title: Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism.
abstract: Understanding cellular life requires a comprehensive knowledge of the essential cellular functions, the components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains of the model bacterium, Bacillus subtilis, whose genomes have been reduced by ∼36%. These strains are fully viable, and their growth rates in complex medium are comparable to those of wild type strains. An in-depth multi-omics analysis of the genome reduced strains revealed how the deletions affect the transcription regulatory network of the cell, translation resource allocation, and metabolism. A comparison of gene counts and resource allocation demonstrates drastic differences in the two parameters, with 50% of the genes using as little as 10% of translation capacity, whereas the 6% essential genes require 57% of the translation resources. Taken together, the results are a valuable resource on gene dispensability in B. subtilis, and they suggest the roads to further genome reduction to approach the final aim of a minimal cell in which all functions are understood.
authors.affiliation: Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Reuß
authors.affiliation: Institute for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany.
authors.forename: Josef
authors.initials: J
authors.lastname: Altenbuchner
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mäder
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
authors.forename: Hermann
authors.initials: H
authors.lastname: Rath
authors.affiliation: Department of Plant Biochemistry, Georg-August-University Göttingen, 37077 Göttingen, Germany.
authors.forename: Till
authors.initials: T
authors.lastname: Ischebeck
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
authors.forename: Praveen Kumar
authors.initials: PK
authors.lastname: Sappa
authors.affiliation: Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, 37077 Göttingen, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Thürmer
authors.affiliation: MaIAGE, INRA Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Cyprien
authors.initials: C
authors.lastname: Guérin
authors.affiliation: MaIAGE, INRA Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Nicolas
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
authors.forename: Leif
authors.initials: L
authors.lastname: Steil
authors.affiliation: Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.
authors.forename: Bingyao
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Department of Plant Biochemistry, Georg-August-University Göttingen, 37077 Göttingen, Germany.|Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany.
authors.forename: Ivo
authors.initials: I
authors.lastname: Feussner
authors.affiliation: Institute for Nonlinear Dynamics, Georg-August-University Göttingen, 37077 Göttingen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Klumpp
authors.affiliation: Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, 37077 Göttingen, Germany.|Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Daniel
authors.affiliation: Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.|Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany.
authors.forename: Fabian M
authors.initials: FM
authors.lastname: Commichau
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Völker
authors.affiliation: Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.|Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Stülke
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D020043:Genes, Essential / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins