Biology subjects

Gallo, A.

Publications and source records attributed to Gallo, A..

10 recordsLinked to original sources

bioRxiv2026

A recently evolved TAF8 isoform arising from an Alu insertion increases TFIID assembly complexity in the human lineage

Despite its centrality in regulating RNA polymerase II transcription in all eukaryotes, the TFIID general transcription factor exhibits several layers of variability across different tissues and developmental stages, representing an underexplored hub of evolutionary innovation. Here, we describe a novel short isoform of TAF8 (TAF8s) - a TFIID scaffold subunit - which evolved from the use of an intronic polyadenylation site (iPAS) in the human lineage. Comparative genomics analyses show that the emergence of TAF8s expression in the human lineage coincides with minute DNA changes in the iPAS at the edge of a FLAM-C Alu element that inserted into intron 5 in the common ancestor of anthropoid primates (Simiiformes). The human-specific TAF8s isoform lacks nearly half of the canonical coding sequence, is widely expressed across human tissues, and constitutes a substantial fraction of the TAF8 transcript pool. TAF8s is translated into a truncated protein isoform that lacks the nuclear-localization signal and localises in the cytoplasm. TAF8s interacts with its histone-fold partner TAF10 and other core TFIID subunits, while entirely losing its interactions with TAF2, thus giving rise to alternative TFIID sub-complexes in human cells. Our study suggests that the TFIID complex underwent a recent diversification through a stepwise evolutionary acquisition of complexity in the TAF8 locus in the human lineage, leading to the expression of a novel truncated pan-isoform that might work as a modulator of TFIID assembly. We discuss the ramifications of our findings in TFIID complex diversification, its evolvability, and the genetics of TAF-related congenital disorders.

molecular biology↗

bioRxiv2025

The RNA-binding activity of SACSIN HEPN domain is connected to ARSACS

Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay (ARSACS) is a neurodegenerative disorder caused by mutations in the SACS gene, though the molecular function of its protein product, SACSIN, remains elusive. Therapeutic strategies for ARSACS are limited, mostly due to the exceptionally large size of SACSIN ([~]520 kDa), which precludes conventional gene therapy and standard molecular delivery methods. Over 200 pathogenic variants, including missense and nonsense mutations, have been identified. Regardless of variant type, patients uniformly exhibit cerebellar ataxia and spasticity. Among them, patients carrying missense mutations within the SACSIN higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain, suggesting that the alteration of the functional role of SACSIN HEPN domain could be linked to the manifestation of ARSACS symptoms. Here, we provide the first direct evidence that SACSIN HEPN domain binds RNA, corroborating the hypothesis that SACSIN functions as an RNA-binding protein. In silico predictions through the catRAPID algorithm as well as AlphaFold 3 revealed the propensity of SACSIN HEPN domain to specifically interact with RNAs. These interactions were validated both in vitro and in cell studies, confirming that SACSIN HEPN domain binds to RNA transcripts. Overall, our study unveils an unknown molecular function of SACSIN that, if altered, can contribute to the development of ARSACS disease. Therefore, paving the way for innovative therapeutic approaches for ARSACS patients.

molecular biology↗

bioRxiv2025

REGULATION OF HDL DYSFUNCTIONALITY BY PHOSPHATIDYLETHANOLAMINE LINKS POLY-UNSATURATED FATTY ACIDS WITH ATHEROSCLEROTIC CARDIOVASCULAR DISEASES

