Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function.

BACKGROUND: Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each family makes it a major task to identify new family members and to provide basis for prediction of enzyme function. A fast and reliable method for de novo annotation of genes encoding carbohydrate-active enzymes is to identify conserved peptides in the curated enzyme families followed by matching of the conserved peptides to the sequence of interest as demonstrated for the glycosyl hydrolase and the lytic polysaccharide monooxygenase families. This approach not only assigns the enzymes to families but also provides functional prediction of the enzymes with high accuracy. RESULTS: We identified conserved peptides for all enzyme families in the CAZy database with Peptide Pattern Recognition. The conserved peptides were matched to protein sequence for de novo annotation and functional prediction of carbohydrate-active enzymes with the Hotpep method. Annotation of protein sequences from 12 bacterial and 16 fungal genomes to families with Hotpep had an accuracy of 0.84 (measured as F1-score) compared to semiautomatic annotation by the CAZy database whereas the dbCAN HMM-based method had an accuracy of 0.77 with optimized parameters. Furthermore, Hotpep provided a functional prediction with 86% accuracy for the annotated genes. Hotpep is available as a stand-alone application for MS Windows. CONCLUSIONS: Hotpep is a state-of-the-art method for automatic annotation and functional prediction of carbohydrate-active enzymes.

Isolated 2-methylbutyrylglycinuria caused by short/branched-chain acyl-CoA dehydrogenase deficiency: identification of a new enzyme defect, resolution of its molecular basis, and evidence for distinct acyl-CoA dehydrogenases in isoleucine and valine metabolism.

Acyl-CoA dehydrogenase (ACAD) defects in isoleucine and valine catabolism have been proposed in clinically diverse patients with an abnormal pattern of metabolites in their urine, but they have not been proved enzymatically or genetically, and it is unknown whether one or two ACADs are involved. We investigated a patient with isolated 2-methylbutyrylglycinuria, suggestive of a defect in isoleucine catabolism. Enzyme assay of the patient's fibroblasts, using 2-methylbutyryl-CoA as substrate, confirmed the defect. Sequence analysis of candidate ACADs revealed heterozygosity for the common short-chain ACAD A625 variant allele and no mutations in ACAD-8 but a 100-bp deletion in short/branched-chain ACAD (SBCAD) cDNA from the patient. Our identification of the SBCAD gene structure (11 exons; >20 kb) enabled analysis of genomic DNA. This showed that the deletion was caused by skipping of exon 10, because of homozygosity for a 1228G-->A mutation in the patient. This mutation was not present in 118 control chromosomes. In vitro transcription/translation experiments and overexpression in COS cells confirmed the disease-causing nature of the mutant SBCAD protein and showed that ACAD-8 is an isobutyryl-CoA dehydrogenase and that both wild-type proteins are imported into mitochondria and form tetramers. In conclusion, we report the first mutation in the SBCAD gene, show that it results in an isolated defect in isoleucine catabolism, and indicate that ACAD-8 is a mitochondrial enzyme that functions in valine catabolism.

Immunoglobulin and complement studies in children with Schönlein-Henoch Syndrome and other vasculitic diseases.

In 35 children with Schönlein-Henoch Syndrome (SHS) serum IgG, IgM, and IgA concentrations were increased in 15%, 21%, and 44% of cases, respectively. Seven children with other vasculitic syndromes (VS) had normal serum Ig concentrations. Serum concentration of IgG subclass IgG1 was increased in 72% of children with SHS and 57% with VS. In SHS this was related to the presence of arthritis, but inversely related to nephritic symptoms. Only a few children had IgG subclasses IgG2, IgG3, or IgG4 concentrations outside the normal ranges. Platelet associated Ig (PAIg) was found in 75% of children with SHS or VS. In SHS the identification of increased amounts of PAIgG was related to the presence of nephritis. The serum concentration of properdin, a component of the alternative complement system, was reduced in 21% of children with SHS. This was related to the presence of abdominal symptoms or nephritis. No cases of retinal vasculitis was observed, but 4 of 22 children with SHS had punctuate retinal haemorrhages. SHS and VS may be clinical variations of the same syndrome. The immunological aspects indicate a close relationship with autoimmune diseases.

Screening for Down's syndrome using an iso-risk curve based on maternal age and serum alpha-fetoprotein level.

On the basis of the significantly different distributions of maternal serum alpha-fetoprotein (AFP) levels in 86 pregnancies associated with fetal Down's syndrome and in 2018 unaffected pregnancies, an iso-risk curve for Down's syndrome was constructed. An iso-risk curve shows, for women of all ages, which combinations of maternal age and level of maternal serum AFP result in the same risk of carrying a fetus with Down's syndrome. A 1:400 risk of Down's syndrome, corresponding to the risk of a 35-year-old woman, was chosen as the lowest risk indicating referral for amniocentesis. If all women, irrespective of their age, are offered amniocentesis, when their risk of carrying a Down's syndrome fetus is 1:400 or higher, 53% of the affected fetuses can be detected as compared with 28% of the affected fetuses diagnosed at present in women above 35 years of age.

The impact of legal termination of pregnancy and of prenatal diagnosis on the birth prevalence of Down syndrome in Denmark.

A considerable reduction in number of livebirths for mothers over 35 was observed in Denmark from 1960 to 1980. Birthrates for those aged 35-39 fell by 58.8%, for those aged 40-44 by 78%. In 1979-1980 100 infants with Down syndrome were born among 116757 newborns, a birth prevalence of 0.86 per 1000, which was significantly lower than the incidence of 1.17 per 1000 when the prenatally diagnosed cases were included. The reduction was noticeable for the age group over 35 where it fell to 1.89 per 1000 for mothers 35-39 and 6.48 per 1000 for mothers over 40. The utilization of prenatal diagnosis was 72 per 100 livebirths for women 35 and older in the Copenhagen area and 56 per 100 livebirths for the rest of the country, with differences in different areas. The number of induced abortions for women 35 years and older was 9265 against 6597 livebirths. The estimated number of Down syndrome cases averted by unrestricted abortion was 61, twice the number prevented by amniocentesis (31), with the greatest impact for mothers over 40. An increased risk of Down syndrome for the age group 35-39 was observed when liveborn and prenatal cases were considered together showing an incidence of 6.89 per 1000, with the highest incidence in the Copenhagen area, 8.70 per 1000, more than double the incidence of 3.04 observed in Copenhagen from 1960 to 1971, for the same age group.

Familial inversion translocation (8;13) with partial trisomy 13 in several family members.

A partial trisomy 13q was observed in siblings with hexadactylia, hypertelorism, hemangioma and severe psychomotor retardation. It originated from a maternal inversion translocation 46,XX,inv(8)(q23q241),t(8;13)(q241;q32). The family showed a pedigree pattern typical for the segregation of a chromosomal translocation. In spite of this the diagnosis was delayed several years, because the bands involved from the two chromosomes were of great similarity. This stresses the importance of reinvestigating families with a clinical suspicion of a chromosomal syndrome, preferentially with prometaphase chromosomes. The identification of a chromosomal rearrangement is essential for genetic counselling and prenatal diagnosis.