Biology subjects

Caffarri, S.

Publications and source records attributed to Caffarri, S..

6 recordsLinked to original sources

bioRxiv2026

in silico Analysis of Phycodnaviridae Tetrapyrrole Enzymes: Subcellular Localization and Functional Divergence from Host Homologs

RationaleRecent viral metagenomic studies have identified a plethora of enzyme-encoding genes in Phycodnaviridae viruses that are not strictly required for viral replication. These enzymes hold an unexpected metabolic potential during the infection process with their specific green algae host. As neither their role in the infection process nor the subcellular localization of these proteins has been experimentally characterized, comparative sequences, structural and biochemical in silico analyses can help generate functional and localization hypotheses. MethodsIn a recent viral metagenomic dataset, we identified a collection of viral homologs involved in bilin biosynthesis: heme oxygenase (vHMOX1) and Phycocyanobilin:Ferredoxin oxidoreductase (vPcyA). Viral and algal homologues were compared through sequence analyses and AlphaFold3 structural predictions. Predicted biochemical properties were analyzed for their compatibility with subcellular compartments. Active site architecture and putative substrate binding were compared between viral and algal proteins using AlphaFold3 and experimentally resolved structures. ResultsViral HMOX1 and PcyA sequences are truncated compared to algal homologs, lacking the N-terminal extension associated with chloroplast targeting. However biochemical properties, including isoelectric point and surface charge distribution, are compatible with localization in chloroplast stroma. Structural comparisons reveal modifications in the viral HMOX1 active site, including partial substrate reorientation and substitutions of key residues, consistent with modified heme-binding properties. In contrast, vPcyA models show no significant differences to their algal counterparts. ConclusionsActive site remodeling in vHMOX1 protein models suggests that these viral homologues may have evolved distinct heme-binding properties. Unlike vPcyA, vHMOX1 homologs appear to have diverged more substantially from their algal counterparts, potentially reflecting functional specialization in the viral infection context. One sentence summary of key findingsOur bioinformatic analyses expand the repertoire of auxiliary metabolic genes in Phycodnaviridae by identifying a conserved heme degradation pathway, non-canonical vHMOX1/PcyA targeting and structural rearrangements surrounding the catalytic sites of viral HMOX1.

biochemistry↗

bioRxiv2025

Guanosine tetraphosphate (ppGpp) signalling promotes high-light tolerance in Arabidopsis thaliana.

Guanosine tetraphosphate (ppGpp) is a hyperphosphorylated nucleotide originally discovered in prokaryotes and found in the chloroplasts of plants and algae. In plants, ppGpp signalling plays a role as a regulator of photosynthetic activity, which is important in acclimation to environmental stresses such as nitrogen limitation. However, the full range of stresses involving ppGpp signalling is not yet known. Here, we investigated the role of ppGpp accumulation in the acclimation of plants to high light. We found that the over-accumulation of ppGpp in transgenic lines that overexpress RSH3 (OX:RSH3) increases tolerance to high light intensity. Although ppGpp leads to higher non-photochemical energy dissipation (NPQ) than in wild-type plants, we show that NPQ is not critical for the enhanced high-light tolerance. Rather, our results show that ppGpp accumulation leads to broad changes in plant physiology that prime plants to resist and subsequently recover from high light exposure. ppGpp levels themselves also increase in response to high light exposure, suggesting that ppGpp signalling may play a physiological role in high light acclimation. Our work highlights the importance of ppGpp signalling in plant stress acclimation.

plant biology↗

bioRxiv2025

Acclimation of photosynthesis began with a Cu-binding superoxide detoxifying enzyme

Plant acclimation is a growing scientific concept, at molecular, cellular and global scales. All photosynthetic organisms that created an oxic atmosphere on earth possess a gene of unknown function "Acclimation of Photosynthesis to the Environment 1". Here we show that APE1 encodes a thylakoid-bound protein with a unique motif that binds copper and detoxifies the superoxide anion radical, O2*-. Maturation of the recombinant APE1 protein from Chlamydomonas reinhardtii requires formation of cysteine disulfide bonds after copper binding or via a high affinity interaction with a copper chaperone (Plastid Copper Chaperone 1) that boosts its scavenging capacity for O2*-. APE1 co-occurs in evolution with Photosystem II oxygen evolving proteins and it is the archaic O2*- detoxifying enzyme for acclimating photosynthesis to an oxygenic environment.

