Biology subjects

Zanzoni, A.

Publications and source records attributed to Zanzoni, A..

11 recordsLinked to original sources

bioRxiv2026

Capturing domain-level detail of molecular interactions in the IMEx Consortium binding domain data set

The machinery of the cell depends on physical interactions, between proteins themselves, and between proteins and other biomolecules. The detailed characterisation of these interactions, including the identification of the precise sequence regions mediating binding events, is essential to understand both normal cell biology and disease mechanisms. Protein binding domains are specific regions of a protein sequence that mediate direct contact with a partner and represent a critical layer of functional annotation, bridging sequence, structure, and cellular function. Here we present the IMEx binding domain dataset, a large-scale, manually curated open-access set of molecular interactions assembled over more than two decades by the International Molecular Exchange (IMEx) Consortium. The dataset compiles experimentally derived binding region annotations from peer-reviewed literature, systematically linked to protein-protein interaction (PPI) records and mapped to standardised protein sequences in UniProtKB. We describe the curation model, data format, and content of the dataset, provide a descriptive and comparative analysis, and demonstrate the utility of the dataset as a gold standard for benchmarking interface prediction and variant effect annotation methods. Its integration with genomic variations further offers a route to elucidate the mechanistic basis of disease-associated mutations. The datasets are freely available through IntAct in the dedicated PSI-MI FeatureTAB format at https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/features/ and are updated and enhanced with every release.

bioinformatics↗

bioRxiv2026

BactMentha: a database of annotated bacteria-host protein interactions

Bacterial pathogens ensure their successful dissemination by employing specialized secretion systems to deliver a wide range of virulence proteins that interact with specific host proteins to modulate the response during infection. These interactions are often mediated by host-like elements, like short linear motifs, which can interfere with host interaction interfaces, enabling bacterial secreted proteins to compete and displace native partners of the targeted proteins. Several resources provide access to bacteria-host protein-protein interaction data. However, some are neither fully functional or up to date. Moreover, most of these databases lack virulence protein annotations, thus hampering hypothesis formulation based on protein interaction analyses. In this context, we have developed BactMentha, a unified resource that integrates bacterial-host protein-protein interactions for three organisms (human, mouse, and rat) with virulence protein annotations and bacterial strain clinical relevance information. BactMentha provides easy access to available experimentally identified binding regions of the interaction partners, complemented with putative interaction interfaces based on predicted structure complexes and on the detection of host-like elements on bacterial protein sequences interacting with human proteins. BactMentha currently contains 11 776 unique protein interactions between 2970 bacterial proteins, of which 684 have at least one virulence annotation, and 5088 host proteins. Experimentally identified binding regions are available for 532 bacteria-host interactions, most of which involve human proteins (440 interactions). Predicted interaction interfaces enabled a 3.7-fold increase in known and putative binding regions in the bacteria-human protein interaction data. By providing easy access to functionally annotated and clinically relevant protein interaction data, enriched with experimentally and predicted interaction interfaces, BactMentha can be instrumental in formulating novel hypotheses and speeding up wet lab research on the molecular mechanisms underlying pathogenic bacterial infections.

bioinformatics↗

bioRxiv2026

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

Bacteria employ molecular mimicry to hijack host cellular functions for their own benefit. Despite the wealth of data mapping human-bacteria interactions, a comprehensive view of how these networks are fine-tuned remains elusive. In particular, there have been no large-scale screenings measuring human-bacterial protein-protein binding affinities to explore their role in functional and pathological outcomes. Here, we report the largest quantitative interactome to date between the family of human PDZ domains and C-terminal PDZ-binding motifs (PBMs) in effectors from pathogenic and resident gut bacteria. We show that bacteria tailor effector sequences to bind PDZ domains with similar or higher binding affinities than human PBMs to hijack their associated cellular functions. For a subset of the dataset, we validate PDZ-PBM interactions with the corresponding full-length proteins and show that for pathogenic E. coli effector NleA, its C-terminal PBM is necessary for interactions with proteins involved in intracellular transport and membrane organization, probably impacting the host glycocalyx to favor infection. Finally, we show that motifs overlapping with effector PBMs target interaction modules other than PDZ domains, adding an additional layer of complexity to the host-microbe molecular dialogue.

