The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation

Microbial interactions with magnetite enhance methane production from hydrocarbon biodegradation

Indigenous microbial communities in fine tailings (FT) biodegrade residual diluent hydrocarbons and support CH4 emissions from oil sands tailings ponds and end-pit lakes. We investigated the effect of added crystalline Fe mineral magnetite on microbial metabolism of hydrocarbons in FT collected from methanogenically less and more active sites of an end-pit lake. Magnetite accelerated CH4 production by enhancing the biodegradation of hydrocarbons, with a more prominent effect on complex/relatively recalcitrant aliphatics (C8-C11 compounds) and monoaromatics. Interestingly, 86-92 % of total magnetite added in FT remained stable even after the metabolism of labile hydrocarbons (∼45 % of total diluent hydrocarbons). This may be due to magnetite enabling mineralogical direct interspecies electron transfer (mDIET) rather than iron reduction to enhance the methanogenic biodegradation of hydrocarbons. Enrichment of Coriobacteriaceae along with Desulfosporosinus, Syntrophus, Peptococcaceae, Smithella, Methanosaeta, and Methanoregula in magnetite-supplemented FT during hydrocarbon biodegradation suggested their potential role in developing mDIET. These results suggest that magnetite, when present, accelerates methanogenesis and potentially may increase rather than suppress CH4 emissions from FT, and also suggest the potential use of magnetite to accelerate bioremediation of other hydrocarbon-contaminated anaerobic environments.

Probing and manipulating the gut microbiome with chemistry and chemical tools

The human gut microbiome represents an extended "second genome" harbouring about 1015 microbes containing >100 times the number of genes as the host. States of health and disease are largely mediated by host-microbial metabolic interplay, and the microbiome composition also underlies the differential responses to chemotherapeutic agents between people. Chemical information will be the key to tackle this complexity and discover specific gut microbiome metabolism for creating more personalised interventions. Additionally, rising antibiotic resistance and growing awareness of gut microbiome effects are creating a need for non-microbicidal therapeutic interventions. We classify chemical interventions for the gut microbiome into categories like molecular decoys, bacterial conjugation inhibitors, colonisation resistance-stimulating molecules, "prebiotics" to promote the growth of beneficial microbes, and inhibitors of specific gut microbial enzymes. Moreover, small molecule probes, including click chemistry probes, artificial substrates for assaying gut bacterial enzymes and receptor agonists/antagonists, which engage host receptors interacting with the microbiome, are some other promising developments in the expanding chemical toolkit for probing and modulating the gut microbiome. This review explicitly excludes "biologics" such as probiotics, bacteriophages, and CRISPR to concentrate on chemistry and chemical tools like chemoproteomics in the gut-microbiome context.

Lysine Phoshoglycerylation Is Widespread in Bacteria and Overlaps with Acylation

Phosphoglycerylation is a non-enzymatic protein modification in which a phosphoglyceryl moiety is covalently bound to the ε-amino group of lysine. It is enriched in glycolytic enzymes from humans and mice and is thought to provide a feedback mechanism for regulating glycolytic flux. We report the first proteomic analysis of this post-translational modification in bacteria by profiling phosphoglyceryl-lysine during the growth of Streptococcus pyogenes in different culture media. The identity of phosphoglyceryl-lysine was confirmed by a previously unknown diagnostic cyclic immonium ion generated during MS/MS. We identified 370 lysine phosphoglycerylation sites in 123 proteins of S. pyogenes. Growth in a defined medium on 1% fructose caused a significant accumulation of phosphoglycerylation compared to growth in a rich medium containing 0.2% glucose. Re-analysis of phosphoproteomes from 14 bacterial species revealed that phosphoglycerylation is generally widespread in bacteria. Many phosphoglycerylation sites were conserved in several bacteria, including S. pyogenes. There was considerable overlap between phosphoglycerylation, acetylation, succinylation, and other acylations on the same lysine residues. Despite some exceptions, most lysine phosphoglycerylations in S. pyogenes occurred with low stoichiometry. Such modifications may be meaningless, but it is also conceivable that phosphoglycerylation, acetylation, and other acylations jointly contribute to the overall regulation of metabolism.

Efficient methane production from agro-industrial residues using anaerobic fungal-rich consortia

