Analysis of Alkaptonuria (AKU) Mutations and Polymorphisms Reveals that the CCC Sequence Motif Is a Mutational Hot Spot in the Homogentisate 1,2 Dioxygenase Gene (HGO)

Abstract

We recently showed that alkaptonuria (AKU) is caused by loss-of-function mutations in the homogentisate 1,2 dioxygenase gene (HGO). Herein we describe haplotype and mutational analyses of HGO in seven new AKU pedigrees. These analyses identified two novel single-nucleotide polymorphisms (INV4+31A-->G and INV11+18A-->G) and six novel AKU mutations (INV1-1G-->A, W60G, Y62C, A122D, P230T, and D291E), which further illustrates the remarkable allelic heterogeneity found in AKU. Reexamination of all 29 mutations and polymorphisms thus far described in HGO shows that these nucleotide changes are not randomly distributed; the CCC sequence motif and its inverted complement, GGG, are preferentially mutated. These analyses also demonstrated that the nucleotide substitutions in HGO do not involve CpG dinucleotides, which illustrates important differences between HGO and other genes for the occurrence of mutation at specific short-sequence motifs. Because the CCC sequence motifs comprise a significant proportion (34.5%) of all mutated bases that have been observed in HGO, we conclude that the CCC triplet is a mutational hot spot in HGO.

Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database

“…In case of so far unpublished mutations, in the figure "HGD variants schematic" only the type of mutation is indicated. HGD haplotypes associated with AKU mutations were constructed based on the analysis of seven single nucleotide polymorphisms and three dinucleotide repeats as reported before (Beltrán-Valero de Bernabé et al 1999;Zatkova et al 2000a). …”

“…In the database was included a column indicating an involvement of the mutation hot-spots ("CCC"triplets, c.342+1G, CpG) that have been identified within HGD gene (Beltrán-Valero de Bernabé et al 1999;Zatkova et al 2000a). A creation or abolition of recognition site of some common restriction enzymes is included for easy identification of each mutation (Fig.…”

“…By reexamination of the mutations and polymorphisms reported in HGD by 1999, Beltrán-Valero de Bernabé et al showed that the "CCC" sequence motif and its inverted complement, "GGG" are preferentially mutated (Beltrán-Valero de Bernabé et al 1999). Subsequently, nucleotide c.342+1G was also described as a mutational hotspot in HGD (Zatkova et al 2000a).…”

Properties and Function of Pyomelanin

“…In addition, deletion of the gene that encodes for HGA-oxidase results in hyper production of pyomelanin while deletion of the gene that encodes for 4-HPPD results in the inability to produce pyomelanin (Coon et al 1994;Ruzafa et al 1995). In humans with loss-of-function mutations in HGA-oxidase, pyomelanin (also known as alkapton or ochronotic pigment) forms in the urine due to the spontaneous auto oxidation of excess HGA (Beltrán-Valero de Bernabé, et al 1999). This condition is known as alkaptonuria in humans and can result in arthritis in adults.…”

A Founder Effect for the HGD G360R Mutation in Italy: Implications for a Regional Screening of Alkaptonuria

“…Subsequently, another ten compound heterozygous patients were reported to carry G360R (Grasko et al 2009;Vilboux et al 2009;Usher et al 2015). Since G360R takes place in a G run, a sequence motif known as a mutational hot spot in HGD (Beltrán-Valero de Bernabé et al 1999), referral of two large, apparently unrelated, South Tyrolean AKU families, has recently renewed our interest in the origin and spread of G360R mutation among populations of European ancestry.…”