Biology subjects

Johnson, X.

Publications and source records attributed to Johnson, X..

9 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

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↗

bioRxiv2025

Nitrogen metabolism profiling reveals cell state-specific pyrimidine synthesis pathway choice

Conventional stable isotope tracing assays track one or several metabolites. However, cells use an array of nutrients to sustain nitrogen metabolic pathways. This incongruency hampers a system level understanding of cellular nitrogen metabolism. Therefore, we created a platform to simultaneously trace 30 nitrogen isotope-labeled metabolites. This platform revealed that while primitive cells engage both de novo and salvage pyrimidine synthesis pathways, differentiated cells nearly exclusively salvage uridine despite expressing de novo pathway enzymes. This link between cell state and pyrimidine synthesis routes persisted in physiological contexts, including primary murine and human tissues and tumor xenografts. Mechanistically, we found that Ser1900 phosphorylation of CAD, the first enzyme of the de novo pathway, was enriched in primitive cells and that mimicking this modification in differentiated cells abrogated their preference for pyrimidine salvage. Collectively, we establish a method for nitrogen metabolism profiling and define a mechanism of cell state-specific pyrimidine synthesis pathway choice.

cell biology↗

bioRxiv2025

NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT

Cells generate purine nucleotides through both de novo purine biosynthesis (DNPB) and purine salvage. Purine accumulation represses energetically costly DNPB through feedback inhibition of the enzymatic steps that produce the precursor phosphoribosylamine. Excessive DNPB is associated with human diseases including neurological dysfunction and hyperuricemia. However, the mechanisms explaining how cells balance DNPB and purine salvage are incompletely understood. Data from a genome-wide CRISPR loss-of-function screen and extensive stable isotope tracing identified Nudix hydrolase 5 (NUDT5) as a suppressor of DNPB during purine salvage. NUDT5 ablation allows DNPB to persist in the presence of either native purines or thiopurine drugs; this renders NUDT5-deficient cells insensitive to thiopurine treatment. Surprisingly, this regulation occurs independently of NUDT5s known function in hydrolyzing ADP-ribose to AMP and ribose-5-phosphate. Rather, NUDT5 interacts with phosphoribosyl pyrophosphate amidotransferase (PPAT), the rate-limiting enzyme in DNPB that generates phosphoribosylamine. Upon induction of purine salvage, the PPAT-NUDT5 interaction is required to trigger disassembly of the purinosome, a cytosolic metabolon involved in efficient DNPB. Mutations that disrupt NUDT5s interaction with PPAT but leave its catalytic activity intact permit excessive DNPB during purine salvage, inducing thiopurine resistance. Collectively, our findings identify NUDT5 as a regulator governing the balance between DNPB and purine salvage, underscoring its impact on nucleotide metabolism and efficacy of thiopurine treatment.

biochemistry↗

bioRxiv2024

Crystal structure of a Photosystem II-related, Manganese-binding, TPM-domain protein at a 1.6 A resolution

Many proteins conserved across oxygenic phototrophs play essential roles in photosynthetic function and acclimation, yet many remain unidentified or poorly characterized. In the green alga Chlamydomonas reinhardtii we identified two paralogous thylakoid lumenal proteins, encoded by Cre15.g636050 (LMTP1) and Cre03.g154600 (TLP26), belonging to the conserved TPM-domain (TLP18.3-Psb32-MOLO1) PF04536 family. We generated C. reinhardtii knock-out mutants for LMTP1 and TLP26 and produced recombinant proteins to assess their biochemical properties. The crystal structures of both proteins reveal the presence of a conserved redox-responsive cysteine pair, novel in TPM-domain proteins, and show that LMTP1 binds manganese. Double mutants lacking both LMTP1 and TLP26 show reduced photosynthetic performance due to effects at the acceptor-side of Photosystem II (PSII); however, these mutants accumulate more chlorophyll and photosynthetic proteins due to increased synthesis rates, a phenotype not observed for the single lmtp1 and tlp26 mutants. We propose that these two TPM-domain proteins, LMTP1 and TLP26, are functionally redundant in maturing nascent PSII intermediates during assembly and repair.

