How pairs of proteins collaborate to splice RNAs into cell-specific products

How pairs of proteins collaborate to splice RNAs into cell-specific products
Figure 1: Illustration depicting the binding mechanism for RNA-recognition motifs (RRMs) of ASD-1 (tan) and SUP-12 (cyan) with the EGL-15 mRNA (pink). The sandwiched guanine nucleotide is shown as a solid pink circle. Credit: Yutaka Muto, RIKEN Center for Life Science Technologies

A team of scientists led by RIKEN researcher Yutaka Muto, in collaboration with Hidehito Kuroyanagi of Tokyo Medical and Dental University and Masatoshi Hagiwara of Kyoto University, has revealed some of the mechanisms that regulate the mysterious RNA splicing process that produces specific protein variants.

Gene expression involves transcription of DNA to messenger RNA (mRNA) followed by translation of mRNA into proteins. Although each gene is coded to produce a single corresponding protein, a mechanism known as alternative makes it possible for mRNA to be translated into any number of different proteins. Each mRNA transcript consists of numerous protein-coding 'exon' segments separated by non-coding 'intron' segments. Alternative splicing is a regulated process in which splicing proteins selectively target different combinations of exons to produce a variety of possible proteins. 

Many splicing proteins rely on elements known as RNA-recognition motifs (RRMs) to recognize target sequences within mRNA introns. Yet these RNA-recognition motifs are very similar to one another, and it has remained unclear exactly how splicing proteins achieve their remarkable selectivity.

Muto, a scientist from the RIKEN Center for Life Science Technologies and Musashino University who started this research while at the recently reorganized RIKEN Systems and Structural Biology Center, focused his team's attention on a pair of proteins, ASD-1 and SUP-12. These proteins are known to collaboratively coordinate alternative splicing of the mRNA encoding the signaling EGL-15 in the worm species Caenorhabditis elegans. EGL-15 undergoes a distinctive splicing event in muscle tissue that contributes critically to sexual development. ASD-1 is expressed throughout the worm's body, whereas SUP-12 is only produced in muscle tissue.

The researchers determined that SUP-12 RRM is not very selective on its own, but gets steered by ASD-1 RRM to the appropriate 12-nucleotide target sequence within the egl-15 mRNA. Detailed structural analysis using nuclear magnetic resonance (NMR) techniques revealed that ASD-1 RRM binding initiates a rearrangement in the RNA that favors SUP-12 RRM binding, resulting in a distinctive complex in which a single guanine nucleotide is essentially wedged between the two proteins (Fig. 1). Altering this single nucleotide was sufficient to eliminate the muscle-specific alternative splicing of EGL-15.

"There have been many reports that multiple splicing regulators cooperate for accurate splicing on a biochemical level, but our work is the first structural explanation for the cooperation between splicing regulatory factors at atomic resolution," says Muto. His team hopes to further determine whether such mechanisms are a general feature of cooperative scenarios. "We would like to advance our structural analysis to take into account the dynamic changes in the structure of the RNA molecule," says Muto.

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More information: Kuwasako, K., Takahashi, M., Unzai, S., Tsuda, K., Yoshikawa, S., He, F., Kobayashi, N., Güntert, P., Shirouzu, M., Ito, T. et al. "RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing." Nature Structural & Molecular Biology  21, 778–786 (2014). DOI: 10.1038/nsmb.2870
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Citation: How pairs of proteins collaborate to splice RNAs into cell-specific products (2014, October 17) retrieved 18 June 2019 from
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Oct 17, 2014
See also: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes."

Also see:

Alternative RNA Splicing in Evolution: http://jonlieffmd...volution

Oct 18, 2014

Excerpt 1) "Alternative splicing (AS), in eukaryotes, is one of the mechanisms of post-transcriptional regulation that generate multiple transcripts from the same gene. These transcripts are then translated into multiple proteins having diverse biological functions."

Excerpt 2) "...the process exploits the dynamic composition of splicing factors under various cell lines or developmental stages to have flexible intermolecular interactions such as protein-RNA, RNA-RNA, and protein-protein interactions [10], [11], [12].

From atoms to ecosystems, nothing known about physics, chemistry, or molecular biology suggests that mutations and/or natural selection lead to the evolution of biodiversity via the conserved molecular mechanisms of nutrient-dependent RNA-mediated amino acid substitutions and protein-protein interactions.

Oct 18, 2014
Instead, all interactions are nutrient-dependent and all are controlled by the metabolism of nutrients to species-specific pheromones, which control the physiology of reproduction.

For examples, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

The model links atoms to ecosystems without the pseudoscientific nonsense of evolutionary theory and details how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms that link ecological variation to ecological adaptations.

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