Exploring the Tomato Root Protein Network Exploited by Core Type 3 Effectors from the Species Complex.

Proteomics has become a powerful approach for the identification and characterization of type III effectors (T3Es). Members of the species complex (RSSC) deploy T3Es to manipulate host cells and to promote root infection of, among others, a wide range of solanaceous plants such as tomato, potato, and tobacco. Here, we used TurboID-mediated proximity labeling (PL) in tomato hairy root cultures to explore the proxeomes of the core RSSC T3Es RipU, RipD, and RipB.

Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.

Unlabelled: In recent years, it has become evident that the true complexity of bacterial proteomes remains underestimated. Gene annotation tools are known to propagate biases and overlook certain classes of truly expressed proteins, particularly proteoforms-protein isoforms arising from a single gene. Recent (re-)annotation efforts heavily rely on ribosome profiling by providing a direct readout of translation to fully describe bacterial proteomes.

Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium.

In bacteria, cell poles function as subcellular compartments where proteins localize during specific lifecycle stages, orchestrated by polar "hub" proteins. Whereas most described bacteria inherit an "old" pole from the mother cell and a "new" pole from cell division, generating cell asymmetry at birth, non-binary division poses challenges for establishing cell polarity, particularly for daughter cells inheriting only new poles. We investigated polarity dynamics in the obligate predatory bacterium , proliferating through filamentous growth followed by non-binary division within prey bacteria.

Exposing the small protein load of bacterial life.

The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs).

Virotrap: Trapping Protein Complexes in Virus-Like Particles.

The discovery of protein-protein interactions can provide crucial information on protein function by linking proteins into known pathways or complexes within the cell. Mass spectrometry (MS)-based methods, such as affinity purification (AP)-MS and proximity-dependent biotin identification (BioID), allowed for a vast increase in the number of reported protein complexes. As a more recent addition to the arsenal of MS-based methods, Virotrap represents a unique technology that benefits from the specific properties of the human immunodeficiency virus-1 (HIV-1) Gag polyprotein.

Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective.

By applying dual proteome profiling to Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters with its epithelial host (here, S. Typhimurium infected human HeLa cells), a detailed interdependent and holistic proteomic perspective on host-pathogen interactions over the time course of infection was obtained.

Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides.

Genomic studies of bacteria have long pointed toward widespread prevalence of small open reading frames (sORFs) encoding for short proteins, <100 amino acids in length. Despite the mounting genomic evidence of their robust expression, relatively little progress has been made in their mass spectrometry-based detection and various blanket statements have been used to explain this observed discrepancy. In this study, we provide a large-scale riboproteogenomics investigation of the challenging nature of proteomic detection of such small proteins as informed by conditional translation data.

Gasdermin D independent canonical inflammasome responses cooperate with caspase-8 to establish host defense against gastrointestinal Citrobacter rodentium infection.

Citrobacter rodentium is an enteropathogen that causes intestinal inflammatory responses in mice reminiscent of the pathology provoked by enteropathogenic and enterohemorrhagic Escherichia coli infections in humans. C. rodentium expresses various virulence factors that target specific signaling proteins involved in executing apoptotic, necroptotic and pyroptotic cell death, suggesting that each of these distinct cell death modes performs essential host defense functions that the pathogen aims to disturb.

Seeking the interspecies crosswalk for filamentous microbe effectors.

Both pathogenic and symbiotic microorganisms modulate the immune response and physiology of their host to establish a suitable niche. Key players in mediating colonization outcome are microbial effector proteins that act either inside (cytoplasmic) or outside (apoplastic) the plant cells and modify the abundance or activity of host macromolecules. We compile novel insights into the much-disputed processes of effector secretion and translocation of filamentous organisms, namely fungi and oomycetes.

Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly.