Anaerobic digestion (AD) emerges as a pivotal technique in climate change mitigation, transforming organic materials into biogas, a renewable energy form. This process significantly impacts energy production and waste management, influencing greenhouse gas emissions. Traditional research has largely focused on anaerobic bacteria and methanogens for methane production. However, the potential of anaerobic lignocellulolytic fungi for degrading lignocellulosic biomass remains less explored. In this study, buffalo rumen inocula were enriched and acclimatized to improve lignocellulolytic hydrolysis activity. Two consortia were established: the anaerobic fungi consortium (AFC), selectively enriched for fungi, and the anaerobic lignocellulolytic microbial consortium (ALMC). The consortia were utilized to create five distinct microbial cocktails-AF0, AF20, AF50, AF80, and AF100. These cocktails were formulated based on varying of AFC and ALMC by weights (w/w). Methane production from each cocktail of lignocellulosic biomasses (cassava pulp and oil palm residues) was evaluated. The highest methane yields of CP, EFB, and MFB were obtained at 337, 215, and 54 mL/g VS, respectively. Cocktails containing a mix of anaerobic fungi, hydrolytic bacteria (Sphingobacterium sp.), syntrophic bacteria (Sphaerochaeta sp.), and hydrogenotrophic methanogens produced 2.1-2.6 times higher methane in cassava pulp and 1.1-1.2 times in oil palm empty fruit bunch compared to AF0. All cocktails effectively produced methane from oil palm empty fruit bunch due to its lipid content. However, methane production ceased after 3 days when oil palm mesocarp fiber was used, due to long-chain fatty acid accumulation. Anaerobic fungi consortia showed effective lignocellulosic and starchy biomass degradation without inhibition due to organic acid accumulation. These findings underscore the potential of tailored microbial cocktails for enhancing methane production from diverse lignocellulosic substrates.

The benzoyl-CoA pathway serves as a genomic marker to identify the oxygen requirements in the degradation of aromatic hydrocarbons

The first step of anaerobic benzoate degradation is the formation of benzoyl-coenzyme A by benzoate-coenzyme A ligase (BCL). The anaerobic route is steered by benzoyl-CoA reductase, which promotes benzoyl-CoA breakdown, which is subsequently oxidized. In certain bacteria at low oxygen conditions, the aerobic metabolism of monoaromatic hydrocarbons occurs through the degradation Box pathway. These pathways have undergone experimental scrutiny in Alphaproteobacteria and Betaproteobacteria and have also been explored bioinformatically in representative Betaproteobacteria. However, there is a gap in our knowledge regarding the distribution of the benzoyl-CoA pathway and the evolutionary forces propelling its adaptation beyond that of representative bacteria. To address these questions, we used bioinformatic procedures to identify the BCLs and the lower pathways that transform benzoyl-CoA. These procedures included the identification of conserved motifs. As a result, we identified two motifs exclusive to BCLs, describing some of the catalytic properties of this enzyme. These motifs helped to discern BCLs from other aryl-CoA ligases effectively. The predicted BCLs and the enzymes of lower pathways were used as genomic markers for identifying aerobic, anaerobic, or hybrid catabolism, which we found widely distributed in Betaproteobacteria. Despite these enhancements, our approach failed to distinguish orthologs from a small cluster of paralogs exhibiting all the specified features to predict an ortholog. Nonetheless, the conducted phylogenetic analysis and the properties identified in the genomic context aided in formulating hypotheses about how this redundancy contributes to refining the catabolic strategy employed by these bacteria to degrade the substrates.

FLAMS: Find Lysine Acylations and other Modification Sites

SUMMARY

Today, hundreds of post-translational modification (PTM) sites are routinely identified at once, but the comparison of new experimental datasets to already existing ones is hampered by the current inability to search most PTM databases at the protein residue level. We present FLAMS (Find Lysine Acylations and other Modification Sites), a Python3-based command line and web-tool that enables researchers to compare their PTM sites to the contents of the CPLM, the largest dedicated protein lysine modification database, and dbPTM, the most comprehensive general PTM database, at the residue level. FLAMS can be integrated into PTM analysis pipelines, allowing researchers to quickly assess the novelty and conservation of PTM sites across species in newly generated datasets, aiding in the functional assessment of sites and the prioritization of sites for further experimental characterization.

AVAILABILITY AND IMPLEMENTATION

FLAMS is implemented in Python3, and freely available under an MIT license. It can be found as a command line tool at https://github.com/hannelorelongin/FLAMS, pip and conda; and as a web service at https://www.biw.kuleuven.be/m2s/cmpg/research/CSB/tools/flams/.

Granular activated carbon and exogenous hydrogen enhanced anaerobic digestion of hypersaline phenolic wastewater via syntrophic acetate oxidation and hydrogenotrophic methanogenesis

High salinity in phenolic wastewater inhibited anaerobes' metabolic activity, thereby affecting the anaerobic biotransformation of phenol. In this study, granular activated carbon (GAC) coupled with exogenous hydrogen (H₂) was used to enhance the anaerobic digestion of phenol. The GAC/H₂ group's accumulative methane production, coenzyme F₄₂₀ concentration, and interspecies electron transfer system activity increased by 24 %, 53 %, and 16 %, respectively, compared with the control group. In the floc sludge of the GAC/H₂ group, the relative abundance of syntrophic acetate-oxidizing bacteria such as Syntrophus and Syntrophorhabdus were 18.7 % and 1.1 % at genus level, respectively, which were around 93.5 and 7.5 times of that of the controlgroup. Moreover, Acinetobacter (77.6 %), Methanobacterium (44.0 %), and Methanosarcina (34.2 %) were significantly enriched on the GAC surface in GAC/H₂ group. Therefore, the coupling of GAC and H₂ provided a novel attempt at anaerobic digestion of hypersaline phenolic wastewater via syntrophic acetate oxidation and hydrogenotrophic methanogenesis pathway.