proteomics

Carboxypeptidase activity drives L,D-transpeptidase essentiality during vegetative growth and sporulation in Clostridioides difficile

This paper identifies DD-CPases as the source of tetrapeptides for LDTs in C. difficile and shows that LDTs are essential due to high DD-CPase activity, not for divisome/elongasome function.

Dissecting functional dynamics of fecal-derived in vitro stable microbial communities with metaproteomics

This study uses metaproteomics to analyze how culture medium and donor-specific factors influence the establishment of in vitro fecal microbial communities over time.

GlRac Regulates an ATG8-Independent Autophagy-Like Pathway in Giardia lamblia

This study identifies an ATG8-independent autophagy-like pathway in Giardia lamblia regulated by GlRac, showing structural and functional similarities to canonical autophagy despite lacking most ATG genes.

ESX-1 remodels the Mycobacterium tuberculosis antigen storage compartment in macrophages

The paper investigates how Mtb remodels antigen storage compartments in macrophages using a split fluorescent protein reporter and subcellular spatial proteomics.

The microbial soy metabolite S-equol mitigates cadmium neurotoxicity in mice

This study shows that S-equol, a microbial metabolite, reduces cadmium-induced neurotoxicity in mice by restoring neural gene expression and is associated with lower levels in humans carrying the apolipoprotein E4 allele.

Dynamic 2'-O-Me of rRNA regulates ribosome translation in Arabidopsis nucleolin1 mutants and during seed-to-seedling transition

This study shows that 2'-O-Me modifications on rRNA are dynamically regulated during seed-to-seedling transition in Arabidopsis and affect ribosome translation.

Bottom-up engineering of EV-mimetic vesicles reveals selective protein loading and modulates cellular uptake and biodistribution

The paper engineers EV-mimetic vesicles to study protein loading and uptake, finding that protein properties influence incorporation and biodistribution.

Small-molecule modulators of HIPK4 activity and proteostasis

This study identifies cyanoquinoline-based HIPK4 inhibitors with nanomolar potency and reveals their cell-type-specific effects on HIPK4 proteostasis and autophagy.

Integrating dorsolateral prefrontal cortex multi-omics and GWAS summary data enhances gene-mapping of Parkinson's disease

This study integrates multi-omics data from DLPFC with GWAS summary data to identify PD risk genes, finding significant overlaps between bulk and cell-type-aware TWAS and PWAS results.

Dimerization of human PARP15 is required for NAD+ binding and automodification

This study shows that dimerization of PARP15 is necessary for NAD+ binding and automodification, supported by structural and biochemical evidence.

Verification Debt in Automated Biological Research Workflows: A Proof-of-Concept

This study examines verification debt in agentic AI workflows for biological research, using Biomni to analyze 10 test cases across proteomics, genomics, and drug discovery.

Analysis of Phycodnaviridae Tetrapyrrole Enzymes: Subcellular Localization and Functional Divergence from Host Homologs

The paper analyzes Phycodnaviridae viral homologs of heme oxygenase-1 and Phycocyanobilin:Ferredoxin oxidoreductase to predict their subcellular localization and functional divergence from host enzymes.

Mucosal architecture, microbiota resilience and metabolic disruption reveal holobiont dynamics during bovine respiratory disease

This study investigates host-microbiota interactions during bovine respiratory disease, finding that antimicrobial treatment has a greater impact on microbial communities and metabolic functions than infection alone.

Mass spectrometric analysis of free methionine oxidation levels in E. coli

This study introduces fMObB, a mass spectrometry method to measure free methionine oxidation in E. coli, revealing higher oxidation under stress and the role of methionine sulfoxide reductases.

Protective near-germline antibodies to malaria elicited by RTS,S/AS01E vaccination in African infants

This study identifies potent antimalarial antibodies in African infants vaccinated with RTS,S/AS01E, showing near-germline configurations and protective efficacy.

An Expanded Lpt Pathway Couples Surface Lipoprotein Export to Outer Membrane Vesicle Biogenesis in Bacteroides

This study identifies LptZ as a critical protein linking surface lipoprotein export to outer membrane vesicle biogenesis in Bacteroides, revealing a novel pathway and expanding the role of the Lpt machinery.

Conserved mycobacteriophage protein uses structural mimicry to displace host initiation factors

The paper identifies a conserved viral protein module that displaces host RNA polymerase sigma factors to control transcription in mycobacteria.

SETD3 ACTIN HISTIDINE METHYLTRANSFERASE REGULATES INTESTINAL EPITHELIAL BARRIER INTEGRITY AND MUCOSAL INFLAMMATION

This study shows that SETD3 methylates actin, enhancing F-actin polymerization and protecting intestinal epithelial barrier integrity, and its loss worsens inflammation and permeability.

A quantitative interactome map reveals affinity tailored hijacking of human cellular functions by resident and pathogenic bacteria

The paper reports a large-scale quantitative interactome of human PDZ domains and bacterial PDZ-binding motifs, showing bacteria tailor effector sequences to bind with similar or higher affinity than human PBMs to hijack host functions.

Monomeric TDP-43 binds GU-rich RNA via its NTD but only its oligomers block cryptic exon inclusion

This study shows that the NTD of TDP-43 binds UG-rich RNA on monomers, while oligomerization is essential for repressing cryptic exons.

Spatial Uncoupling of Protein Synthesis from Viral Factories during Rabies Virus Infection

This study shows that during rabies virus infection, protein synthesis occurs outside viral factories (Negri bodies) and newly synthesized viral proteins are later targeted to these compartments.

Unexpected ribosome turnover during prolonged translation inhibition

This study shows that prolonged translation inhibition by cycloheximide causes proteasome-dependent degradation of ribosomal RNA and proteins, revealing a new quality control pathway called GRIP.

BactMentha: a database of annotated bacteria-host protein interactions

BactMentha is a database of annotated bacteria-host protein interactions for human, mouse, and rat, including virulence proteins and predicted interaction interfaces.

A 10-year longitudinal study reveals bat-driven SARSr-CoV evolution

This study tracks SARSr-CoV evolution in Rhinolophus bats over 10 years, revealing host factors driving viral diversification and adaptation.

Characterization of the dual functions of Leishmania CK1.2 in both the parasite and the macrophage

This study identifies L-CK1.2 interacting partners in Leishmania and host macrophages, revealing its dual role in parasite survival and host immune processes.

Dynamic membrane organization coordinates protein-O-mannosylation and proteostasis in mycobacteria.

The paper identifies a dynamic membrane platform in mycobacteria that coordinates protein-O-mannosylation and proteostasis through a hierarchically organized network.

Templated paired helical filament formation and tau fold-dependent inclusion morphologies in primary neurons

This study shows that primary neurons can propagate Alzheimer's disease paired helical filaments and that tau filament folds determine inclusion morphologies.

Evolutionary conservation and divergence of CXCL17 orthologs: functional evidence in reptiles and loss in the avian lineage

This study identifies functional CXCL17 orthologs in reptiles and shows their loss in birds, using bioinformatics and recombinant protein assays.

ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications

ProteomeScout v4 provides an open-source ecosystem for aggregating and harmonizing post-translational modification data with web and code-based access tools.

Ref(2)P/p62 protein pleomorphism confers tissue-specific function

One Drosophila Ref(2)P polypeptide takes different structures in midgut and muscle, driving autophagy or mitochondria-associated degradation; deleting disordered region IDR2 switches muscle Ref(2)P to midgut state.