title: Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
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.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain maria.lluch@crg.es luis.serrano@crg.es.
authors.forename: Maria
authors.initials: M
authors.lastname: Lluch-Senar
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Delgado
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Wei-Hua
authors.initials: WH
authors.lastname: Chen
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Verónica
authors.initials: V
authors.lastname: Lloréns-Rico
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Francis J
authors.initials: FJ
authors.lastname: O'Reilly
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany.
authors.forename: Judith Ah
authors.initials: JA
authors.lastname: Wodke
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: E Besray
authors.initials: EB
authors.lastname: Unal
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Yus
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Sira
authors.initials: S
authors.lastname: Martínez
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Nichols
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Tony
authors.initials: T
authors.lastname: Ferrar
authors.affiliation: Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Vivancos
authors.affiliation: Department of General Microbiology, Institute for Microbiology and Genetics, Göttingen, Germany.
authors.forename: Arne
authors.initials: A
authors.lastname: Schmeisky
authors.affiliation: Department of General Microbiology, Institute for Microbiology and Genetics, Göttingen, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Stülke
authors.affiliation: Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Vera
authors.initials: V
authors.lastname: van Noort
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gavin
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany Max-Delbrück-Centre (MDC) for Molecular Medicine, Berlin, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain maria.lluch@crg.es luis.serrano@crg.es.
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics*; D020043:Genes, Essential; D016680:Genome, Bacterial; D009177:Mycoplasma pneumoniae / Q000235:genetics*; D016366:Open Reading Frames; D011487:Protein Conformation; D022661:RNA, Untranslated / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D022661:RNA, Untranslated
keywords: minimal genome; non‐coding RNAs; small proteins