AimsLow plasma high-density lipoprotein (HDL)-cholesterol levels are associated with increased risk of atherosclerotic cardiovascular disease (ASCVD), potentially reflecting impaired antiatherogenic HDL functions. These latter are strongly influenced by the HDL phospholipidome, which is frequently altered in ASCVD patients. Several studies reported that plasma levels of phosphatidylethanolamine (PE) species, particularly PE (36:5), were positively associated with ASCVD, but the underlying mechanisms remain unclear. Plasma PE (36:5) exists as eicosapentaenoic (EPA)-PE and arachidonic acid (ARA)-PE, with the latter predominating in ASCVD. This study investigated whether the association of PE (36:5) with ASCVD might result from an impairment of the antiatherogenic functions of HDL. Methods and ResultsTotal PE and PE (36:5) content of large HDL isolated from 86 women with metabolic syndrome was positively associated with carotid intima-media thickness in multivariate regression analysis adjusted for traditional risk factors. In TgCETP x Ldlr-/- mice fed a high-cholesterol diet, the atherosclerotic plaque size was greater when reconstituted HDL (rHDL) containing ARA-PE was injected retro-orbitally, compared with injection of control rHDL containing only phosphatidylcholine (PC). In vitro, PE rHDL showed reduced cholesterol efflux capacity and impaired anti-inflammatory activity in THP-1 macrophages, together with diminished anti-oxidative activity against LDL oxidation compared to control rHDL. Strikingly, ARA-PE rHDL profoundly weakened of the HDL functions, while EPA-PE counteracted the ARA-PE-induced dysfunction and potentiated the functionality of rHDL. ConclusionThis study reveals a causal link between PE species, particularly ARA-PE, and HDL dysfunction, contributing to atherosclerosis. EPA-PE can restore HDL function, supporting the therapeutic potential of EPA reducing ASCVD risk.

cell biology↗

bioRxiv2024

Sustainable in situ extraction of microalgae-derived terpenoids using functionalized silica microparticles

Chlamydomonas reinhardtii is a green microalga that has been genetically engineered to produce heterologous terpenoid metabolites. While this green biochemical approach for producing high-value chemicals holds tremendous potential, the current in situ extraction methods, utilizing traditional solvents such as dodecane and perfluorinated chemicals, present separation challenges, unfavorable economics, and risk of cell toxicity. Here, we develop a low-cost solvent-free approach based on silanized silica particles to fill the technology gap. We determine the feasibility and specificity of three differently coated (C11, C16, C18) silica particles to extract nine terpenoid metabolites from C. reinhardtii cultures during cultivation. The results reveal that the extraction efficiencies of functionalized particles, particularly those coated with C18, demonstrated high potential as an alternative to traditional extraction methods. While the extraction efficiencies of coated microparticles are for most compounds lower than those observed for dodecane-based extractions, it holds higher potential for larger-scale cultivations where the use of dodecane is restricted due to its flammability and tendency to form emulsions. In addition, the present study provides insights into the optimization of particle-to-culture volume ratio, particle saturation, and the required number of product elution steps, and proves the feasibility of an upscaled extraction of the sesquiterpenoid patchoulol as a representative metabolite in 5 L hanging bag reactors. This study paves the way for a circular bioprocess where product capture with traditional solvent overlays is impractical due to the formation of emulsions, and at the same time allows for an easy product recovery (solid-liquid separation) and reuse of functionalized particles over numerous cycles.

bioengineering↗

bioRxiv2024

Superhydrophobic Sand Mulch and Date Palm Biochar Dramatically Boost Growth of Moringa oleifera in Sandy Soil: Insights into Evapotranspiration Budgeting and Metabolomic Profiling

In response to the challenge of nutrient-deficient sandy soils and water scarcity due to excessive evaporative water loss in arid regions, we developed and tested two complementary soil amendment technologies: Superhydrophobic sand (SHS) mulch and an enriched date palm biochar. In a greenhouse pot experiment, we investigated the stand-alone and synergistic effects of SHS mulch (10 mm-thickness) and biochar (2% w/w) on Moringa oleifera plants under normal (N, 100% field capacity) and reduced (R, 50% of N) irrigation scenarios. Under N and R, SHS mulch reduced evaporation by 71% and 64%, respectively; while SHS+biochar reduced evaporation by 61% and 47%, respectively, in comparison with the control (p < 0.05). Total transpiration significantly increased in SHS plants by 311% and 385% under N and R, respectively. Compared with the control, transpiration increased in biochar-amended plants by 103% and 110%; whereas, its combination with SHS increased transpiration by 288% and 301% under N and R, respectively (p < 0.05). Irrespective of the irrigation regimes, we found superior effects of SHS, biochar, and their combination on plant height (62-140%), trunk diameter (52-91%), leaf area index (57-145%), leaf chlorophyll content index (11-19%), stomatal conductance (51-175%), as well as shoot (390-1271%) and root (52-142%) biomass, in comparison with the controls. Metabolomics analysis showed significantly higher relative abundance of amino acids, sugars, fatty acids, and organic acids in the leaves of control plants relative to other treatments, as a response to water or nutrient stress induced by excessive water loss through evaporation. Next, we found a higher concentration of D-Mannose, D-Fructose, glucose, and malic acid in plants grown with SHS or biochar treatment under N and R irrigation, attributed to increased water/nutrient-use efficiency and carbon assimilation because of higher photosynthesis rates than in the control plants. Our results show that, our complementary technologies could address the challenge of water loss via evaporation from soil and maximize soil nutrient retention for improving plant growth in arid regions. This could underscore the success and sustainability of irrigated agriculture and greening efforts in arid lands.

