title: Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.
abstract: We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated '-omics' data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes.
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
authors.forename: Wei-Hua
authors.identifier: http://orcid.org/0000-0001-5160-4398
authors.initials: WH
authors.lastname: Chen
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
authors.forename: Vera
authors.initials: V
authors.lastname: van Noort
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Lluch-Senar
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
authors.forename: Marco L
authors.initials: ML
authors.lastname: Hennrich
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain Theoretical Biophysics, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.
authors.forename: Judith A H
authors.initials: JA
authors.lastname: Wodke
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Yus
authors.affiliation: Bioinformatics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Andreu
authors.initials: A
authors.lastname: Alibés
authors.affiliation: Bioinformatics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Guglielmo
authors.initials: G
authors.lastname: Roma
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Pesavento
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Typas
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany gavin@embl.de.
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gavin
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain luis.serrano@crg.eu.
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany Max-Delbrück-Centre (MDC) for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany bork@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data; D005786:Gene Expression Regulation; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009177:Mycoplasma pneumoniae / Q000235:genetics* / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D022661:RNA, Untranslated / Q000235:genetics; D049490:Systems Biology / Q000379:methods / Q000706:statistics & numerical data
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D022661:RNA, Untranslated