Versatile and stable vectors for efficient gene expression in Ralstonia eutropha H16.

The Gram-negative β-proteobacterium Ralstonia eutropha H16 is primarily known for polyhydroxybutyrate (PHB) production and its ability to grow chemolithoautotrophically by using CO2 and H2 as sole carbon and energy sources. The majority of metabolic engineering and heterologous expression studies conducted so far rely on a small number of suitable expression systems. Particularly the plasmid based expression systems already developed for the use in R. eutropha H16 suffer from high segregational instability and plasmid loss after a short time of fermentation. In order to develop efficient and highly stable plasmid expression vectors for the use in R. eutropha H16, a new plasmid design was created including the RP4 partitioning system, as well as various promoters and origins of replication. The application of minireplicons derived from broad-host-range plasmids RSF1010, pBBR1, RP4 and pSa for the construction of expression vectors and the use of numerous, versatile promoters extend the range of feasible expression levels considerably. In particular, the use of promoters derived from the bacteriophage T5 was described for the first time in this work, characterizing the j5 promoter as the strongest promoter yet to be applied in R. eutropha H16. Moreover, the implementation of the RP4 partition sequence in plasmid design increased plasmid stability significantly and enables fermentations with marginal plasmid loss of recombinant R. eutropha H16 for at least 96 h. The utility of the new vector family in R. eutropha H16 is demonstrated by providing expression data with different model proteins and consequently further raises the value of this organism as cell factory for biotechnological applications including protein and metabolite production.

[1]  D. Helinski,et al.  Characterization of the stable maintenance properties of the par region of broad-host-range plasmid RK2 , 1996, Journal of bacteriology.

[2]  T. Gerngross,et al.  A Novel High-Cell-Density Protein Expression System Based on Ralstonia eutropha , 2002, Applied and Environmental Microbiology.

[3]  K. Timmis,et al.  Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. , 1981, Gene.

[4]  O. Lenz,et al.  A hydrogen-sensing system in transcriptional regulation of hydrogenase gene expression in Alcaligenes species , 1997, Journal of bacteriology.

[5]  H. Bujard,et al.  Promoters recognized by Escherichia coli RNA polymerase selected by function: highly efficient promoters from bacteriophage T5 , 1985, Journal of bacteriology.

[6]  Steven W. Singer,et al.  Engineering of Ralstonia eutropha H16 for Autotrophic and Heterotrophic Production of Methyl Ketones , 2013, Applied and Environmental Microbiology.

[7]  V. de Lorenzo,et al.  Site-specific deletions of chromosomally located DNA segments with the multimer resolution system of broad-host-range plasmid RP4 , 1995, Journal of bacteriology.

[8]  B. Friedrich,et al.  Denitrification by Alcaligenes eutrophus is plasmid dependent , 1985, Journal of bacteriology.

[9]  M. Inouye,et al.  Toxin-antitoxin systems in bacteria and archaea. , 2011, Annual review of genetics.

[10]  Jong Park,et al.  Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production , 2011, BMC Systems Biology.

[11]  A. Steinbüchel,et al.  Cloning of the Alcaligenes eutrophus genes for synthesis of poly-beta-hydroxybutyric acid (PHB) and synthesis of PHB in Escherichia coli , 1988, Journal of bacteriology.

[12]  A. Steinbüchel,et al.  Application of a KDPG-aldolase gene-dependent addiction system for enhanced production of cyanophycin in Ralstonia eutropha strain H16. , 2006, Metabolic engineering.

[13]  Mechthild Bömeke,et al.  Genome-wide transcriptome analyses of the 'Knallgas' bacterium Ralstonia eutropha H16 with regard to polyhydroxyalkanoate metabolism. , 2010, Microbiology.

[14]  B. Bowien,et al.  Genetics and control of CO2 assimilation in the chemoautotroph Ralstoniaeutropha , 2002, Archives of Microbiology.

[15]  R. Tait,et al.  Genetic map of the crown gall suppressive IncW plasmid pSa , 2004, Molecular and General Genetics MGG.

[16]  H. Schwab,et al.  Detection of a new enzyme for stereoselective hydrolysis of linalyl acetate using simple plate assays for the characterization of cloned esterases from Burkholderia gladioli. , 1998, Journal of biotechnology.

[17]  R. Meyer Identification of the mob Genes of Plasmid pSC101 and Characterization of a Hybrid pSC101-R1162 System for Conjugal Mobilization , 2000, Journal of bacteriology.

[18]  D. Roop,et al.  Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. , 1995, Gene.

[19]  T. Fukui,et al.  Microbial synthesis of poly((R)-3-hydroxybutyrate-co-3-hydroxypropionate) from unrelated carbon sources by engineered Cupriavidus necator. , 2009, Biomacromolecules.

[20]  A. Steinbüchel,et al.  Bacterial and other biological systems for polyester production. , 1998, Trends in biotechnology.

[21]  Anne Pohlmann,et al.  Autotrophic Production of Stable-Isotope-Labeled Arginine in Ralstonia eutropha Strain H16 , 2012, Applied and Environmental Microbiology.

