Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease

In eukaryotes, precise pre-mRNA processing, including alternative splicing, is essential to carry out the intricate protein translation process. Both point mutations (that alter the translated protein sequence) and synonymous mutations (that do not alter the translated protein sequence) are capable of affecting the splicing process. Synonymous mutations are known to affect gene expression via altering mRNA stability, mRNA secondary structure, splicing processes, and translational kinetics. In higher eukaryotes, precise splicing is regulated by three weakly conserved cis-elements, 5' and 3' splice sites and the branch site. Many other cis-acting elements (exonic/intronic splicing enhancers and silencers) and trans-acting splicing factors (serine and arginine-rich proteins and heterogeneous nuclear ribonucleoproteins) have also been found to enhance or suppress the splicing process. The appearance of synonymous mutations in cis-acting elements can alter the splicing process by changing the binding pattern of splicing factors to exonic splicing enhancers or silencer motifs. This results in exon skipping, intron retention, and various other forms of alternative splicing, eventually leading to the emergence of a wide range of diseases. The focus of this review is to elucidate the role of synonymous mutations and their impact on abnormal splicing mechanisms. Further, this study highlights the function of synonymous mutation in mediating abnormal splicing in cancer and development of X-linked, and autosomal inherited diseases.

New KEL*01M and KEL*02M alleles: structural modeling to assess the impact of amino acid changes

BACKGROUND

The KELL antigens are carried by the well-folded and highly polymorphic glycoprotein KELL, belonging to the M13 family of metalloproteases. Anti-KEL, particularly anti-KEL1, are clinically significant. We retrospectively investigated genomic DNA from samples with uncertain KEL1 or KEL2 phenotype and identified six novel Kmod alleles. We then considered a model of the protein three-dimensional (3D) structure to assess the impacts of the amino acid changes.

STUDY DESIGN AND METHODS

The 19 exons of the KEL gene were polymerase chain reaction amplified and sequenced. Modeling was performed using the experimental 3D structure of human endothelin-converting enzyme-1 in the presence of the metabolite phosphoramidon.

RESULTS

We identified four novel KEL*01M alleles with amino acid substitutions p.Arg447Trp, p.Gly641Arg, p.Ala645Val, and p.Gly703Arg found buried within helices of the ectodomain catalytic lobe. We also revealed one new KEL*02M allele with p.Gly263Glu in contact with solvent (water) located within the second lobe of the ectodomain. One sample with c.575G>C transversion (p.Arg192Pro) on a KEL*02 background showed a weakened reactivity for KEL1. According to our 3D modeling, these amino acid substitutions may have a profound impact on the protein structure.

CONCLUSION

This study is especially interesting with regard to the description of four new KEL*01M alleles. Indeed, to date only two KEL*01M alleles have been described and our data suggest a nonnegligible incidence of KEL1 variants. Serologic KEL2-negative results as well as any ambiguity implying either KEL1 or KEL2 in donors should always be confirmed by means of genotyping analysis and discrepancies between these methods require sequencing of KEL gene.

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

SCOPE

Synonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health.

PURPOSE

This synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics.

PHYSIOLOGICAL AND MEDICAL RELEVANCE

Understanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.

Novel alleles at the Kell blood group locus that lead to Kell variant phenotype in the Dutch population

BACKGROUND

Alloantibodies directed against antigens of the Kell blood group system are clinically significant. In the Netherlands, the KEL1 antigen is determined in all blood donors. In this study, after phenotyping of KEL:1-positive donors, genotyping analysis was conducted in KEL:1,-2 donors to identify possible KEL*02 variant alleles.

STUDY DESIGN AND METHODS

A total of 407 donors with the KEL:1,-2 phenotype were genotyped for the KEL*01/02 polymorphism, followed by direct sequencing of the KEL gene if the KEL*02 allele was detected. Two K0 patients were also included. Transcript analysis was conducted in two probands with the KEL*02. M05 allele defined by a synonymous mutation (G573G). Flow cytometry analysis to determine the expression of Kell antigen was performed.

RESULTS

Thirty KEL:1,-2 individuals (30/407, 7.4%) with discrepant KEL*01/02 genotype were identified. Seven novel alleles were identified: KEL*02(R86Q, R281W)mod, KEL*02(L133P)null, KEL*02(436delG)null, KEL*02(F418S)null, KEL*02(R492X)null, KEL*02(L611R)null, and KEL*02(R700X)null. Nine variant alleles described before were detected: KEL*02N.06, KEL*02N.15, KEL*02N.17, KEL*02N.19, KEL*02N.21, KEL*02M.02, KEL*02M.04, KEL*02M.05, and KEL*02(Q362K)mod. A transcript lacking Exon 16 was identified in two probands with the KEL*02M.05 allele as described before. Finally, flow cytometry analysis showed a decreased total Kell expression and a relatively increased KEL1 expression in individuals with the KEL:1,2null or KEL:1,2mod phenotype, compared to KEL:1,2 controls.

CONCLUSION

In 7.4% of a group of tested KEL:1,-2 Dutch donors, a KEL*02null or KEL*02mod allele was found. A relatively increased KEL1 antigen expression in KEL:1,2null and KEL:1,2mod individuals suggest that the expression of Kell-XK complexes depends on the availability of the XK protein.