plant biology↗

bioRxiv2023

An organic extract from ascidian Ciona robusta induces cytotoxic autophagy in human malignant cell lines

The last decades have seen an increase in the isolation and characterization of anticancer compounds derived from marine organisms, especially invertebrates, and their use in clinical trials. In this regard, ascidians, which are included in the subphylum Tunicata, represent successful examples with two drugs, Aplidine(C) and Yondelis(C), that reached the market as orphan drugs against several malignancies. Here, we report that an organic extract prepared from homogenized tissues of the Mediterranean ascidian Ciona robusta inhibited cell proliferation in HT-29, Hep G2, and U2 OS human cells with the former resulting as the most sensitive to the extract (EC50 = 250 {micro}g/ml). We demonstrated that the ascidian organic extract was not cytotoxic on HT-29 cells induced to differentiate with sodium butyrate, suggesting a preference for the mixture for the malignant phenotype. Finally, we reported that the cell death induced by the organic extract was mediated by the activation of a process of cytotoxic autophagy as a result of the increased expression of the LC3-II marker and the number of autophagic vacuoles, which almost doubled in treated HT-29 cells. In summary, although the detailed chemical composition of the Ciona robusta extract is still undetermined, our data suggest the presence in it of bioactive compounds possessing anticancer activity.

pharmacology and toxicology↗

bioRxiv2023

HSV-1 miRNAs are posttranscriptionaly edited in latently infected human ganglia

Viruses use miRNAs to enable efficient replication, control host defense mechanisms, and regulate latent infection. Herpes simplex virus 1 (HSV-1) expresses multiple miRNAs, whose functions are largely unknown. The evolutionary conservation of many HSV-1 miRNAs in the closely related HSV-2 suggests their functional importance. miRNAs, similar to other transcripts, can undergo various posttranscriptional modifications that may affect their biogenesis, stability and targeting. To investigate whether editing occurs in HSV-1 miRNAs, we sequenced samples from latently infected human ganglia. We show that one of the six HSV-1 miRNAs (miR-H2 to -H8) that define HSV-1 latency, miR-H2, exhibits A-to-I hyperediting within the miRNA seed sequence. We observed the same specific miR-H2 hyperediting phenomenon in miRNAs isolated from the ganglia of latently infected mice and, to a lesser extent, during productive infection in cultured cells. Curiously, we found no evidence of editing of the encoded HSV-2 homolog in latently infected mice or in cultured cells. The efficient loading of the edited miRNAs onto the RISC complex, indicates their ability to function as miRNAs. To investigate the potential of the edited miRNA to alter mRNA targeting, we predicted the host and viral targets for the modified miRNAs. Nucleotide substitution in the seed region significantly increased the number of potential host and viral targets. Most notably, ICP4, an essential viral protein, was predicted to be an additional target. Using transfection assays, we demonstrated that edited miRNAs have the potential to regulate ICP4 in addition to the previously identified target ICP0. Our study identifies a specific hyperedited HSV-1 mRNA, miR-H2, and highlights how the virus can use a single miRNA to target multiple transcripts during persistent, latent infection. ImportanceHerpes simplex virus 1 is an important human pathogen and intensively studied for many decades. Nevertheless, the molecular mechanisms regulating its establishment, maintenance, and reactivation from latency are poorly understood. Here, we show that HSV- 1 encoded miR-H2 is post-transcriptionally edited in latently infected human tissues. Hyperediting of viral miRNAs increases the targeting potential of these miRNAs and may play an important role in regulating latency. We show that the edited miR-H2 (miR-H2-e) can target ICP4, an essential viral protein. Interestingly, we found no evidence of hyperdating of its homolog, miR-H2, which is expressed by the closely related virus HSV-2. The discovery of posttranslational modifications of viral miRNA in the latency phase suggests that these processes may also be important for other non-coding viral RNA in the latency phase, including the intron LAT, which in turn may be crucial for understanding the biology of this virus.

