Biology subjects

Siponen, M.

Publications and source records attributed to Siponen, M..

4 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

Thriving Across Depths: How Blue Light Shapes a Large PSI Supercomplex and Specic Photosynthetic Traits in the seagrass Posidonia oceanica.

Photosynthetic organisms rely on finely tuned mechanisms to optimize photosynthesis under different light conditions. While these processes are well-characterized in land plants, the adaptive strategies of marine plants remain largely unexplored. The Mediterranean seagrass Posidonia oceanica (Alismatales), a key ecosystem engineer thriving from the surface up to 40m depth and one of the largest long-term blue carbon sinks in coastal environments. Here, we investigate how P. oceanica adjusts its photosynthetic apparatus in response to varying light spectra encountered at different seawater depths. Contrary to land plants, P. oceanica maintains a relatively high PSI/PSII ratio and a high content of the major light-harvesting complex II (LHCII), regardless of depth. Notably, the antenna size of the photosystems remains stable across depths, although we document significant depth-dependent reorganization of the thylakoid membrane ultrastructure. Moreover, we identify a novel large PSI-LHCII supercomplex (L-PSI-LHCII) in P. oceanica, characterized by additional Lhca proteins, reduced red-shifted absorption, and increased chlorophyll b content. Ultrafast spectroscopy reveals the distinct energy transfer dynamics within this complex. The presence of a similar supercomplex in other marine plants, such as Zostera marina, suggests a conserved adaptive strategy among seagrasses.

plant biology↗

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↗