A plant biologist’s toolbox to study translation
- 1Plant and Microbial Biology, Program in Genetics, North Carolina State University, United States
Across a broad range of species and biological questions, more and more studies are incorporating translation data to better assess how gene regulation occurs at the level of protein synthesis. The inclusion of translation data improves upon, and has been shown to be more accurate than, transcriptional studies alone. However, there are many different techniques available to measure translation and it can be difficult, especially for young or aspiring scientists, to determine which methods are best applied in specific situations. We have assembled this review in order to enhance the understanding and promote the utilization of translational methods in plant biology. We cover a broad range of methods to measure changes in global translation (e.g., radiolabeling, polysome profiling, or puromycylation), translation of single genes (e.g., fluorescent reporter constructs, toeprinting, or ribosome density mapping), sequencing-based methods to uncover the entire translatome (e.g., Ribo-seq, or TRAP), and mass spectrometry-based methods to identify changes in the proteome (e.g., SILAC or BONCAT). The benefits and limitations of each method are discussed with a particular note of how applications from other model systems might be extended for use in plants. In order to make this burgeoning field more accessible to students and newer scientists, our review includes an extensive glossary to define key terms.
Keywords: translation, ribosome, Ribo-seq, TRAP, polysome profiling, toeprinting, reporter, amino acid tagging
Received: 27 Mar 2018;
Accepted: 04 Jun 2018.
Edited by:Philippe Giegé, Centre national de la recherche scientifique (CNRS), France
Reviewed by:Rémy MERRET, UMR5096 Laboratoire Génome et développement des plantes, France
Etienne Delannoy, UMR9213 Institut des Sciences des Plantes de Paris Saclay (IPS2), France
Copyright: © 2018 Mazzoni-Putman and Stepanova. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Anna N. Stepanova, North Carolina State University, Plant and Microbial Biology, Program in Genetics, 112 Derieux Place, Campus Box 7614, Raleigh, 27695-7614, NC, United States, firstname.lastname@example.org