

The preeminent source of biological methane on Earth is methyl coenzyme M reductase (Mcr)-dependent archaeal methanogenesis. A growing body of evidence suggests a diversity of archaea possess Mcr, however, experimental validation of hypothesized methane metabolisms has been missing. Here, we provide evidence of a functional Mcr-based methanogenesis pathway in a novel member of the family Archaeoglobaceae, designated Methanoproducendum nevadense, which we enriched from a terrestrial hot spring on the polysaccharide xyloglucan. Our incubation assays demonstrate methane production that is highly sensitive to the Mcr-inhibitor bromoethanesulfonate, stimulated by xyloglucan and xyloglucan-derived sugars, concomitant with the consumption of molecular hydrogen, and causing a deuterium fractionation in methane characteristic of hydrogenotrophic and methylotrophic methanogens. Combined with the recovery and analysis of a high-quality M. nevadense metagenome-assembled genome encoding a divergent Mcr and diverse potential electron and carbon transfer pathways, our observations suggest methanogenesis in M. nevadense occurs via Mcr and is fueled by the consumption of cross-fed byproducts of xyloglucan fermentation mediated by other community members. Phylogenetic analysis shows close affiliation of the M. nevadense Mcr with those from Korarchaeota, Nezhaarchaeota, Verstraetearchaeota, and other Archaeoglobales that are divergent from well-characterized Mcrs. We propose these archaea likely also use functional Mcr complexes to generate methane on the basis of our experimental validation in M. nevadense. Although our stable isotope approach reveals that microbial methanogenesis contributes only a small proportion of the overall methane abundance in the native habitat, divergent Mcr-encoding archaea may be underestimated sources of biological methane in terrestrial and marine hydrothermal environments.

microbiology↗

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↗

bioRxiv2021

Bacterial growth in multicellular aggregates leads to the emergence of complex lifecycles

In response to environmental stresses such as starvation, many bacteria facultatively aggregate into multicellular structures that can attain new metabolic functions and behaviors. Despite the ubiquity and relevance of this form of collective behavior, we lack an understanding of how the spatiotemporal dynamics of aggregate development emerge from cellular physiology. Here, we show that the coupling between growth and spatial gradient formation leads to the emergence of a complex lifecycle, akin to those known for multicellular bacteria. Under otherwise carbon-limited growth conditions, the marine bacterium Vibrio splendidus 12B01 forms multicellular groups to collectively harvest carbon from the brown-algal polysaccharide alginate. This is achieved during growth on dissolved alginate polymer through formation of spherical, clonal clusters of cells that grow up to 40 {micro}m in radius. Clusters develop striking spatial patterning as they grow due to phenotypic differentiation of sub-populations into a shell of static cells surrounding a motile core. Combining in situ measurements of cell physiology with transcriptomics, we show that shell cells express adhesive type IV pili, while motile core cells express carbon storage granules. The emergence of shell and core phenotypes is cued by opposing gradients of carbon and nitrogen that form within cell clusters due to local metabolic activity. Eventually, the shell ruptures, releasing the carbon-storing core, and we show that carbon-storing cells more readily propagate on alginate than non-carbon storing cells. We propose that phenotypic differentiation promotes the resilience of 12B01 groups by enabling clonal groups to grow larger and propagate more effectively. Phenotypic differentiation may be a widespread, but overlooked, strategy among bacteria to enhance resilience in the context of resource limitation.

microbiology↗

bioRxiv2018

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; rG16) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Candidatus Bathyarchaeota and Candidatus Syntrophoarchaeum MAGs. rG16 is basal to members of the class Archaeoglobi, and encodes the genes for {beta}-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. rG16 also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. As the first Archaeoglobi with the MCR complex, rG16 extends our understanding of the evolution and distribution of novel MCR encoding lineages among the Archaea.

microbiology↗