Exploring thylakoid emergence: evolution of membrane biogenesis and photosystem II assembly in early‐diverging cyanobacteria

Summary Thylakoid membranes (TM) in cyanobacteria and chloroplasts host the light‐dependent reactions of oxygenic photosynthesis. Gloeobacterales , the earliest‐diverging cyanobacterial lineage, lack TM and perform photosynthesis in the cytoplasmic membrane (CM), representing an ancestral state relative to other cyanobacteria (Phycobacteria). This study investigates the evolutionary origin of TM. Phylogenomic analyses were performed across a phylogenetically diverse set of cyanobacteria, including extensive representation of basal lineages ( Gloeobacterales , Thermostichales , Gloeomargaritales , and Pseudanabaenales ), as well as micro‐ and macrocyanobacteria, using orthologous proteins involved in membrane dynamics and photosystem II (PSII) assembly, together with structural modeling using AlphaFold3. We identified two candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH (Stomatin, Prohibitin, Flotillin, en HflK/C) family member Slr1106, proposed to have been acquired by lateral gene transfer. Analysis of 36 PSII assembly factors revealed modifications in late‐stage assembly, notably in manganese homeostasis. Structural changes in the YidC translocase may have facilitated the relocation of linear electron transfer components from the CM to TM. Altogether, these phylogenetic and functional prediction analyses provide new insight into the molecular innovations that led to TM emergence, including membrane trafficking systems, PSII assembly changes, and protein targeting adaptations.