plant biology↗

bioRxiv2024

A cytochrome P450 involved in apocarotenoid signaling enhances plant photosynthetic capacity and photooxidative stress tolerance

{beta}-cyclocitric acid and its precursor {beta}-cyclocitral are signaling apocarotenoids which trigger defense and detoxification mechanisms enhancing plant tolerance to abiotic stresses. From a transcriptomic analysis of Arabidopsis plants exposed to each apocarotenoid over several exposure times, we identified a gene (CYP81D11) encoding a cytochrome P450 that is strongly induced under all conditions and is under the control of the TGAII-SCL14 transcription regulator. Overexpressing the CYP81D11 gene in Arabidopsis led to a very tolerant phenotype to high light stress while a CYP81D11- deficient mutant was photosensitive. The transcriptomic profile of the CYP81D11 overexpressor revealed a selective upregulation of genes related to photosynthesis and the response to high light stress. Photosynthetic electron transport, CO2 fixation and biomass production were noticeably improved by high expression levels of CYP81D11. These effects occurred in high light, not in low light, and were associated with a noticeable reduction of singlet oxygen photoproduction. These findings indicate that CYP81D11 is a key component of {beta}-cyclocitral-induced stress tolerance, acting through enhancement of the photosynthetic capacity of leaves. This gene could be a new target for improving photosynthesis, particularly in sunny environments.

plant biology↗

bioRxiv2021

A ppGpp-mediated brake on photosynthesis is required for acclimation to nitrogen limitation in Arabidopsis.

Guanosine pentaphosphate and tetraphosphate (together referred to as ppGpp) are hyperphosphorylated nucleotides found in bacteria and the chloroplasts of plants and algae. In plants and algae artificial ppGpp accumulation can inhibit chloroplast gene expression, and influence photosynthesis, nutrient remobilisation, growth, and immunity. However, it is so far unknown whether ppGpp is required for abiotic stress acclimation in plants. Here, we demonstrate that ppGpp biosynthesis is necessary for acclimation to nitrogen starvation in Arabidopsis. We show that ppGpp is required for remodeling the photosynthetic electron transport chain to downregulate photosynthetic activity and for protection against oxidative stress. Furthermore, we demonstrate that ppGpp is required for coupling chloroplastic and nuclear gene expression during nitrogen starvation. Altogether, our work indicates that ppGpp is a pivotal regulator of chloroplast activity for stress acclimation in plants.

plant biology↗

bioRxiv2020

ACCLIMATION OF PHOTOSYNTHESIS TO THE ENVIRONMENT 1 regulates Photosystem II Supercomplex dynamics in response to light in Chlamydomonas reinhardtii

Photosynthetic organisms require acclimation mechanisms to regulate photosynthesis in response to light conditions. Here, two mutant alleles of ACCLIMATION OF PHOTOSYNTHESIS TO THE ENVIRONMENT 1 (ape1) have been characterized in Chlamydomonas reinhardtii. The ape1 mutants are photosensitive and show PSII photoinhibition during high light acclimation or under high light stress. The ape1 mutants retain more PSII super-complexes and have changes to thylakoid stacking relative to control strains during photosynthetic growth at different light intensities. The APE1 protein is found in all oxygenic phototrophs and encodes a 25 kDa thylakoid protein that interacts with the Photosystem II core complex as monomers, dimers and supercomplexes. We propose a model where APE1 bound to PSII supercomplexes releases core complexes and promotes PSII heterogeneity influencing the stacking of Chlamydomonas thylakoids. APE1 is a regulator in light acclimation and its function is to reduce over-excitation of PSII centres and avoid PSII photoinhibition to increase the resilience of photosynthesis to high light.

plant biology↗