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Ribosome profiling provides novel insights into translation dynamics in bacteria

Brinkman, Lester (2019) Ribosome profiling provides novel insights into translation dynamics in bacteria. Colloquium, Molecular Biology and Biotechnology.

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Abstract

Ribosome profiling provides a snapshot of mRNA’s which are actively being translated. This technique has been revived in the last decade through the upcoming of next generation sequencing. In short, ribosome occupancy on mRNA’s is determined by sequencing ribosome-protected mRNA fragments1. Also, by using specific nucleases, the mRNA footprint can now be determined to a single nucleotide resolution in eukaryotes, yielding reading frame information. Due to available ribosome inhibitors for eukaryotes, stalling ribosomes at the translation initiation site could be investigated2. This confirmed that protein isoforms can be formed by alternative in-frame initiation sites. Also regulatory roles for short open reading frames were discovered. In prokaryotes, the development of ribosome profiling lagged behind, among other things because ribosome inhibitors were lacking. Recently however, specific ribosome inhibitors have been identified that stall prokaryotic ribosomes at the initiation site, leading to the systematic investigation of translation initiation sites in E. coli3,4. These studies showed that alternative translation initiation evens occur, both within and outside of annotated open reading frames. While some of these alternative initiation events produced protein isoforms, others contain regulatory functions. Furthermore small open reading frames were discovered to be translated. However due to their small size, functional analysis of small proteins is often complicated, leaving a cryptic function for a large fraction of these small proteins. References: 1. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S. & Weissman, J. Genome-Wide Analysis in Vivo of Translation with nucleotide resolution using Ribosome profiling. Science (80-. ). 324, 218–324 (2009). 2. Ingolia, N. T., Lareau, L. F. & Weissman, J. S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789–802 (2011). 3. Meydan, S. et al. Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol. Cell 74, 1–13 (2019). 4. Weaver, J., Mohammad, F., Buskirk, A. R. & Storz, G. Identifying Small Proteins by Ribosome Profiling with Stalled initiation complexes. Mol. Biol. Physiol. 10, e02819-18 (2019).

Item Type: Thesis (Colloquium)
Supervisor:
Supervisor nameSupervisor E mail
Linskens, M.H.K.M.H.K.Linskens@rug.nl
Degree programme: Molecular Biology and Biotechnology
Thesis type: Colloquium
Language: English
Date Deposited: 27 May 2019
Last Modified: 14 Jun 2019 09:57
URI: http://fse.studenttheses.ub.rug.nl/id/eprint/19538

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