Biology subjects

Fucile, G.

Publications and source records attributed to Fucile, G..

5 recordsLinked to original sources

bioRxiv2026

Mass spectrometric identification of a PSI-LHCI-cytochrome b6f complex in both Arabidopsis stn7 and pph1

Native PAGE separation of digitonin-solubilized thylakoid stroma lamellae resolves PSI and cytochrome b6f into separate bands. Mass spectrometric analysis of the 1D native gel bands showed that the bands are baskets of co-migrating complexes along the molecular size axis. Hierarchical clustering confirmed the separation of dimeric cytochrome b6f from PSI in 1D LN-PAGE. Interval-zone free-flow electrophoresis separated the same extracts by charge in a flowing buffer film, and the continuous fractionation indicated co-migration of complexes without the in-gel structural hindrances. A second-dimension LN-PAGE separated the complexes co-migrating in iZE into complexes with defined molecular size, allowing in-gel mass spectrometry identification in the gel bands. Both genotypes showed a 720 kDa fluorescent band in which cytochrome f (PetA) and cytochrome b6 (PetB) join the PSI-LHCI node (stn7, d = 0.50; pph1, d = 0.34). Lhcb1 and Lhcb2 are absent from the 720 kDa node. The 753 kDa band is specific to pph1 (d = 0.38). Phosphorylated LHCII1,2 joins PSI-LHCI there, and PetB is detected in every slice of that band without becoming a leaf of the tree.

plant biology↗

bioRxiv2025

Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE

Genome organization into higher-order active and inactive compartments exhibits cell-type specific patterns, which are widely implicated in the regulation of transcriptional activity. During embryogenesis, epigenetic regulation controls cell type specification along cellular lineages with similar transcriptional identities through the coordinated action of chromatin states. However, prevalent single-molecule variability in higher-order chromosome conformation and a lack of precise cell lineage information have previously limited our understanding of the relationship between conformation and transcriptional activity in vivo. Specifically, how the conformation-transcription relationship is inherited along cellular lineages through cell divisions is poorly understood. Here, we developed a novel algorithm for cell lineage identification (C. elegans Sinkhorn-based Cell ALignmEnt, CeSCALE) combined with single cell genomics to reveal that local conformation-transcription fingerprints are associated with, and inherited along the stereotyped cellular lineages of C. elegans embryos. Inspired by Optimal Transport theory, CeSCALE provides a fully automated framework for quantifying lineage-resolved individual cell phenotypes in situ, across a wide developmental window. Combining CeSCALE with single-molecule chromosome tracing uncovered higher-order interchromosomal block associations, which surprisingly coalesce transcriptionally diverse domains and are independent of lineage identity. Instead, by integrating lineage-resolved chromosome conformations with single-cell transcriptomics, we find that local conformation-transcription spatial relationships ( fingerprints), containing both hubs and islands of transcriptional activity, are robustly inherited along lineages. Finally, we find that the canalization of these fingerprints represent the rewiring of chromatin states at key developmental stages. Our results suggest that local chromatin environments, but not large-scale compartments, coordinate the dramatically changing transcriptome during embryogenesis.

developmental biology↗

bioRxiv2024

Bacterial RNA promotes proteostasis through inter-tissuecommunication in C. elegans

Life expectancy has been increasing over the last decades, which is not matched by an increase in healthspan. Besides genetic composition, environmental and nutritional factors influence both health- and lifespan. Diet is thought to be a major factor for healthy ageing. Here, we show that dietary RNA species extend healthspan in C. elegans. Inherent bacterial-derived double stranded RNA reduces protein aggregation in a C. elegans muscle proteostasis model. This beneficial effect depends on low levels of systemic selective autophagy, the RNAi machinery in the germline, even when the RNA is delivered through ingestion in the intestine and the integrity of muscle cells. Our data suggest a requirement of inter-organ communication between the intestine, the germline and muscles. Our results demonstrate that bacterial-derived RNAs elicit a systemic response in C. elegans, which protects the animal from protein aggregation during ageing. We provide evidence that low stress levels are beneficial for healthspan. One-Sentence SummaryBacteria-derived dietary cues and inter-tissue communication promote proteostasis and fitness in C. elegans

cell biology↗

bioRxiv2022

High-resolution crystal structure of a metabolic switch protein in a complex with monomeric c-di-GMP reveals a potential mechanism for c-di-GMP dimerization

Bacterial second messengers c-di-GMP and (p)ppGpp have broad functional repertoires ranging from growth and cell cycle control to the regulation of biofilm formation and virulence. The recent identification of SmbA, an effector protein from Caulobacter crescentus that is jointly targeted by both signaling molecules, has opened up studies on how these global bacterial networks interact. C-di-GMP and (p)ppGpp compete for the same SmbA binding site, with a dimer of the former ligand inducing a conformational change of loop 7 leading to downstream signaling. Here, we report a crystal structure of a partial loop 7 deletion mutant, SmbA{Delta}loop in complex with c-di-GMP determined at 1.4 [A] resolution. SmbA{Delta}loop binds monomeric c-di-GMP strengthening the view that loop 7 is required for c-di-GMP dimerization. In the crystal, SmbA{Delta}loop forms a 2-fold symmetric dimer via isologous interactions with the two symmetric halves of c-di-GMP. Structural comparisons of SmbA{Delta}loop with wild-type SmbA in complex with dimeric c-di-GMP or ppGpp support the idea that loop 7 is critical for SmbA function by interacting with downstream partners. These results underscore the flexibility of c-di-GMP in binding to the symmetric interface between protein subunits. It is envisaged that such isologous interactions of c-di-GMP will be observed in hitherto unrecognized targets.

biochemistry↗

bioRxiv2018

Asymmetric Distribution of Glucose Transporter mRNA Provides Growth Advantage

Asymmetric localization of mRNA is important for cell fate decisions in eukaryotes and provides the means for localized protein synthesis in a variety of cell types. Here we show that hexose transporter mRNAs are retained in the mother cell of S. cerevisiae until metaphase-anaphase transition (MAT) and then are released into the bud. The retained mRNA was translationally inactive but bound to ribosomes before MAT. Importantly, when cells were shifted from starvation to glucose-rich conditions, HXT2 mRNA, but none of the other HXT mRNAs, was enriched in the bud after MAT. This enrichment was dependent on the Ras/cAMP/PKA pathway, the APC ortholog Kar9 and nuclear segregation into the bud. Competition experiments between strains that only expressed one hexose transporter at a time revealed that HXT2 only cells grow faster than their counterparts when released from starvation. Therefore, asymmetric distribution of HXT2 mRNA provides a growth advantage for young daughters, who are better prepared for nutritional changes in the environment. Our data provide evidence that asymmetric mRNA localization is an important factor in determining cellular fitness.

cell biology↗