Butenko, I. | bioRxiv Science

bioRxiv2026

The proteome as a whole: from a passive reflection of the transcriptome to an active cellular organizer

Despite advances in proteomics, the proteome is still often viewed as a passive reflection of the transcriptome. Using Mycoplasma gallisepticum as a minimal cell model, we analyzed large-scale datasets across multiple stress conditions to investigate whether the proteome functions as an integrated regulatory system. The proteome remained quantitatively stable under stress, yet the bacteria adapted successfully. We identified a minimal core of 17 major proteins constituting 35% of cellular protein mass. These proteins exhibit distinct physicochemical properties--higher positive charge, lower hydrophilicity, and enrichment in intrinsically disordered regions--suggesting they shape cytoplasmic organization and may drive liquid-liquid phase separation. Minor proteins form tightly correlated clusters, while stress conditions trigger rearrangement of protein complexes without abundance changes, representing an energy-efficient adaptation strategy. Cross linking mass spectrometry revealed condition specific interactome remodeling, which may underlie mycoplasma adaptation to diverse stresses. Our findings suggest that the proteome operates as an active cellular organizer, where physicochemical properties and dynamic complex rearrangements enable adaptation independently of transcriptional control. This framework may inform synthetic biology efforts to engineer minimal cells.

synthetic biology↗

bioRxiv2017

Distinct types of short open reading frames are translated in plant cells

Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of ten plant species examined. Mass spectrometry analysis of proteomic and peptidomic datasets suggested that 584 sORFs located on distinct parts of mRNAs and long non-coding RNAs (lncRNAs) are translated, including 73 conservative sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Alternative splicing is likely involved in the excision of translatable sORFs from such transcripts. We identified a group of sORFs homologous to known protein domains and suggested they function as small interfering peptides. Functional analysis of candidate lncRNA-encoded peptides showed it to be involved in regulating growth and differentiation in moss. The high evolutionary rate and wide translation of sORFs suggest that they may provide a reservoir of potentially active peptides and their importance as a raw material for gene evolution. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.

plant biology↗