Biology subjects

Falciatore, A.

Publications and source records attributed to Falciatore, A..

9 recordsLinked to original sources

bioRxiv2025

A photoprotection dial maps holistic light-stress response in diatoms

Cellular responses to light stress operate on two timescales: short-term responses, driven by dynamic photosynthetic mechanisms such as non-photochemical quenching (NPQ), and long-term responses, characterized by various physiological and metabolic shifts driven by changes in gene expression. Understanding the coordination within and between these layers represents a major challenge in photosynthesis research. We achieved this in the diatom Phaeodactylum tricornutum using an adjustable "photoprotection dial" across 10 mutant strains expressing different constitutive levels of the Lhcx1 protein, which determine their latent NPQ capacity. Crucially, a near-identical initial state is preserved among strains, which allows a precise mapping of the causal chain of events initiated by NPQ induction under high light. This unlocks exceptional leverage to examine holistic interactions between functional photosynthesis and gene expression within their natural regulatory architecture. We observe that increasing NPQ maintains the PSII primary acceptor QA in a more oxidized state with little effect on linear electron flow. This oxidation limits PSII photodamage and promotes cyclic electron flow around PSI, which in turn is consistent with enhanced ATP production supporting PSII repair. Moreover, transcriptomic analysis across high-light exposure time suggests that the expression of nearly half of the genome is modulated via NPQ-driven effects. Gene expression profile clustering reveals distinct and coherent transcriptomic regulatory networks. The short-term response is characterized by a strong downregulation of light-harvesting-related genes -- independently of NPQ -- and an upregulation of oxidative stress response genes that scales inversely with NPQ magnitude. In the long term, most of the transcriptome is deeply impacted by high-light stress in a widely NPQ-dependent manner, highlighting the critical role of this process in shaping photophysiology, which in turn influences gene expression. By engineering a native functional feedback loop into an experimental dial, our approach establishes a generalizable framework for studying the complex interplay between physiology and system-wide biological regulation.

plant biology↗

bioRxiv2025

The first photosynthetic mutant in diatoms targets the subunit γ of plastidial ATP synthase and reveals a key role of thylakoid electrochemical proton gradient in photosynthesis regulation and heterotrophic metabolism.

Diatoms are major phytoplanktonic algae with secondary endosymbiotic plastids that differ in cellular and regulatory traits from those of the green lineage. Here we exploited the heterotrophic growth ability of Cyclotella cryptica to create the first diatom photosynthetic mutant by CRISPR-Cas inactivation of the nucleus-encoded ATP synthase subunit {gamma}. These mutants showed impaired phototrophic capacity and altered thylakoids morphology. In absence of {gamma}-ATP, protons that accumulate in the thylakoid lumen slow down the cytochrome b6f complex, thus keeping the electron carriers downhill oxidized. These results, reversible when the proton gradient is suppressed, demonstrate the existence of a photosynthetic control in diatoms. At variance with the wild type, {gamma} ATP synthase mutants cannot grow heterotrophically in darkness nor in the light when photosystem II is inhibited. This requirement of heterotrophic growth on photosynthetic electron transfer or on the presence of plastidial ATP synthase suggests that the proton motive force (pmf) is a central integrator of the metabolic interaction between photosynthesis and heterotrophy. Our results establish C. crytica as a robust model for analysis of photosynthetic function, regulation and metabolic integration in organisms with secondary plastids. TeaserMutagenesis in the facultative autotroph diatom Cyclotella cryptica enables exploration of essential plastid functions in diatoms

plant biology↗

bioRxiv2024

Circadian regulation of key physiological processes by the RITMO1 clock protein in the marine diatom Phaeodactylum tricornutum

O_LIPhasing biological and physiological processes to periodic light-dark cycles is crucial for the life of most organisms. Marine diatoms, as many phytoplanktonic species, exhibit biological rhythms, yet their molecular timekeepers remain largely uncharacterized. Recently, the bHLH-PAS protein RITMO1 has been proposed to act as a regulator of circadian rhythms. C_LIO_LIIn this study, we first determined the physiological conditions to monitor circadian clock activity and its perturbation in the diatom model species Phaeodactylum tricornutum by using cell fluorescence as a circadian output. Employing ectopic overexpression, targeted gene mutagenesis, and functional complementation, we then investigated the role of RITMO1 in various circadian processes. C_LIO_LIOur findings reveal that RITMO1 significantly influences the P. tricornutum circadian rhythms not only of cellular fluorescence, but also of photosynthesis and of the expression of clock-controlled genes, including transcription factors and putative clock input/output components. RITMO1 effects on rhythmicity are unambiguously detectable under free running conditions. C_LIO_LIBy uncovering the complex regulation of biological rhythms in P. tricornutum, these results provide a key step in understanding the endogenous regulators of phytoplankton physiological responses to environmental changes. Furthermore, these studies position diatoms as instrumental and novel model systems for elucidating key mechanistic principles of oscillator functions in marine ecosystems. C_LI

