title: A particular silent codon exchange in a recombinant gene greatly influences host cell metabolic activity.
abstract: BACKGROUND
  Recombinant protein production using Escherichia coli as expression host is highly efficient, however, it also induces strong host cell metabolic burden. Energy and biomass precursors are withdrawn from the host's metabolism as they are required for plasmid replication, heterologous gene expression and protein production. Rare codons in a heterologous gene may be a further drawback. This study aims to investigate the influence of particular silent codon exchanges within a heterologous gene on host cell metabolic activity. Silent mutations were introduced into the coding sequence of a model protein to introduce all synonymous arginine or leucine codons at two randomly defined positions, as well as substitutions leading to identical amino acid exchanges with different synonymous codons. The respective E. coli clones were compared during cultivation in a mineral autoinduction medium using specialized online and offline measuring techniques to quantitatively analyze effects on respiration, biomass and protein production, as well as on carbon source consumption, plasmid copy number, intracellular nucleobases and mRNA content of each clone.
  
  
  RESULTS
  Host stain metabolic burden correlates with recombinant protein production. Upon heterologous gene expression, tremendous differences in respiration, biomass and protein production were observed. According to their different respiration activity the E. coli clones could be classified into two groups, Type A and Type B. Type A clones tended to higher product formation, Type B clones showed stronger biomass formation. Whereas codon usage and intracellular nucleobases had no influence on the Type-A-Type-B-behavior, plasmid copy number, mRNA content and carbon source consumption strongly differed between the two groups.
  
  
  CONCLUSIONS
  Particular silent codon exchanges in a heterologous gene sequence led to differences in initial growth of Type A and Type B clones. Thus, the biomass concentration at the time point of induction varied. In consequence, not only plasmid copy number and expression levels differed between the two groups, but also the kinetics of lactose and glycerol consumption. Even though the underlying molecular mechanisms are not yet identified we observed the astonishing phenomenon that particular silent codon exchanges within a heterologous gene tremendously affect host cell metabolism and recombinant protein production. This could have great impact on codon optimization of heterologous genes, screening procedures for improved variants, and biotechnological protein production processes.
authors.affiliation: AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany. natalie.rahmen@avt.rwth-aachen.de.
authors.forename: Natalie
authors.initials: N
authors.lastname: Rahmen
authors.affiliation: Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany. christian.schlupp@rwth-aachen.de.
authors.forename: Christian D
authors.initials: CD
authors.lastname: Schlupp
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Japan. hitoshi_mitsunaga@bio.eng.osaka-u.ac.jp.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Mitsunaga
authors.affiliation: Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany. a.fulton@fz-juelich.de.
authors.forename: Alexander
authors.initials: A
authors.lastname: Fulton
authors.affiliation: AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany. tita.aryani@rwth-aachen.de.
authors.forename: Tita
authors.initials: T
authors.lastname: Aryani
authors.affiliation: Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany. lara.esch@rwth-aachen.de.
authors.forename: Lara
authors.initials: L
authors.lastname: Esch
authors.affiliation: Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany. schaffrath@bio3.rwth-aachen.de.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Schaffrath
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Japan. fukusaki@bio.eng.osaka-u.ac.jp.
authors.forename: Eiichiro
authors.initials: E
authors.lastname: Fukuzaki
authors.affiliation: Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany. karl-erich.jaeger@fz-juelich.de.|Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany. karl-erich.jaeger@fz-juelich.de.
authors.forename: Karl-Erich
authors.initials: KE
authors.lastname: Jaeger
authors.affiliation: AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany. jochen.buechs@avt.rwth-aachen.de.
authors.forename: Jochen
authors.initials: J
authors.lastname: Büchs
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D018533:Biomass; D002244:Carbon / Q000378:metabolism; D003062:Codon; D004926:Escherichia coli / Q000378:metabolism*; D018628:Gene Dosage; D008049:Lipase / Q000235:genetics; D060847:Metabolic Engineering; D055442:Metabolome; D016297:Mutagenesis, Site-Directed; D010957:Plasmids / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D011994:Recombinant Proteins / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D012333:RNA, Messenger; D011994:Recombinant Proteins; D002244:Carbon; D008049:Lipase