Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection
Michaela Kreitmeier,
Zachary Ardern,
Miriam Abele,
Christina Ludwig,
Siegfried Scherer,
Klaus Neuhaus
Affiliations
Michaela Kreitmeier
Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
Zachary Ardern
Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Corresponding author
Miriam Abele
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
Christina Ludwig
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
Siegfried Scherer
Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
Klaus Neuhaus
Core Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany; Corresponding author
Summary: The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
