Open AccessA streamlined ribosome profiling protocol for the characterization of microorganisms
Author(s) -
Haythem Latif,
Richard Szubin,
Jiaying Tan,
Elizabeth Brunk,
Anna Lechner,
Karsten Zengler,
Bernhard Ø. Palsson
Publication year - 2015
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/000114302
Subject(s) - computational biology , profiling (computer programming) , ribosome profiling , ribosome , biology , genetics , computer science , rna , gene , operating system
Ribosome profiling is a powerful tool for characterizing in vivo protein translation at the genome scale, with multiple applications ranging from detailed molecular mechanisms to systems-level predictive modeling. Though highly effective, this intricate technique has yet to become widely used in the microbial research community. Here we present a streamlined ribosome profiling protocol with reduced barriers to entry for microbial characterization studies. Our approach provides simplified alternatives during harvest, lysis, and recovery of monosomes and also eliminates several time-consuming steps, in particular size-selection steps during library construction. Furthermore, the abundance of rRNAs and tRNAs in the final library is drastically reduced. Our streamlined workflow enables greater throughput, cuts the time from harvest to the final library in half (down to 3-4 days), and generates a high fraction of informative reads, all while retaining the high quality standards of the existing protocol.