Supplementary - Polyploid Achromatium sp. expresses protein variants based on environmental cues

Abstract

Achromatium spp. are giant bacteria harboring hundreds of non-clonal chromosomes per cell. The allelic divergence they exhibit could be a mechanism to enable fine-tuned responses to environmental changes, enabling this organism to broaden its ecological range. However, while ubiquitous in freshwater and marine environments, Achromatium has not been obtained in culture, leaving the role and functioning of its genomic and proteomic diversity poorly understood. Here, we incubated freshly collected freshwater Achromatium under three temperature conditions to conduct comparative mass spectrometry-based proteomics experiments. These were interpreted against an Achromatium-specific protein atlas developed from curated published and new assemblies from marine and freshwater environments. This de novo assembled atlas allowed a twenty-fold increase in the number of identified proteins compared to mass spectrometry data searches against the UniProt database. Predicted proteins from the Achromatium atlas were grouped into orthologs, 5% of which showed temperature-associated detection of distinct protein variants within the group. This provides the first indication that Achromatium uses distinct protein variants under different environmental conditions, enabling it to swiftly respond to environmental changes through differential expression from its cache of chromosomes.