The genetic code as expressed through relationships between mRNA structure and protein function

Abstract

Structured RNA elements within messenger RNA often direct or modulate the cellular production of active proteins. As reviewed here, RNA structures have been discovered that govern nearly every step in protein production: mRNA production and stability; translation initiation, elongation, and termination; protein folding; and cellular localization. Regulatory RNA elements are common within RNAs from every domain of life. This growing body of RNA-mediated mechanisms continues to reveal new ways in which mRNA structure regulates translation. We integrate examples from several different classes of RNA structure-mediated regulation to present a global perspective that suggests that the secondary and tertiary structure of RNA ultimately constitutes an additional level of the genetic code that both guides and regulates protein biosynthesis.

RNA secondary structure modeling at consistent high accuracy using differential SHAPE

“…of RNA structure and RNA-ligand interactions in most phases of gene regulation (Mauger et al 2013). Moreover, an accurate secondary structure model is critical for and can dramatically facilitate tertiary structure modeling (Hajdin et al 2010;Bailor et al 2011).…”

“…Defining the secondary structure of an RNA is also a critical first step in tertiary structure modeling (Hajdin et al 2010;Weeks 2010;Bailor et al 2011). The structures of RNA molecules modulate the numerous functions of RNA and the interactions of RNAs with proteins, small molecules, and other RNAs in splicing, translation, and other regulatory machineries (Mauger et al 2013). …”

Imaging Genetic Information

“…Second, RNA is produced in a single-strand form, as opposed to a double-strand form, making it more accessible to a simple complementary antisense probe. While it is produced in a single-strand form, self-complementary sequences within the RNA form duplexes leading to a folded structure, much of which would be inaccessible to an antisense probe [36,37]. RNA also associates with proteins [38], which would also limit its accessibility to an antisense probe and also be initially produced and sequestered within the nucleus or mitochondria.…”

The many faces of proteins

“…Four contributions cover RNA-related topics [24][25][26][27]. RNA structures are known to govern nearly every step in protein synthesis [24].…”

“…RNA structures are known to govern nearly every step in protein synthesis [24]. Recent work suggested that some ribosomal subpopulations may have the property to influence the functions of the proteins they produce, and specific ribosomes were engineered to allow discrimination between different mRNA templates or with unique decoding properties [25].…”