The cytosolic carboxypeptidase 6 (CCP6) catalyzes the deglutamylation of polyglutamate side chains, a post-translational modification that affects proteins such as tubulins or nucleosome assembly proteins. CCP6 is involved in several cell processes, such as spermatogenesis, antiviral activity, embryonic development, and pathologies like renal adenocarcinoma. In the present work, the cellular role of CCP6 has been assessed by BioID, a proximity labeling approach for mapping physiologically relevant protein-protein interactions (PPIs) and bait proximal proteins by mass spectrometry.

Rhizogenic protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development.

Rhizogenic strains comprise biotrophic pathogens that cause hairy root disease (HRD) on hydroponically grown and crops, besides being widely explored agents for the creation of hairy root cultures for the sustainable production of plant-specialized metabolites. Hairy root formation is mediated through the expression of genes encoded on the T-DNA of the root-inducing (Ri) plasmid, of which several, including (), play a major role in hairy root development. Despite decades of research, the exact molecular function of the proteins encoded by the genes remains enigmatic.

Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis.

The chaperone SecB has been implicated in de novo protein folding and translocation across the membrane, but it remains unclear which nascent polypeptides SecB binds, when during translation SecB acts, how SecB function is coordinated with other chaperones and targeting factors, and how polypeptide engagement contributes to protein biogenesis. Using selective ribosome profiling, we show that SecB binds many nascent cytoplasmic and translocated proteins generally late during translation and controlled by the chaperone trigger factor. Revealing an uncharted role in co-translational translocation, inner membrane proteins (IMPs) are the most prominent nascent SecB interactors.

Identification of Plant Protein-Metabolite Interactions by Limited Proteolysis-Coupled Mass Spectrometry (LiP-MS).

The interactions between metabolites and proteins constitute crucial events in cell signaling and metabolism. In recent years, large-scale proteomics techniques have emerged to identify and characterize protein-metabolite interactions. However, their implementation in plants is generally lagging behind, preventing a complete understanding of the regulatory mechanisms governing plant physiology.

To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in .

Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.

Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates.

N-terminal acetylation (Nt-acetylation) catalyzed by conserved N-terminal acetyltransferases or NATs embodies a modification with one of the highest stoichiometries reported for eukaryotic protein modifications to date. Comprising the catalytic N-alpha acetyltransferase (NAA) subunit NAA10 plus the ribosome anchoring regulatory subunit NAA15, NatA represents the major acetyltransferase complex with up to 50% of all mammalian proteins representing potential substrates. Largely in consequence of the essential nature of NatA and its high enzymatic activity, its experimentally confirmed mammalian substrate repertoire remained poorly charted.

N-Terminal Acetyltransferase Naa40p Whereabouts Put into N-Terminal Proteoform Perspective.

The evolutionary conserved N-alpha acetyltransferase Naa40p is among the most selective N-terminal acetyltransferases (NATs) identified to date. Here we identified a conserved N-terminally truncated Naa40p proteoform named Naa40p25 or short Naa40p (Naa40). Intriguingly, although upon ectopic expression in yeast, both Naa40p proteoforms were capable of restoring N-terminal acetylation of the characterized yeast histone H2A Naa40p substrate, the Naa40p histone H4 substrate remained N-terminally free in human haploid cells specifically deleted for canonical Naa40p27 or 237 amino acid long Naa40p (Naa40), but expressing Naa40.

Follicular fluid during individual oocyte maturation enhances cumulus expansion and improves embryo development and quality in a dose-specific manner.

We evaluated the effect of supplementation of different concentrations of bovine follicular fluid (FF) during in vitro maturation (IVM) on oocyte development and blastocyst quality in group and individual culture conditions. To do so, in vitro maturation medium (TCM-199 with 20 ng/mL epidermal growth factor and 50 μg/mL gentamycin) was supplemented with 0 (control), 1, 5, or 10% of FF. Follicular fluid was collected from slaughterhouse-derived ovaries, selecting follicles between 12 and 20 mm in diameter.

Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency.

[Figure: see text].