Biology subjects

Stock, L.

Publications and source records attributed to Stock, L..

4 recordsLinked to original sources

bioRxiv2026

Alkane-oxidizing consortia produce substantial amounts of disaccharides

1Consortia of archaea and partner bacteria couple the anaerobic oxidation of alkanes to sulfate reduction. While catabolic pathways in anaerobic alkane-oxidizing archaea (ANKA) are increasingly understood, their anabolic capacities remain poorly characterized. Here, we examined nine enrichment cultures dominated by ANKA and their partner bacteria for small-molecular compounds using solvent extraction and gas chromatographic analysis of derivatized extracts. All hydrocarbon-degrading cultures contained substantial amounts of disaccharides in their metabolite pools. Cold-adapted methane-oxidizing cultures dominated by ANME-2c and Seep-SRB2 contained up to 1.5 mg of trehalose per mg soluble protein. Trehalose was also abundant in ethane-oxidizing cultures of Candidatus Ethanoperedens and its distinct partner SRBs, accounting for up to 75 % of the extracted metabolites. In contrast, thermophilic ANKA cultures dominated by ANME-1 or Ca. Syntropharchaeum and Ca. Desulfofervidus contained an abundant as-yet-unidentified glucose-containing disaccharide. Metagenomic analysis revealed widespread trehalose metabolism genes among partner Desulfobacterota and in ANME-2c and Ca. Ethanoperedens, but a lower potential in ANME-1 and Syntropharchaeum, consistent with metabolite profiles. If exogenous trehalose was added to the Ethane50 culture, we observed rapid metabolization by heterotrophic microorganisms, but poor assimilation by the Ca. Ethanoperedens/ Ca. Desulfofervidus core community, indicating that ANKA/SRB consortia do not consume externally supplied trehalose. Instead, Ca. Ethanoperedens/ Ca. Desulfofervidus, as well as other ANKA/SRB consortia, may use the disaccharides as energy-storage molecules, osmolytes, or components of the extracellular matrix. Notably, the disaccharides produced by the consortia also sustain ancillary heterotrophs, thereby linking alkane oxidation to broader sedimentary carbon cycling.

microbiology↗

bioRxiv2025

Marine cold seep ANME-2/SRB consortia produce their lipid biomass from inorganic carbon

In cold seeps, anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) oxidize methane to inorganic carbon (IC) coupled to sulfate reduction. While catabolic pathways are well resolved, carbon flow into biomass remains unclear. We conducted lipid stable isotope probing (lipid-SIP) experiments with Astoria Canyon sediments dominated by ANME-2/SRB consortia and incubated samples with either 13C-labeled methane (13CH4) or dissolved IC (DI13C). Lipid-specific {delta}13C analysis showed higher 13C incorporation from DI13C than from 13CH4. After 30 days, {delta}13C values were up to +417{per thousand} in SRB-specific fatty acids (e.g., C16:1{omega}5c, cyC17:0{omega}5,6) and +126{per thousand} in ANME-2-specific isoprenoid lipids (e.g., archaeol, crocetane). Based on these values, we calculated carbon assimilation rates and found that both partners primarily assimilate IC. Remarkedly, IC assimilation in SRB lipids was eight times higher than in ANME lipids, suggesting that ANME either rely on fixation of internally generated CO2 from 13C-label-free methane before it can be exchanged with the environment or they utilize an additional, yet unknown carbon source for lipid biosynthesis. By examining the step-wise 13C-enrichment of ANME- and SRB-derived lipids, we further delineate biosynthetic pathways for archaeal and bacterial diether lipid formation and highlight crocetane as a bilayer-modulating isoprenoid hydrocarbon potentially affecting membrane fluidity and proton permeability. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/667857v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@a70354org.highwire.dtl.DTLVardef@cb95acorg.highwire.dtl.DTLVardef@1cf6d5corg.highwire.dtl.DTLVardef@114b912_HPS_FORMAT_FIGEXP M_FIG C_FIG Lipid-SIP experiments in Astoria Canyon sediments revealed that both ANME-2 and SRB primarily assimilate inorganic carbon (IC), not methane, into biomass. SRB-specific lipids showed eightfold higher I13C-assimilation than ANME lipids, suggesting SRB directly assimilate environmental IC, while ANME rely on internally produced CO2 or alternative carbon sources, potential provided by SRBs.

microbiology↗

bioRxiv2021

SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available, or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the master UPR sensor IRE1 kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1 as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1 through autophosphorylation, but its RNase activity fails to splice XBP1. Moreover, while IRE1 was dispensable for replication in human cells for all coronaviruses tested, it was required for maximal expression of genes associated with several key cellular functions, including the interferon signaling pathway, during SARS-CoV-2 infection. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1, perhaps as a strategy to eliminate detection by the host immune system. IMPORTANCESARS-CoV-2 is the third lethal respiratory coronavirus after MERS-CoV and SARS-CoV to emerge this century, causing millions of deaths world-wide. Other common coronaviruses such as HCoV-OC43 cause less severe respiratory disease. Thus, it is imperative to understand the similarities and differences among these viruses in how each interacts with host cells. We focused here on the inositol-requiring enzyme 1 (IRE1) pathway, part of the host unfolded protein response to virus-induced stress. We found that while MERS-CoV and HCoV-OC43 fully activate the IRE1 kinase and RNase activities, SARS-CoV-2 only partially activates IRE1, promoting its kinase activity but not RNase activity. Based on IRE1-dependent gene expression changes during infection, we propose that SARS-CoV-2 prevents IRE1 RNase activation as a strategy to limit detection by the host immune system.

microbiology↗

bioRxiv2018

Binding of general anesthetics to ion channels

The direct-site hypothesis assumes general anesthetics bind ion channels to impact protein equilibrium and function, inducing anesthesia. Despite advancements in the field, a first-principle all-atom demonstration of this structure-function premise misses. We focus on clinically used sevoflurane interaction to anesthetic-sensitive Kv1.2 mammalian channel to resolve if sevoflurane binds the proteins well-characterized open and closed structures in a conformation-dependent manner to shift channel equilibrium. We employ an innovative approach relying on extensive docking calculations and free-energy perturbation and find sevoflurane binds open and closed structures at multiple sites under complex saturation and concentration effects. Results point to a non-trivial interplay of conformation-dependent modes of action involving distinct binding sites that increase channel open-probability at diluted ligand concentrations. Given the challenge in exploring more complex processes potentially impacting channel-anesthetic interaction, the result is reassuring as demonstrates that the process of multiple binding events alone may account for open-probability shifts recorded in measurements.

biophysics↗