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.

Details

Title
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium
Author
Lluch-Senar, Maria 1 ; Delgado, Javier 1 ; Wei-Hua, Chen 2 ; Lloréns-Rico, Verónica 1 ; O'Reilly, Francis J 2 ; Judith AH Wodke 3 ; Unal, E Besray 1 ; Yus, Eva 1 ; Martínez, Sira 1 ; Nichols, Robert J 4 ; Ferrar, Tony 1 ; Vivancos, Ana 5 ; Schmeisky, Arne 6 ; Stülke, Jörg 6 ; Vera van Noort 7 ; Anne-Claude Gavin 2 ; Bork, Peer 8 ; Serrano, Luis 9 

1  EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain 
2  European Molecular Biology Laboratory, Heidelberg, Germany 
3  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 
4  Department of Genetics, Stanford University, Stanford, CA, USA 
5  Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain 
6  Department of General Microbiology, Institute for Microbiology and Genetics, Göttingen, Germany 
7  Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium 
8  European Molecular Biology Laboratory, Heidelberg, Germany; Max-Delbrück-Centre (MDC) for Molecular Medicine, Berlin, Germany 
9  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 
Section
Reports
Publication year
2015
Publication date
Jan 2015
Publisher
EMBO Press
e-ISSN
17444292
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.15252/msb.20145558
ProQuest document ID
2290245966
Copyright
© 2015. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.