microbiology↗

bioRxiv2022

Cadmium treatment induces endoplasmic reticulum stress and unfolded protein response in Arabidopsis thaliana

We report about the response of Arabidopsis thaliana to chronic and temporary Cd2+ stress, and the Cd2+ induced activation of ER stress and unfolded protein response (UPR). Cd2+-induced UPR proceeds mainly through the bZIP60 arm, which in turn activates relevant ER stress marker genes such as BiP3, CNX, PDI5 and ERdj3B in a concentration- (chronic stress) or time- (temporary stress) dependent manner. A more severe Cd-stress triggers programmed cell death (PCD) through the activation of the NAC089 transcription factor. Toxic effects of Cd2+ exposure are reduced in the Atbzip28/bzip60 double mutant in terms of primary root length and fresh shoot weight, likely due to reduced UPR and PCD activation. We also hypothesised that the enhanced Cd2+ resistance of the Atbzip28/bzip60 double mutant is due to an increase in brassinosteroids signaling, since the amount of the brassinosteroid insensitive1 receptor (BRI1) protein decreases under Cd2+ stress only in Wt plants. These data highlight the complexity of the UPR pathway, since the ER stress response is strictly related to the type of the treatment applied and the multifaceted connections of ER signaling. The reduced sensing of Cd2+ stress in plants with UPR defects can be used as a novel strategy for phytoremediation.

plant biology↗

bioRxiv2021

ADAR2-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair

The maintenance of genomic stability requires the coordination of multiple cellular tasks upon the appearance of DNA lesions. RNA editing, the post-transcriptional sequence alteration of RNA, has a profound effect on cell homeostasis, but its implication in the response to DNA damage was not previously explored. Here we show that, in response to DNA breaks, an overall change of the Adenosine-to-Inosine RNA editing is observed, a phenomenon we call the RNA Editing DAmage Response (REDAR). REDAR relies on the checkpoint kinase ATR and the recombination factor CtIP. Moreover, depletion of the RNA editing enzyme ADAR2 renders cells hypersensitive to genotoxic agents, increases genomic instability and hampers homologous recombination by impairing DNA resection. Such a role of ADAR2 in DNA repair goes beyond the recoding of specific transcripts, but depends on ADAR2 editing DNA:RNA hybrids to ease their dissolution. One sentence summaryDNA recombination requires RNA editing of DNA:RNA hybrids to ease their melting and facilitate DNA end resection

genetics↗

bioRxiv2019

The interaction between non-fusogenic Sec22b-Stx complexes and Extended-Synaptotagmins promotes neurite growth and ramification

Axons and dendrites are long and often ramified neurites that need particularly intense plasma membrane (PM) expansion during the development of the nervous system. Neurite growth depends on non-fusogenic Sec22b-Stx1 SNARE complexes at endoplasmic reticulum (ER)-PM contacts. Here we show that Sec22b interacts with the endoplasmic reticulum lipid transfer proteins Extended-Synaptotagmins (E-Syts) and this interaction depends on the Longin domain of Sec22b. Overexpression of E-Syts stabilizes Sec22b-Stx1 association, whereas silencing of E-Syts has the opposite effect. Overexpression of wild-type E-Syt2, but not mutants unable to transfer lipids or attach to the ER, increase the formation of axonal filopodia and ramification of neurites in developing neurons. This effect is inhibited by a clostridial neurotoxin cleaving Stx1, expression of Sec22b Longin domain and a Sec22b mutant with extended linker between SNARE and transmembrane domains. We conclude that Sec22b-Stx1 ER-PM contact sites contribute to PM expansion by interacting with lipid transfer proteins such as E-Syts.

cell biology↗