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Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein

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Abstract

Poly(A) binding protein (PAB1) is involved in a number of RNA metabolic functions in eukaryotic cells and correspondingly is suggested to associate with a number of proteins. We have used mass spectrometric analysis to identify 55 non-ribosomal proteins that specifically interact with PAB1 from Saccharomyces cerevisiae. Because many of these factors may associate only indirectly with PAB1 by being components of the PAB1-mRNP structure, we additionally conducted mass spectrometric analyses on seven metabolically defined PAB1 deletion derivatives to delimit the interactions between these proteins and PAB1. These latter analyses identified 13 proteins whose associations with PAB1 were reduced by deleting one or another of PAB1’s defined domains. Included in this list of 13 proteins were the translation initiation factors eIF4G1 and eIF4G2, translation termination factor eRF3, and PBP2, all of whose previously known direct interactions with specific PAB1 domains were either confirmed, delimited, or extended. The remaining nine proteins that interacted through a specific PAB1 domain were CBF5, SLF1, UPF1, CBC1, SSD1, NOP77, yGR250c, NAB6, and GBP2. In further study, UPF1, involved in nonsense-mediated decay, was confirmed to interact with PAB1 through the RRM1 domain. We additionally established that while the RRM1 domain of PAB1 was required for UPF1-induced acceleration of deadenylation during nonsense-mediated decay, it was not required for the more critical step of acceleration of mRNA decapping. These results begin to identify the proteins most likely to interact with PAB1 and the domains of PAB1 through which these contacts are made.

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Acknowledgments

We would like to thank A. Jacobson for providing HA-tagged versions of UPF1 and the upf1Δ-containing strain. This research was supported by NIH grants GM78087 and GM82048 to C.L.D. and from the ARRA initiative of 2009. Partial funding was provided by the New Hampshire Agricultural Experiment Station to C.L.D. This is Scientific Contribution Number 2450.

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  1. Department of Molecular, Cellular, and Biomedical Sciences, Rudman Hall, University of New Hampshire, Durham, NH, 03824, USA

    Roy Richardson, Clyde L. Denis, Chongxu Zhang, Yueh-Chin Chiang, Xin Wang, Darren J. Lee & Gang Yao

  2. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK, 5230, Denmark

    Maria E. O. Nielsen, Morten Kierkegaard & Jens S. Andersen

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  1. Roy Richardson
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Correspondence to Clyde L. Denis.

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Communicated by T. Ito.

R. Richardson and C. L. Denis contributed equally to this manuscript.

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Richardson, R., Denis, C.L., Zhang, C. et al. Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein. Mol Genet Genomics 287, 711–730 (2012). https://doi.org/10.1007/s00438-012-0709-5

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