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Restricted protein rate of evolution due to splicing constrain

Posted by pbio on 07 May 2009 at 22:16 GMT

Author: Franco Pagani
Position: MD,
Institution: International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
Additional Authors: Francisco, E. , Baralle
Submitted Date: March 27, 2007
Published Date: March 30, 2007
This comment was originally posted as a “Reader Response” on the publication date indicated above. All Reader Responses are now available as comments.

The recent paper by Parmley et al (1) used a bioinformatics approach to test the hypothesis previously put forward by us (2) that the selection acting on splicing regulatory elements may impose some constrains on the rate of protein evolution. The observed lowest rate of evolution near the exon-intron junctions due to putative splicing enhancers, led the Authors to conclude that human proteins may not be optimized as they could, as their sequence is serving two conflicting roles.
These conclusions neatly reproduced those published few years ago by our laboratory (3). In fact the conflict between ensuring splicing efficiency and preserving coding capacity is not a new concept in clinical genetics and evolution and it was suggested to be the molecular explanation of disease splicing susceptibility in human exons. Indeed, we proposed some years ago the idea of a restricted protein rate of evolution due to splicing constrain based on the studies of splicing affecting genomic variants in human disease (2). We stated that the unexpected high coexistence of exonic splicing regulatory elements with amino-acid coding capacity would restrict the evolutionary selection of codon variants that could improve protein function. It follows that at least in a fraction of the exons present in the genome, suboptimal protein function might be tolerated to allow for the persistence of sequences that are essential for exon inclusion. We then experimentally validated this hypothesis by studying the effect on splicing of synonymous and non-synonymous substitutions in mammalian CFTR exon 12 (3, 4). This exon has a human-lineage specific low level of skipping and comparative analysis with the mouse CFTR exon 12 splicing showed that the combination of the mouse synonymous variations with the human missense mutations is incompatible with normal RNA processing. The fact that in mammalian CFTR exon 12 natural synonymous and non synonymous substitutions outside their species-specific context are not tolerated by the splicing machinery confirmed our proposal. The conflict between splicing modulation and protein optimization could explain why CFTR exon 12 is highly susceptible to splicing derangements by several natural and side-directed synonymous and non-synonymous substitutions (3-5). Since then, although not as extensively as the CFTR exon 12 case, another example, the NF 1 exon 37, has been studied experimentally (6).
As our work was not referenced in the Parmley et al paper, we feel that may be an advantage for the PLos readers to be aware of the already available experimental evidences in the literature and of their implications in clinical genetics.

1. Parmley, J.L., Urrutia, A.O., Potrzebowski, L., Kaessmann, H. and Hurst, L.D. (2007) Splicing and the evolution of proteins in mammals. PLoS Biol, 5, e14.
2. Pagani, F. and Baralle, F.E. (2004) Genomic variants in exons and introns: identifying the splicing spoilers. Nat Rev Genet, 5, 389-96.
3. Pagani, F., Raponi, M. and Baralle, F.E. (2005) Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci U S A, 102, 6368-72.
4. Raponi, M., Baralle, F.E. and Pagani, F. (2007) Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12. Nucleic Acids Res, 35, 606-13.
5. Pagani, F., Stuani, C., Tzetis, M., Kanavakis, E., Efthymiadou, A., Doudounakis, S., Casals, T. and Baralle, F.E. (2003) New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12. Hum Mol Genet, 12, 1111-20.
6. Baralle, M., Skoko, N., Knezevich, A., De Conti, L., Motti, D., Bhuvanagiri, M., Baralle, D., Buratti, E. and Baralle, F.E. (2006) NF1 mRNA biogenesis: effect of the genomic milieu in splicing regulation of the NF1 exon 37 region. FEBS Lett, 580, 4449-56.

No competing interests declared.