systems biology↗

bioRxiv2026

Epromoter 3D interaction-associated regulation in T-acute Lymphoblastic Leukemia

Background: Promoters have been traditionally seen as contiguous gene-adjacent cis-regulatory elements. Yet, substantial studies corroborate that Epromoters (promoters with enhancer activity) engage in distal forms of gene regulation. Although in the three-dimensional (3D) space enhancer-promoter networks have been well studied, the contribution of the circuits of promoter-promoter (P-P) interactions is poorly understood. Furthermore, whether the regulatory aspects of P-P interactions in cancer may be controlled by physical 3D-mediated Epromoter interactions remains elusive. Results: We show that Epromoter-mediated 3D interactions regulate target genes and participate in cluster co-regulation, playing a critical role in T-cell acute Lymphoblastic Leukemia (T-ALL). To achieve this, we first leveraged survival CRISPR screenings in T-ALL model cells (Jurkat) to identify potential Epromoters. By integrating these findings with an H3K27ac HiChIP dataset from T-ALL cells, we characterized a set of Epromoters that establish 3D genome interactions with other promoters. We observed that promoters organize into dense, promoter-rich genomic clusters, and that among them, the clusters enriched with Epromoters actively regulate complex gene expression networks. To investigate gene coregulation, we integrated transcriptomic data from T-ALL patients and found that promoter-promoter (P-P) pairs exhibit positive correlation at multiple levels, and that several Jurkat Epromoter candidate clusters are significantly co-regulated in the patient cohort. To experimentally validate these candidates, we utilized CRISPRi to inhibit Epromoters, which revealed direct transcriptional regulation of multiple target genes within each hub. Finally, we performed cell competition assays to confirm that these Epromoters are vital for T-ALL cell survival. Conclusions: Our analysis provides support for the role of Epromoters in the regulation of 3D P-P interactions and co-regulation of promoter hubs, and how these interactions play a critical part in T-ALL cell survival.

cancer biology↗

bioRxiv2024

InteractORF, predictions of human sORF functions from an interactome study

Short open reading frames (sORFs) are widespread yet often poorly annotated, and an increasing number are known to encode functional sORF-encoded peptides (sPEPs, or microproteins). Here, we use a system approach to determine the functions of sPEPs in three tissues: monocytes, skeletal muscle and brain. We first predicted interactions between sPEPs and canonical proteins and characterized their interaction interfaces. sPEPs preferentially target specific canonical partners rather than interacting promiscuously, and two functional groups emerge from their interaction features. A small subset (~2%) exhibits canonical protein-like features, with structured domains interacting with diverse proteins involved in tissue-specific functions. In contrast, most sPEPs contain short linear motifs with extensive phosphorylation potential, suggesting they may be involved in signaling. We then constructed the first sPEP-containing interactome networks and infer sPEP functions from network topology. Most sPEPs appear to act as regulatory elements modulating diverse cellular processes rather than acting directly as functional components. Knowledge-based validations using characterized sPEPs, show that our framework can capture context-specific functions beyond current annotations. Together with their limited evolutionary constraint, the pervasive regulatory roles of sPEPs suggest that they constitute a reservoir of functional novelty and an evolutionarily flexible layer of cellular regulation.

bioinformatics↗

bioRxiv2023

Modulation of human kinase activity through direct interaction with SARS-CoV-2 proteins

The dysregulation of cellular signaling upon SARS-CoV-2 infection is mediated via direct protein interactions, with the human protein kinases constituting the major impact nodes in the signaling networks. Here, we employed a targeted yeast two-hybrid matrix approach to identify direct SARS-CoV-2 protein interactions with an extensive set of human kinases. We discovered 51 interactions involving 14 SARS-CoV-2 proteins and 29 human kinases, including many of the CAMK and CMGC kinase family members, as well as non-receptor tyrosine kinases. By integrating the interactions identified in our screen with transcriptomics and phospho-proteomics data, we revealed connections between SARS-CoV-2 protein interactions, kinase activity changes, and the cellular phospho-response to infection and identified altered activity patterns in infected cells for AURKB, CDK2, CDK4, CDK7, ABL2, PIM2, PLK1, NEK2, TRIB3, RIPK2, MAPK13, and MAPK14. Finally, we demonstrated direct inhibition of the FER human tyrosine kinase by the SARS-CoV-2 auxiliary protein ORF6, hinting at pressures underlying ORF6 changes observed in recent SARS-CoV-2 strains. Our study expands the SARS-CoV-2 - host interaction knowledge, illuminating the critical role of dysregulated kinase signaling during SARS-CoV-2 infection.

biochemistry↗

bioRxiv2023

A gut meta-interactome map reveals modulation of human immunity by microbiome effectors

The molecular mechanisms by which the gut microbiome influences human health remain largely unknown. Pseudomonadota is the third most abundant phylum in normal gut microbiomes. Several pathogens in this phylum can inject so-called virulence effector proteins into host cells. We report the identification of intact type 3 secretion systems (T3SS) in 5 - 20% of commensal Pseudomonadota in normal human gut microbiomes. To understand their functions, we experimentally generated a high-quality protein-protein meta-interactome map consisting of 1,263 interactions between 289 bacterial effectors and 430 human proteins. Effector targets are enriched for metabolic and immune functions and for genetic variation of microbiome-influenced traits including autoimmune diseases. We demonstrate that effectors modulate NF-{kappa}B signaling, cytokine secretion, and adhesion molecule expression. Finally, effectors are enriched in metagenomes of Crohns disease, but not ulcerative colitis patients pointing toward complex contributions to the etiology of inflammatory bowel diseases. Our results suggest that effector-host protein interactions are an important regulatory layer by which the microbiome impacts human health.

