Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium |
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| Authors: | Verónica Lloréns‐Rico Francis J O'Reilly Judith AH Wodke E Besray Unal Eva Yus Sira Martínez Robert J Nichols Tony Ferrar Ana Vivancos Arne Schmeisky Jörg Stülke Vera van Noort Anne‐Claude Gavin Peer Bork Luis Serrano |
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| Affiliation: | 1. EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain;2. Universitat Pompeu Fabra (UPF), Barcelona, Spain;3. European Molecular Biology Laboratory, Heidelberg, Germany;4. Theoretical Biophysics, Humboldt‐Universit?t zu Berlin, Berlin, Germany;5. Department of Genetics, Stanford University, Stanford, CA, USA;6. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain;7. Department of General Microbiology, Institute for Microbiology and Genetics, G?ttingen, Germany;8. Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium;9. Max‐Delbrück‐Centre (MDC) for Molecular Medicine, Berlin, Germany;10. Institució Catalana de Recerca i Estudis Avan?ats (ICREA), Barcelona, Spain |
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| Abstract: | Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes. In larger proteins, essentiality applied to individual domains and not entire proteins, a notion we could confirm by expression of truncated domains. The fraction of essential non-coding RNAs (ncRNAs) non-overlapping with essential genes is 5% higher than of non-transcribed regions (0.9%), pointing to the important functions of the former. We found that the minimal essential genome is comprised of 33% (269,410 bp) of the M. pneumoniae genome. Our data highlight an unexpected hidden layer of smORFs with essential functions, as well as non-coding regions, thus changing the focus when aiming to define the minimal essential genome. |
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| Keywords: | minimal genome non-coding RNAs small proteins |
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