Evaluation of Affinity-Tagged Protein Expression Strategies using Local and Global Isotope Ratio Measurements

Journal Article · Thu Jan 01 04:00:00 EST 2009 · Journal of Proteome Research

DOI:https://doi.org/10.1021/pr801088f· OSTI ID:958954

Khalsa-Moyers, Gurusahai K ^[1]; Lankford, Patricia K ^[1]; Owens, Elizabeth T ^[1]; McKeown, Catherine K ^[1]; Lu, Tse-Yuan S ^[1]; Foote, Linda J ^[1]; Morrell-Falvey, Jennifer L ^[1]; McDonald, W Hayes ^[1]; Pelletier, Dale A ^[1]

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1. ORNL

Protein enrichments of engineered, affinity-tagged (or bait ) fusion proteins with interaction partners are often laden with background, non-specific proteins, due to interactions that occur in vitro as an artifact of the technique. Furthermore, the in vivo expression of the bait protein may itself affect physiology or metabolism. In this study, intrinsic affinity purification challenges were investigated in a model protein complex, DNA-dependent RNA polymerase (RNAP), encompassing chromosome- and plasmid-encoding strategies for bait proteins in two different microbial species: Escherichia coli and Rhodopseudomonas palustris. Isotope ratio measurements of bait protein expression strains relative to native, wild-type strains were performed by liquid chromatography tandem mass spectrometry (LC-MS-MS) to assess bait protein expression strategies in each species. Authentic interacting proteins of RNAP were successfully discerned from artifactual co-isolating proteins by the isotopic differentiation of interactions as random or targeted (I-DIRT) method (A. J. Tackett et al. J. Proteome Res. 2005, 4 (5), 1752-1756). To investigate broader effects of bait protein production in the bacteria, we compared proteomes from strains harboring a plasmid that encodes an affinity-tagged subunit (RpoA) of the RNAP complex with the corresponding wild-type strains using stable isotope metabolic labeling. The ratio of RpoA abundance in plasmid strains versus wild type was 0.8 for R. palustris and 1.7 for E. coli. While most other proteins showed no appreciable difference, proteins significantly increased in abundance in plasmid-encoded bait-expressing strains of both species included the plasmid encoded antibiotic resistance protein, GenR and proteins involved in amino acid biosynthesis. Together, these local, complex-specific and more global, whole proteome isotopic abundance ratio measurements provided a tool for evaluating both in vivo and in vitro effects of plasmid-encoding strategies for bait protein expression. This approach has the potential for enabling discovery of protein-protein interactions among the growing number of sequenced microbial species without the need for development of chromosomal insertion systems.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 958954
• Journal Information: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 7 Vol. 8
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
ABUNDANCE
AFFINITY
AMINO ACIDS
ESCHERICHIA COLI
EVALUATION
IN VITRO
IN VIVO
ISOTOPE RATIO
MASS SPECTROSCOPY
PROTEINS
RNA POLYMERASES
STABLE ISOTOPES
STRAINS