microbiology↗

bioRxiv2022

mimicINT: a workflow for microbe-host protein interaction inference

BackgroundThe increasing incidence of emerging infectious diseases is posing serious global threats. Therefore, there is a clear need for developing computational methods that can assist and speed up experimental research to better characterize the molecular mechanisms of microbial infections. MethodsIn this context, we developed mimicINT, an open-source computational workflow for large-scale protein-protein interaction inference between microbe and human by detecting putative molecular mimicry elements mediating the interaction with host proteins: short linear motifs (SLiMs) and host-like globular domains. mimicINT exploits these putative elements to infer the interaction with human proteins by using known templates of domain-domain and SLiM-domain interaction templates. mimicINT also provides (i) robust Monte-Carlo simulations to assess the statistical significance of SLiM detection which suffers from false positives, and (ii) an interaction specificity filter to account for differences between motif-binding domains of the same family. We have also made mimicINT available via a web server. ResultsIn two use cases, mimicINT can identify potential interfaces in experimentally detected interaction between pathogenic Escherichia coli type-3 secreted effectors and human proteins and infer biologically relevant interactions between Marburg virus and human proteins. ConclusionsThe mimicINT workflow can be instrumental to better understand the molecular details of microbe-host interactions.

bioinformatics↗

bioRxiv2021

A pathogen-encoded signaling receptor mediating host-like interactions through intrinsic disorder

The translocated intimin receptor (Tir) is a central effector of Attaching and Effacing (A/E) pathogens responsible for worldwide foodborne disease cases. Tir acts as a cell-surface receptor in host cells, rewiring intracellular processes to assist infection by targeting multiple host proteins. We sought to understand the basis for Tir binding diversity in signaling. Here, we establish that Tir is a disordered protein with host-like binding motifs. A trait we find prevalent in several other effectors secreted by A/E bacteria. We disclose that Tir has a disordered C-terminal intracellular tail (C-Tir) with non-random structural preferences at phosphorylation sites, including host-like tyrosine-based motifs, with versatile lipid- and SH2 domain binding capability pre-phosphorylation. We show that multi-site tyrosine phosphorylation enables C-Tir to engage SH2 domains in a multivalent manner, consistent with Tirs scaffold/hub role for host proteins. Last, we uncover Tirs ability to dimerizes via its partially disordered N-terminal intracellular domain. Collectively, our findings provide an updated picture of Tirs intracellular side, highlighting its ability to mimic host disordered membrane receptors versatility as a molecular strategy for host evasion. SummaryTir is a cell-surface receptor secreted by life-threatening pathogens. Upon delivery into host cells, Tir inserts the host plasma membrane providing a means for these extracellular pathogens to control host intracellular processes. To prevent pathogens from relying on Tir, it is essential to understand its intracellular mechanics. This paper provides a coherent picture of the intracellular side of Tir, highlighting its ability to copycat the interactions of disordered intracellular domains of host immune receptors. This copycatting allows the bacterial pathogens to modulate critical host processes, allowing infection to spread further without triggering the immune system response. This work proposes that other bacterial secreted pathogenic proteins exploit intrinsic disorder to hijack human cells, suggesting a widespread host subversion mechanism.

biophysics↗

bioRxiv2019

The role of 3’UTR-protein complexes in the regulation of protein multifunctionality and subcellular localization

Multifunctional proteins often perform their different functions when localized in different subcellular compartments. However, the mechanisms leading to their localization are largely unknown. Recently, 3UTRs were found to regulate the cellular localization of newly synthesized proteins through the co-translational formation of 3UTR-protein complexes. Here, we investigate the formation of 3UTR-protein complexes involving multifunctional proteins by exploiting large-scale protein-protein and protein-RNA interaction networks. Focusing on 238 human extreme multifunctional (EMF) proteins, we predicted 1411 3UTR-protein complexes involving 128 EMF proteins and evaluated their role in regulating protein cellular localization and multifunctionality. Notably, we find that EMF proteins lacking localization addressing signals, yet present at both the nucleus and cell surface, often form 3UTR-protein complexes. In addition, they provide EMF proteins with the diversity of interaction partners necessary to their multifunctionality. Archetypal moonlighting proteins are also predicted to form 3UTR-protein complexes thereby reinforcing our findings. Finally, our results indicate that the formation of 3UTR-protein complex may be a common phenomenon in human cells, affecting up to 20% of the proteins in the human interactome.

systems biology↗

bioRxiv2016

Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence factors

F. nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood.\n\nWe devised a computational strategy to identify putative secreted F. nucleatum proteins (FusoSecretome) and to infer their interactions with human proteins based on the presence of host molecular mimicry elements. FusoSecretome proteins share similar features with known bacterial virulence factors thereby highlighting their pathogenic potential. We show that they interact with human proteins that participate in infection-related cellular processes and localize in established cellular districts of the host-pathogen interface. Our network-based analysis identified 31 functional modules in the human interactome preferentially targeted by 138 FusoSecretome proteins, among which we selected 26 as main candidate virulence proteins, representing both putative and known virulence proteins. Finally, 6 of the preferentially targeted functional modules are implicated in the onset and progression of inflammatory bowel diseases and colorectal cancer.\n\nOverall, our computational analysis identified candidate virulence proteins potentially involved in the F. nucleatum - human cross-talk in the context of gastrointestinal diseases.

bioinformatics↗