molecular biology↗

bioRxiv2024

Phytochromes Enable Social Behavior in Marine Diatoms

The phytochrome superfamily, a group of proteins that enable some organisms to detect changes in light intensity and quality, is widespread in terrestrial and marine microbes, fungi, algae, and plants. In terrestrial plants, these photosensory receptors monitor variations in the light environment by sensing red (R) and far-red (FR) regions of the spectrum and trigger important developmental, metabolic, and physiological responses. However, the role of these photosensors in marine microbes, living in environments where, due to absorption of water molecules R and FR radiation does not penetrate beyond the upper few meters, remains controversial. Here, we investigate the role of phytochromes in light perception of the marine diatom Phaeodactylum tricornutum and their involvement in light-driven collective behavior. We perform experiments comparing the social conduct of wild-type and phytochrome knock-out strains to different light wavelengths. Our results show that cell movements become synchronized in a coordinated wobbling dance upon activation of their phytochromes by blue or far-red light, therefore, demonstrating the key role of phytochrome in light-mediated diatom collective behaviour. Furthermore, our experiments suggest that the observed phytochrome-mediated concerted dance implies a form of intercell communication, proposedly mediated by variable R/FR autofluorescence emission in the frequency range of diatom wobbling movements. Our findings provide new insights into communication pathways in aquatic microorganisms and emphasize the importance of social conduct in the sea at all ecological levels.

ecology↗

bioRxiv2024

DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes

Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology and biotechnology. Since the first genome sequencing in 2008, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and two other diatoms to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize precomputed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. Significance statementIn recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web-based server that integrates public diatom omics data (genomics, transcriptomics, epigenomics, proteomics, sequence variants) to connect individual diatom genes to broader-scale functional processes.

genomics↗

bioRxiv2023

Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations

1.Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes. Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40{degrees} to 78{degrees}N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: while MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the large outlier chromosome (BOC), a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome (SOC), associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish Bathycoccus prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets. 2. Significance statementEukaryotic phytoplankton are key to ocean ecosystems, yet their intraspecific genomic diversity is poorly understood. We present 28 high-quality genomes and their annotations of the cosmopolitan microalga Bathycoccus, revealing whole genome structural variations, chromosomal haplotype diversity linked to mating and viral resistance, and offering a genomic framework that complements metagenomic data to establish this picoalga as a model for functional and ecological studies.

genomics↗

bioRxiv2023

Diatom phytochromes integrate the entire visible light spectra for photosensing in marine environments

Aquatic life is strongly structured by light gradients, with gradual decrease in light intensity and differential attenuation of sunlight wavelengths with depth. How phytoplankton perceive these variations is unknown. By providing the first in vivo quantitative assessment of the action of marine diatom phytochrome photoreceptors (DPH), we show that they efficiently trigger photoreversible responses across the entire light spectrum, unlike current models of phytochrome photosensing. The distribution and activity of DPHs in the environment indicate that they are extremely sensitive detectors of spectral light variations related to depth and optical properties of the water column in temperate and polar oceans, revealing a completely novel view of how light is perceived in the marine environment.

plant biology↗

bioRxiv2019

ProfileView: multiple probabilistic models resolve protein families functional diversity

Sequence functional classification has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple probabilistic models whose construction explores evolutionary information in available databases, and a new definition of a representation space where to look at sequences from the point of view of probabilistic models combined together. ProfileView classifies families of proteins for which functions should be discovered or characterised within known groups. We validate ProfileView on seven classes of widespread proteins, involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterize the functions. Furthermore, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of new biological functions. ProfileView proves to outperform three functional classification approaches, CUPP, PANTHER, and a recently developed neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.

bioinformatics↗

bioRxiv2018

A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum

Periodic light-dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular foundations controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we unveil the function of a Phaeodactylum tricornutum bHLH-PAS protein, PtbHLH1a, in the regulation of light-dependent diurnal rhythms. Peak expression of PtbHLH1a mRNA occurs toward the end of the light period and it adjusts to photoperiod changes. Ectopic over-expression of PtbHLH1a results in lines showing a phase shift in diurnal cell fluorescence, compared to the wild-type cells, and with altered cell cycle progression and gene expression. Reduced oscillations in gene expression are also observed in overexpression lines compared to wild-type in continuous darkness, showing that the regulation of rhythmicity by PtbHLH1a is not directly dependent on light inputs and cell division. PtbHLH1a homologs are widespread in diatom genomes which may indicate a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but underinvestigated branch of the tree of life.\n\nSIGNIFICANCE STATEMENTMost organisms experience diurnal light-dark changes and show rhythms of basic biological processes such that they occur at optimal times of the day. The ocean harbours a huge diversity of organisms showing light-dependent rhythms, but their molecular foundations are still largely unknown. In this study, we discover a novel protein, PtbHLH1a that regulates cell division, gene expression and the diurnal timing of these events in the marine diatom Phaedoactylum tricornutum. The identification of PtbHLH1a-like genes in many diatom species suggests a conserved function in diurnal rhythm regulation in the most species-rich group of algae in the ocean. This study unveils critical features of diatom biology and advances the field of marine rhythms and their environmental regulation.

molecular biology↗