Biology subjects

Deobald, D.

Publications and source records attributed to Deobald, D..

5 recordsLinked to original sources

bioRxiv2026

Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase

The Wood-Ljungdahl pathway is one of biologys most ancient routes for carbon fixation and energy metabolism, used by organisms such as methanogenic archaea. One of its central metabolic complexes is the acetyl-CoA decarbonylase/synthase (ACDS) complex, catalyzing acetyl-CoA synthesis and cleavage through the co-ordinated action of carbon monoxide dehydrogenase (CODH), acetyl-CoA synthase (ACS), and corrinoid iron-sulfur protein (CoFeSP). Unlike bacterial CODH/ACS, archaeal ACDS lacks a stable bifunctional CODH-ACS architecture, raising the question of how reactive CO and methyl intermediates are efficiently transferred between catalytic modules. Using cryo-electron microscopy, crosslinking mass spectrometry, small-angle X-ray scattering, and biophysical analyses, we resolved the organization and dynamics of the [~]2 MDa archaeal ACDS supercomplex from Methanosarcina acetivorans. We identified CoFeSP as a central architectural scaffold that self-assembles into hexa- to octameric oligomers via a conserved N-terminal region of the CdhD subunit. This scaffold likely tethers CODH and ACS through conserved disordered terminal regions, positioning the catalytic modules in the complexs periphery. We propose a mechanism in which ACS transiently alternates between CODH and CoFeSP, enabling efficient CO and methyl-group transfer without stable binary complexes. This dynamic organization represents a fundamental difference to the stable bifunctional CODH/ACS in bacteria, highlighting how transient interactions enable efficient acetyl-CoA metabolism in archaea.

biochemistry↗

bioRxiv2026

Comprehensive study on ferredoxin isoforms in the cyanobacterium Synechocystis sp. PCC 6803

Ferredoxins are central to cellular metabolism by mediating electron flow in energy conversion reactions. The focus of this study was to systematically examine twelve ferredoxin and ferredoxin-like proteins from Synechocystis sp. PCC 6803 to identify their properties, activities, and functions in electron transfer. Using electron paramagnetic resonance spectroscopy, we detected cluster types consistent with major ferredoxin families including plant-type [2Fe-2S], adrenodoxin, thioredoxin, and bacterial-type [4Fe- 4S] ferredoxins. In addition, we found that the ssr3184 ferredoxin-like protein exchanged between a [3Fe-4S] or a [4Fe-4S] cluster, pointing to a possible functional change in response to changes in oxygen or cellular redox poise. Electrochemical measurements demonstrated that these ferredoxins constitute a broad potential window, from -243 mV to -520 mV vs SHE. Investigations on their capacity to support electron-transfer focused on reactions with two major redox hubs: Photosystem I and pyruvate:ferredoxin oxidoreductase and included testing of binding interactions with nitrite reductase. Expression profiling under multiple environmental conditions was also used to predict function and revealed distinct regulatory patterns. Collectively, these findings identified a group of core ferredoxins that directly support photosynthetic electron transfer, and more specialized ones that may serve other functions. In summary, Synechocystis utilizes a suite of ferredoxins to maintain cellular redox homeostasis under dynamic environmental conditions.

biochemistry↗

bioRxiv2026

Structural Basis of Membrane Potential Coupled Vectorial CO2 Hydration by the DAB2 Complex in Chemolithoautotrophs

The fixation of dissolved inorganic carbon (DIC) such as CO2 and bicarbonate by autotrophic microorganisms is fundamental to the global primary production. Many autotrophs depend on a diversity of CO2-concentrating mechanisms (CCMs) to overcome the inefficiency of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and the limited supply of DIC. While cyanobacterial CCMs are well characterized, analogous systems in chemolithoautotrophs, specifically active DIC uptake systems have long been overlooked. Here, we present the first cryo-EM structural analysis of DAB2, an essential membrane-associated protein complex for CO2 uptake in Halothiobacillus neapolitanus. The cytoplasmic subunit DabA2 displays a {beta}-carbonic anhydrase-like fold including a zinc ion, while the transmembrane subunit DabB2 resembles the proton-conducting subunits of respiratory Complex I. Purified DAB2 binds CO2 independent of proton motive force (PMF) however, did not spontaneously hydrate CO2. This suggests that CO2 hydration is PMF-dependent and may involve a gating mechanism. Structural analysis reveals an unconventional deeply buried active site only accessible via gated substrate tunnels, implying that substrate access, product release, and catalytic activation are tightly regulated. A unique transmembrane helix of DabA2 constitutes part of the proton conduction pathway and potentially couples proton translocation to enzymatic turnover. These features define a vectorial CO2 hydration mechanism that prohibits reverse bicarbonate dehydration and requires a proton gradient to initiate catalytic turnover. Our findings establish DAB2 as a prototype of a previously unrecognized family of PMF-driven carbonic anhydrases, elucidating a novel strategy for CO2 capture in non-photosynthetic autotrophs and expanding the mechanistic landscape of bacterial CCMs.

biochemistry↗

bioRxiv2025

Sequential exposure to anoxic/oxic conditions leads to biotransformation and detoxification of sitagliptin in urban hyporheic zones

Pharmaceuticals are increasingly recognized as contaminants of concern in aquatic environments. Sitagliptin, an antidiabetic drug that carries a trifluoromethyl group, which is a precursor of the persistent trifluoroacetic acid, is excreted largely unmetabolized and inefficiently removed in wastewater treatment plants, leading to its widespread detection in surface waters. The hyporheic zone -- a region between surface water and groundwater -- serves as a natural bioreactor with high microbial activity and diverse redox conditions, offering the potential for sitagliptin attenuation. This study explored the biotransformation of sitagliptin in hyporheic sediments under varying redox conditions through batch experiments and field observations. Furthermore, we showed that batch experiments can complement field observations to capture both mechanistic insights and their environmental relevance. Batch experiments revealed amide hydrolysis and N-acetylation of sitagliptin under anoxic conditions, with subsequent deamination and oxidation of transformation products under oxic conditions. Metagenome-resolved metaproteomics suggested Pseudomonas asiatica as a key player in the oxic transformation. Field analysis of pore water samples identified up to 6.47 {micro}g L-{superscript 1} sitagliptin and ten transformation products with concentrations of up to 4.82 {micro}g L-{superscript 1}. Amide hydrolysis products were the most abundant transformation products and preferentially formed under anoxic conditions. All investigated transformation products exhibited lower cytotoxicity and oxidative stress response than sitagliptin in in vitro bioassays, highlighting the detoxification potential of the hyporheic zone. By identifying conditions that promote sitagliptin transformation and characterizing its transformation products toxicologically, our work provides parameters for enhanced sitagliptin removal in aquatic environments and improved risk assessment of fluorinated trace organic contaminants. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/657625v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@b43cf4org.highwire.dtl.DTLVardef@10dd64eorg.highwire.dtl.DTLVardef@170ca9corg.highwire.dtl.DTLVardef@5e433_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Analyzing bacterial community compositions by GroEL-taxoproteomics

Profiling bacterial populations in mixed communities is a common task in microbiology. 16S rRNA-based sequencing is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by SDS-PAGE to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw data set obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.

microbiology↗