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Determining the mechanism of elongation factor P -dependent regulation of gene expression

Elgamal, Sara
http://orcid.org/0000-0003-2274-9891
http://rave.ohiolink.edu/etdc/view?acc_num=osu1448624003

Abstract Details

2015, Doctor of Philosophy, Ohio State University, Microbiology.
Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the efp deficient strain, with up to a 45-fold increase in ribosome density observed at the pausing site. The unexpectedly low fraction of PPX motifs that produce a pause in translation led us to investigate the possible role of sequences upstream of PPX. Our data indicate that EF-P dependent pauses are strongly affected by sequences upstream of the PPX pattern. We found that residues as far as 3 codons upstream of the ribosomal peptidyl-tRNA site had a dramatic effect on whether or not a particular PPX motif triggered a ribosomal pause, while internal Shine Dalgarno sequences upstream of the motif had no effect on EF-P dependent translation efficiency. Increased ribosome occupancy at particular stall sites did not reliably correlate with a decrease in total protein levels, suggesting that in many cases other factors compensate for the potentially deleterious effects of stalling on protein synthesis. These findings indicate that the ability of a given PPX motif to initiate an EF-P-alleviated stall is strongly influenced by its local context, and that other indirect post-transcriptional effects determine the influence of such stalls on protein levels within the cell.
Michael Ibba, Dr. (Advisor)
Irina Artsimovitch, Dr. (Committee Member)
Kurt Fredrick, Dr. (Committee Member)
Jane Jackman, Dr. (Committee Member)
135 p.
Biochemistry; Genetics; Microbiology
Elongation factor P; Ribosome profiling; Protein Translation; pausing; Proline

Recommended Citations

Citations

  • Elgamal, S. (2015). Determining the mechanism of elongation factor P -dependent regulation of gene expression [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1448624003

    APA Style (7th edition)

  • Elgamal, Sara. Determining the mechanism of elongation factor P -dependent regulation of gene expression. 2015. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1448624003.

    MLA Style (8th edition)

  • Elgamal, Sara. "Determining the mechanism of elongation factor P -dependent regulation of gene expression." Doctoral dissertation, Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1448624003

    Chicago Manual of Style (17th edition)

osu1448624003
377
© 2015, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.