Hazkani-Covo, E. | Search bioRxiv

bioRxiv2026

Expansion of Plant Redox Protein Network Predated Plant Terrestrialization

The evolutionary transition of the green plant lineage (Viridiplantae) from aquatic environments to terrestrial habitats required unprecedented adaptations of cellular metabolism to severe environmental stressors, including desiccation, high irradiance, and rapid temperature fluctuations. Redox regulation, mediated by oxidation and reduction of reactive cysteine residues (RCys), plays a crucial role in translating environmental fluctuations into rapid cellular responses. Although comparative genomics has revealed expansions in multiple cellular systems preceding terrestrialization, the evolutionary history of redox-regulated protein networks remains elusive. This work integrated large-scale phylogenomic reconstructions across 37 Viridiplantae species with five independent Arabidopsis thaliana redox proteomics datasets to trace the evolutionary trajectory of RCys. The analysis showed that the ancestral core, consisting of plastid-localized regulatory cysteines, was already established at the base of the green lineage. Furthermore, an expansion driven by gains of RCys via amino acid replacements within pre-existing proteins occurred in the common ancestor of Zygnematophyceae and land plants. These findings suggest that a targeted incorporation of thiol-based regulatory switches provided early land plant ancestors with enhanced protein functional plasticity necessary to cope with the challenges of terrestrial environments. HighlightsO_LIThe foundational plastid-localized redox core was established at the root of Viridiplantae. C_LIO_LINovel regulatory switches were integrated into conserved machinery via amino acid replacement. C_LIO_LIA punctuated burst of redox innovation at Zygnematophyceae and Embryophyta last common ancestor preceded plant terrestrialization. C_LIO_LIRedox acquisition rates declined sharply following the successful colonization of land. C_LI

evolutionary biology↗

bioRxiv2018

Count does not recover major events of gene flux in real biological data

In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional birth-and-death phylogenetic models to investigate prokaryote genome evolution to claim that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here we test the ability of Count, a birth-and-death based program, to recover known events of mass acquisition and differential loss using plastid genomes and eukaryotic protein families that were acquired from plastids. Count showed a strong bias towards reconstructed histories having gene acquisitions distributed uniformly across the tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, Count recovered gradual and continuous lateral gene transfer among lineages, even when massive gains followed by gradual differential loss is the true evolutionary process that generated the gene distribution data.

evolutionary biology↗