[22]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[23]  O. Lenz,et al.  The Maturation Factors HoxR and HoxT Contribute to Oxygen Tolerance of Membrane-Bound [NiFe] Hydrogenase in Ralstonia eutropha H16 , 2011, Journal of bacteriology.

[24]  E. Lanka,et al.  KorB protein of promiscuous plasmid RP4 recognizes inverted sequence repetitions in regions essential for conjugative plasmid transfer. , 1992, Nucleic acids research.

[25]  Christopher M Thomas,et al.  Complete Nucleotide Sequence of Birmingham IncPα Plasmids: Compilation and Comparative Analysis , 1994 .

[26]  A. Steinbüchel,et al.  Plasmid addiction systems: perspectives and applications in biotechnology , 2010, Microbial biotechnology.

[27]  C. S. Kristensen,et al.  Analysis of the multimer resolution system encoded by the parCBA operon of broad‐host‐range plasmid RP4 , 1994, Molecular microbiology.

[28]  Sriram Srinivasan,et al.  High level recombinant protein expression in Ralstonia eutropha using T7 RNA polymerase based amplification. , 2004, Protein expression and purification.

[29]  M. Rohde,et al.  A gene complex coding for the membrane-bound hydrogenase of Alcaligenes eutrophus H16 , 1992, Journal of bacteriology.

[30]  C. Batt,et al.  Comparative study of promoters for the production of polyhydroxyalkanoates in recombinant strains of Wautersia eutropha , 2005, Applied Microbiology and Biotechnology.

[31]  G. Ditta,et al.  Plasmids related to the broad host range vector, pRK290, useful for gene cloning and for monitoring gene expression. , 1985, Plasmid.

[32]  T. Fukui,et al.  Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses , 2013, BMC Microbiology.

[33]  Keiji Matsumoto,et al.  Construction of a stable plasmid vector for industrial production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) by a recombinant Cupriavidus necator H16 strain. , 2013, Journal of bioscience and bioengineering.

[34]  O. Lenz,et al.  A novel multicomponent regulatory system mediates H2 sensing in Alcaligenes eutrophus. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[35]  E. Chiellini,et al.  Continuous production of poly([R]-3-hydroxybutyrate) by Cupriavidus necator in a multistage bioreactor cascade , 2011, Applied Microbiology and Biotechnology.

[36]  Nathan J Hillson,et al.  Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production , 2013, Microbial Cell Factories.

[37]  T. Fukui,et al.  Evaluation of promoters for gene expression in polyhydroxyalkanoate-producing Cupriavidus necator H16 , 2011, Applied Microbiology and Biotechnology.

[38]  Anne Pohlmann,et al.  Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16 , 2006, Nature Biotechnology.

[39]  A. Pühler,et al.  A Broad Host Range Mobilization System for In Vivo Genetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria , 1983, Bio/Technology.

[40]  D. Helinski,et al.  Role of the parCBA Operon of the Broad-Host-Range Plasmid RK2 in Stable Plasmid Maintenance , 1998, Journal of bacteriology.

[41]  T. Gerngross,et al.  Production of recombinant proteins using multiple‐copy gene integration in high‐cell‐density fermentations of Ralstonia eutropha , 2003, Biotechnology and bioengineering.

[42]  Q. Zeng,et al.  Elucidation of β-Oxidation Pathways in Ralstonia eutropha H16 by Examination of Global Gene Expression , 2010, Journal of bacteriology.

[43]  B. Gronenborn Overproduction of phage Lambda repressor under control of the lac promotor of Escherichia coli , 1976, Molecular and General Genetics MGG.

[44]  A. Steinbüchel,et al.  Establishment of an alternative phosphoketolase-dependent pathway for fructose catabolism in Ralstonia eutropha H16 , 2011, Applied Microbiology and Biotechnology.

[45]  S. Srivastava,et al.  Mutagenesis of Alcaligenes eutrophus by insertion of the drug-resistance transposon Tn5 , 1982, Archives of Microbiology.

[46]  H. Schwab,et al.  Partitioning of broad-host-range plasmid RP4 is a complex system involving site-specific recombination , 1990, Journal of bacteriology.

[47]  Anthony J. Sinskey,et al.  Production of Poly(3-Hydroxybutyrate-co-3-Hydroxyhexanoate) from Plant Oil by Engineered Ralstonia eutropha Strains , 2011, Applied and Environmental Microbiology.

[48]  J. Brosius,et al.  Spacing of the -10 and -35 regions in the tac promoter. Effect on its in vivo activity. , 1985, The Journal of biological chemistry.

[49]  A. Sinskey,et al.  Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16 , 2012, Applied and Environmental Microbiology.

[50]  T. Fukui,et al.  Engineering of Ralstonia eutropha for production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from fructose and solid-state properties of the copolymer. , 2002, Biomacromolecules.

[51]  J. Pogliano,et al.  ParE toxin encoded by the broad‐host‐range plasmid RK2 is an inhibitor of Escherichia coli gyrase , 2002, Molecular microbiology.