Biology subjects

Souza, D. P.

Publications and source records attributed to Souza, D. P..

7 recordsLinked to original sources

bioRxiv2026

To Kill or not to Kill: A Conserved trans-intoxication protection factor Blocks X-T4SS-Mediated Fratricide through Interaction with VirB5

Bacteria can outcompete rivals by using specialized secretion systems to deliver toxic effectors into prey cells. How these systems distinguish prey from kin remains a fundamental unanswered question. In many Xanthomonadales (Lysobacterales) species, the antibacterial type IV secretion system (X-T4SS) mediates cell-cell contact-dependent killing of competing bacteria. Here, we identified XAC2611, a chromosomally encoded, cysteine-rich DUF4189 protein, as essential for preventing X-T4SS-mediated fratricide among sibling cells in Xanthomonas citri. XAC2611 homologs are found within or proximal to the genomic loci coding almost all identified X-T4SS. Live-cell microscopy and biochemical data reveal that XAC2611 is abundantly produced and widely distributed throughout the periplasm of recipient cells and is required to prevent X. citri cells from intoxicating each other in a contact-dependent manner. We also show that XAC2611 homologs from Stenotrophomonas maltophilia protect X. citri cells from attack by S. maltophilia. Protein-protein interaction assays show that XAC2611 interacts directly with the VirB5 subunit. Since VirB5 is predicted to be localized at the tip of the X-T4SS pilus, its interaction with XAC2611 in a neighboring sister cell could block X-T4SS-mediated effector delivery. We therefore name this family of proteins trans-intoxication protection factors (Tpfs).

microbiology↗

bioRxiv2026

A conserved archaeal ribosome-associated factor linking bacterial hibernation and eukaryotic energy sensing

Ribosome hibernation helps cells survive stress by reversibly silencing translation and limiting degradation of ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation remains poorly understood. Using cryoEM to analyze lysates from a model archaeon, we identified AHA (AMPK{gamma}-HPF from Archaea), a broadly conserved ribosome-associated protein factor composed of two distinct modules. Structural analyses showed that AHAs C-terminal domain binds the small subunit, while its N-terminal region recognizes the large subunit, occluding the mRNA channel and the A- and P-tRNA binding sites and thereby enforcing translational silencing. Consistent with this proposed function, {Delta}AHA cells displayed reduced viability, depletion of ribosomal proteins during stationary phase, and impaired recovery upon return to growth. Phylogenetic analyses revealed that AHAs C-terminal domain shares homology with the bacterial Hibernation Promoting Factor (HPF), indicating an origin in the last universal common ancestor (LUCA) and thereby identifying HPF as a universal hibernation module. Strikingly, we observed two AMP molecues bound to AHAs N-terminal CBS-tetrad, which we found was structurally and evolutionary related to the eukaryotic energy sensor AMPK{gamma}, thus linking energy sensing between archaea and eukaryotes. Together, these findings uncover a widespread archaeal ribosome hibernation factor and establish a direct evolutionary link between prokaryotic translational silencing and eukaryotic energy sensing.

biochemistry↗

bioRxiv2025

Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism

The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex conserved in all domains of life. However, whether membrane fission was an ancestral ESCRT-III activity predating eukaryogenesis remains unknown. Here we show that ESCRT-IIIA from Asgard Heimdallarchaeota, the closest archaeal relatives of eukaryotes, performs membrane fission through an N-terminal amphipathic helix, which we term Hofund. In eukaryotes, Hofund is fragmented across ESCRT-IIIA paralogs, and disrupting these regions causes severe fission defect in yeast. Remarkably, Heimdallarchaeota Hofund restores fission when fused to defective eukaryotic paralogs. These findings suggest that ESCRT-III-mediated fission arose before eukaryogenesis and later diversified to support the regulatory complexity of eukaryotic compartmentalization.

cell biology↗

bioRxiv2024

Evolutionarily conserved principles of ESCRT-III-mediated membrane remodelling revealed by a two-subunit Asgard archaeal system

ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis we demonstrate that the two ESCRT-III proteins present in our closest archaeal relatives are evolutionarily related to B-type and A-type eukaryotic paralogues, which initiate and execute membrane remodelling, respectively. This deep homology is reflected in ESCRT-III structure and function as demonstrated by the fact that ESCRT-IIIB assembles into parallel arrays on planar membranes to initiate membrane deformation, and is required to recruit ESCRT-IIIA to generate composite polymers. ESCRT-IIIA homopolymers can then remodel membranes into tubes, as a likely prelude to scission. Taken together, this analysis reveals a set of conserved principles governing ESCRT-III-dependent membrane remodelling that first emerged with the evolution of a two-component ESCRT-III system in the Asgard archaea, and which continue to underlie complex multi-component, ESCRT-III-dependent membrane remodelling in eukaryotes.

