Biology subjects

Fortunato, S.

Publications and source records attributed to Fortunato, S..

3 recordsLinked to original sources

bioRxiv2026

Chloroplast ABC peptide transporters TAP1, NAP8, and ATH12 are essential for heat-induced peptide export and play a key role in thermotolerance in Arabidopsis thaliana.

ATP-binding cassette (ABC) transporters mediate substrate translocation across membranes by using energy from ATP hydrolysis. While ABC peptide exporters have been characterized in the mitochondria of metazoans and yeast, corresponding chloroplast peptide transport systems in plants remain uncharacterized. Using in silico and experimental approaches, we identify three previously uncharacterized Arabidopsis thaliana ABCB half-transporters - TAP1, NAP8, and ATH12 - that localize to the chloroplast inner envelope and form homodimers. These proteins are phylogenetically related to known peptide exporters, and functional complementation in Saccharomyces cerevisiae demonstrates that each plant transporter can rescue the heat sensitivity of a{Delta} mdl1 mutant, indicating conserved peptide export activity. In chloroplast peptide efflux assays, peptide export upon heat stress was strongly reduced only in the tap1 nap8 ath12 triple mutant, but not in single or double mutants, indicating functional redundancy. Furthermore, mass spectrometry of chloroplast supernatants revealed an abundance of thylakoid-derived hydrophilic peptides in the wild type, predicted to have antioxidant activity. Under heat stress, the triple mutant displayed increased sensitivity, characterized by reduced biomass, chlorophyll and carotenoid content, and compromised photosynthetic efficiency. Comprehensive analyses revealed altered redox homeostasis in the triple mutant, including modified antioxidant dynamics, differential antioxidant enzyme activities, and distinct gene expression profiles compared with the wild type. Our findings demonstrate that TAP1, NAP8, and ATH12 constitute a chloroplast peptide export system required for efficient peptide release under heat stress, with a role in Arabidopsis thermotolerance. These results provide new insights into organellar peptide transport and its integration with stress mitigation mechanisms in plants.

plant biology↗

bioRxiv2024

Cell Type Differentiation Using Network Clustering Algorithms

Single cell RNA-seq (scRNA-seq) technologies provide unprecedented resolution representing transcriptomics at the level of single cell. One of the biggest challenges in scRNA-seq data analysis is the cell type annotation, which is usually inferred by cell separation approaches. In-silico algorithms that accurately identify individual cell types in ongoing single-cell sequencing studies are crucial for unlocking cellular heterogeneity and understanding the biological basis of diseases. In this study, we focus on robustly identifying cell types in single-cell RNA sequencing data; we conduct a comparative analysis using methods established in biology, like Seurat, Leiden, and WGCNA, as well as Infomap, statistical inference via Stochastic Block Models (SBM), and single-cell Graph Neural Networks (scGNN). We also analyze preprocessing pipelines to identify and optimize key components in the process. Leveraging two independent datasets, PBMC and ROSMAP, we employ clustering algorithms on cell-cell networks derived from gene expression data. Our findings reveal that while clusters detected by WGCNA exhibit limited correspondence with cell types, those identified by multiresolution Infomap and Leiden, and SBM show a closer alignment, with Infomap standing out as a particularly effective approach. Infomap notably offers valuable insights for the precise characterization of cellular landscapes related to neurodegenration and immunology in scRNA-seq.

bioinformatics↗

bioRxiv2024

A system biology-oriented investigation of Arabidopsis proteomes altered in chloroplast biogenesis and retrograde signaling reveals adaptive responses at whole cell level.

Communication across different plant cell compartments relies on an intricate network of molecular interactions, required for the orchestration of organelle development and adaptation to the environment. In this scenario, the Pentatricopeptide Repeat (PPR) Protein GENOMES UNCOUPLED1 (GUN1) plays a key role in transferring information from both developing and mature chloroplasts to the nucleus with the aim to coordinate gene expression between the two genomes. However, its role and the related signaling molecules are still under debate. To help shed light on this matter, we attempted the holistic description of Arabidopsis thaliana proteome upon perturbation of chloroplast biogenesis by lincomycin (Lin), in a genetic context devoid of GUN1-dependent plastid-to-nucleus signaling pathway. Furthermore, the topological analysis of protein-protein interaction (PPI) and protein co-expression networks allowed the identification of protein hubs/bottlenecks characterizing genotypes and conditions, such as proteases, HSPs/Chaperones and redox proteins. Taken together, our findings indicate that GUN1 is required to orchestrate a plastid-located response to plastid protein synthesis inhibition while, in its absence, the reorganization of the activities associated with extra-plastid compartments, such as cytosol, vacuole and mitochondria, prevails. From this landscape, we documented a new role of the Oxygen Evolving Complex subunit PsbO, which appears to be an unconventional photosynthetic protein, as it accumulates in non-photosynthetic plastids and plays a central role in promoting chloroplast breakdown when plastid functions are altered.

systems biology↗