plant biology↗

bioRxiv2022

OHP2 is not required for psbA translation in Chlamydomonas

In land plants and cyanobacteria, co-translational association of chlorophyll (Chl) to the nascent D1 polypeptide, a reaction center protein of photosystem II (PSII), requires a Chl binding complex consisting of a short-chain dehydrogenase (HCF244/Ycf39) and One-Helix Proteins of the LHC superfamily (OHP1 and OHP2 in chloroplasts). Here, we show that an ohp2 mutant of the green alga Chlamydomonas reinhardtii fails to accumulate core PSII subunits, in particular D1. Extragenic suppressors arise at high frequency, suggesting the existence of another route for Chl association to PSII. The ohp2 mutant can be complemented by the Arabidopsis ortholog. In contrast to land plants, where psbA translation is prevented in the absence of OHP2, ribosome profiling experiments show that the Chlamydomonas mutant translates the psbA transcript over its full length. Pulse labelling suggests that D1 is degraded during or immediately after translation. The translation of other PSII subunits is affected by assembly-controlled translational regulation (the CES process). Proteomics show that HCF244, a translation factor which associates with and is stabilized by OHP2 in land plants, still partly accumulates in the Chlamydomonas ohp2 mutant, explaining the persistence of psbA translation. Several Chl biosynthesis enzymes overaccumulate in the mutant membranes. Partial inactivation of the D1-degrading FtsH protease restores a low level of PSII activity in an ohp2 background, but not photoautotrophy. Taken together, our data suggest that OHP2 is not required for psbAD1 translation in Chlamydomonas, but necessary for its stabilization.

plant biology↗

bioRxiv2021

Trehalose-6-phosphate links singlet oxygen-induced signalling with metabolic signalling in Chlamydomonas reinhardtii

Using a novel mutant screen, we identified TREHALOSE 6-PHOSPHATE PHOSPHATASE 1 (TSPP1) as a functional enzyme dephosphorylating trehalose 6-phosphate (Tre6P) to trehalose in Chlamydomonas reinhardtii. The tspp1 knock-out results in reprogramming of the cell metabolism via significantly altered transcriptome. As a secondary effect, tspp1 also shows impairment in 1O2-induced chloroplast retrograde signalling. From transcriptomic analysis and metabolite profiling, we conclude that accumulation or deficiency of certain metabolites directly affect 1O2-signalling. 1O2-inducible GLUTATHIONE PEROXIDASE 5 (GPX5) gene expression is suppressed by increased content of fumarate, an intermediate in the tricarboxylic acid cycle (TCA cycle) in mitochondria and dicarboxylate metabolism in the cytosol, while it is promoted by another TCA cycle intermediate, aconitate. Furthermore, genes encoding known essential components of chloroplast-to-nucleus 1O2-signalling, PSBP2, MBS, and SAK1, show decreased transcript levels in the tspp1 mutant, which can be rescued by exogenous application of aconitate. We demonstrate that chloroplast retrograde signalling involving 1O2 depends on mitochondrial and cytosolic processes and that the metabolic status of the cell determines the response to 1O2.

cell biology↗

bioRxiv2020

Regulation of light harvesting in Chlamydomonas: two protein phosphatases are involved in state transitions

Protein phosphorylation plays important roles in short-term regulation of photosynthetic electron transfer. In a mechanism known as state transitions, the kinase STATE TRANSITION 7 (STT7) of Chlamydomonas reinhardtii phosphorylates components of light-harvesting antenna complex II (LHCII). This reversible phosphorylation governs the dynamic allocation of a part of LHCII to photosystem I or photosystem II, depending on light conditions and metabolic demands. Little is however known in the green alga on the counteracting phosphatase(s). In Arabidopsis, the homologous kinase STN7 is specifically antagonized by PROTEIN PHOSPHATASE 1/THYLAKOID-ASSOCIATED PHOSPHATASE 38 (PPH1/TAP38). Furthermore, the paralogous kinase STN8 and the countering phosphatase PHOTOSYSTEM II PHOSPHATASE (PBCP), which count subunits of PSII amongst their major targets, influence thylakoid architecture and high-light tolerance. Here we analyze state transitions in C. reinhardtii mutants of the two homologous phosphatases, CrPPH1 and CrPBCP. The transition from state 2 to state 1 is retarded in pph1, and surprisingly also in pbcp. However both mutants can eventually return to state 1. In contrast, the double mutant pph1;pbcp appears strongly locked in state 2. The complex phosphorylation patterns of the LHCII trimers and of the monomeric subunits are affected in the phosphatase mutants. Their analysis indicates that the two phosphatases have different yet overlapping sets of protein targets. The dual control of thylakoid protein de-phosphorylation and the more complex antenna phosphorylation patterns in Chlamydomonas compared to Arabidopsis are discussed in the context of the stronger amplitude of state transitions and the more diverse LHCII isoforms in the alga.

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↗