evolutionary biology↗

bioRxiv2023

The protective function of an immunity protein against the cis-toxic effects of a Xanthomonas Type IV Secretion System Effector

Many bacterial species use specialized secretion systems to translocate proteinaceous toxic effectors into target bacterial cells. In most cases, effectors are encoded in bicistronic operons with their cognate immunity proteins. The current model is that immunity proteins could, in principle, provide protection in two different ways: i) by avoiding self-intoxication (suicide or cis-intoxication) or ii) by inhibiting intoxication due to "friendly-fire" translocation from neighboring sister cells (fratricide or trans-intoxication). Here, we set out to distinguish between these two protection mechanisms in the case of the bactericidal Xanthomonas citri Type IV Secretion System (X-T4SS), where killing is due to the action of a cocktail of secreted effectors (X-Tfes) that are inhibited by their cognate immunity proteins (X-Tfis). We use a set of X. citri mutants lacking multiple X-Tfe/X-Tfi pairs to show that X-Tfis are not absolutely required to protect against trans-intoxication. Our investigation then focused on the in vivo function of the lysozyme-like effector X-TfeXAC2609 and its cognate immunity protein X-TfiXAC2610. We observe the accumulation of damage in the X. citri cell envelope and inhibition of biofilm formation due to the action of X-TfeXAC2609 in the absence of X-TfiXAC2610. We show that X-TfeXAC2609 toxicity is independent of an active X-T4SS and that X-TfiXAC2610 protects the cell colony against X-TfeXAC2609-induced cis-intoxication via autolysis. In vitro assays employing X-TfiXAC2610 mutants were used to test and validate an AlphaFold2-derived model of the X-TfeXAC2609-X-TfiXAC2610 complex which presents topological similarities with the distantly related Tse1/Tsi1 complex from P. aeruginosa and the the i-type lysozyme from Meretrix lusoria (MI-iLys) in complex with PliI-Ah from Aeromonas hydrophila. While immunity proteins in other systems have been shown to protect against attacks by sister cells (trans-intoxication), this is the first description of an antibacterial secretion system in which the immunity proteins are dedicated to protecting cells against cis-intoxication.

biochemistry↗

bioRxiv2020

Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodelling superfamily

Membrane remodelling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, CdvB in TACK archaea and ESCRT-III in eukaryotes. Here, we show that these protein families are homologous and share a common evolutionary origin. Using cryo-electron microscopy we present structures for Vipp1 rings over a range of symmetries. Each ring is built from rungs that stack and spontaneously self-organise to form domes. Rungs are assembled from a polymer that is strikingly similar in structure to ESCRT-III. A tilt between rungs generates the dome-shaped curvature with constricted open ends and an inner membrane-binding lumen. Overall, our results reveal conserved mechanistic principles that underlie Vipp1, PspA and ESCRT-III dependent membrane remodelling across all domains of life. One sentence summaryEvolutionary and structural analyses of Vipp1/IM30 rings reveal ESCRT-III-like polymers that remodel membranes in bacteria.

microbiology↗

bioRxiv2018

Metanalysis of genome-wide association studies for panic disorder suggest pathways and mechanisms of pathogenesis

Panic disorder (PD) is characterized by abrupt surges of intense fear and distress. There is evidence for a genetic component in this disorder. We ran a meta-analysis of genome-wide association studies of patients with PD, and found 25 single-nucleotide polymorphisms that were associated with the disorder. Causal gene prediction based on these polymorphisms uncovered 20 hits. Exploratory analyses suggested that these genes formed interactor networks, which was enriched in signaling pathways associated with immune and inflammatory responses, as well as growth factors and other developmental mediators. A subset of genes is enriched in limbic regions of the human brain and in microglia and myelinating oligodendrocytes of mice. While these genes were not associated with relevant neurobehavioral phenotypes in mutant mice, expression levels of several causal genes in the amygdala, prefrontal cortex, hippocampus, hypothalamus, and adrenal gland of recombinant mouse strains was associated with endophenotypes of fear conditioning. Drug repositioning prediction was unsuccessful, but this does not discard these genes and pathways as targets for investigational drugs. In general, ASB3, EIF2S2, RASGRF2, and TRMT2B (and its coded proteins) emerged as interesting targets for mechanistic research on PD. These exploratory findings point towards hypotheses of pathogenesis and neuropharmacology that need to be further investigated.

neuroscience↗