Understanding the Role of Argininosuccinate Lyase Transcript Variants in the Clinical and Biochemical Variability of the Urea Cycle Disorder Argininosuccinic Aciduria

Hu, Liyan; Pandey, Amit V.; Eggimann, Sandra; Rüfenacht, Véronique; Möslinger, Dorothea; Nuoffer, Jean-Marc; Häberle, Johannes

doi:10.1074/jbc.m113.503128

Cited by 10 publications

(12 citation statements)

References 50 publications

(52 reference statements)

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“…We have previously shown that 293 T cells were an ideal ASL expression system lacking endogenous ASL but allowing for high ectopic ASL expression (Hu et al 2013). Cells were grown, maintained and transiently transfected as described before (Hu et al 2013).…”

Section: Expression Of Asl Constructs In Human Embryonic Kidney 293t mentioning

confidence: 99%

“…Full-length ASL cDNA (1395 bp, RefSeq NM_000048.3) was cloned into the expression vector pcDNA3 (Invitrogen, Carlsbad, CA, USA) at BamHI and NotI restriction sites yielding pcDNA3-ASL-WT (P-WT) as described previously (Hu et al 2013). The mutant plasmids were constructed based on P-WT by site-directed mutagenesis (Phusion Site-directed mutagenesis Kit, Finnzymes, Espoo, Finland) according to manufacturer's protocol.…”

Section: Construction Of Recombinant Asl Mutationsmentioning

confidence: 99%

“…The tetrameric 3D structure of ASL (NCBI NP_000039.2, Uniprot P04424) sequence (AA 1-464) was built using the in-silico mutagenesis of ASL structure (PDB 1 K62) as described previously (Hu et al 2013). Structural mutagenesis was performed with programs YASARA (Krieger et al 2004) and WHATIF (Vriend 1990).…”

Section: D Protein Model and In-silico Mutagenesis Of Aslmentioning

confidence: 99%

“…Cells were grown, maintained and transiently transfected as described before (Hu et al 2013). In brief, 293 T cells were grown in Dulbecco's modified Eagle's medium+GlutaMAX (DMEM, Gibco, Paisley, UK) supplemented with 10 % fetal bovine Secondary structure information was extracted from the known crystal structures of ASL (PDB 1 K62) and figure was created with the program CLC Workbench.…”

Section: Expression Of Asl Constructs In Human Embryonic Kidney 293t mentioning

confidence: 99%

“…In the present study, we use our recently established eukaryotic expression system in human embryonic kidney 293 T cell lysates (Hu et al 2013) to investigate all naturally occurring ASL mutations up until now identified in patients with a variant biochemical or clinical phenotype in an attempt to better understand the cause of the broad variation in ASLD phenotypes. We found evidence for thermal instability as well as low expression levels pointing towards a hampered stability in these mutant ASL proteins, hereby contributing to our understanding of the underlying pathology in a part of ASLD.…”

Section: Introductionmentioning

confidence: 99%

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Unstable argininosuccinate lyase in variant forms of the urea cycle disorder argininosuccinic aciduria

Pandey

Balmer

et al. 2015

J of Inher Metab Disea

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Loss of function of the urea cycle enzyme argininosuccinate lyase (ASL) is caused by mutations in the ASL gene leading to ASL deficiency (ASLD). ASLD has a broad clinical spectrum ranging from life-threatening severe neonatal to asymptomatic forms. Different levels of residual ASL activity probably contribute to the phenotypic variability but reliable expression systems allowing clinically useful conclusions are not yet available. In order to define the molecular characteristics underlying the phenotypic variability, we investigated all ASL mutations that were hitherto identified in patients with late onset or mild clinical and biochemical courses by ASL expression in human embryonic kidney 293 T cells. We found residual activities >3% of ASL wild type (WT) in nine of 11 ASL mutations. Six ASL mutations (p.Arg95Cys, p.Ile100Thr, p.Val178Met, p.Glu189Gly, p.Val335Leu, and p.Arg379Cys) with residual activities ≥16% of ASL WT showed no significant or less than twofold reduced Km values, but displayed thermal instability. Computational structural analysis supported the biochemical findings by revealing multiple effects including protein instability, disruption of ionic interactions and hydrogen bonds between residues in the monomeric form of the protein, and disruption of contacts between adjacent monomeric units in the ASL tetramer. These findings suggest that the clinical and biochemical course in variant forms of ASLD is associated with relevant residual levels of ASL activity as well as instability of mutant ASL proteins. Since about 30% of known ASLD genotypes are affected by mutations studied here, ASLD should be considered as a candidate for chaperone treatment to improve mutant protein stability.

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Section: Expression Of Asl Constructs In Human Embryonic Kidney 293t mentioning

confidence: 99%

Section: Construction Of Recombinant Asl Mutationsmentioning

confidence: 99%

Section: D Protein Model and In-silico Mutagenesis Of Aslmentioning

confidence: 99%

Section: Expression Of Asl Constructs In Human Embryonic Kidney 293t mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Unstable argininosuccinate lyase in variant forms of the urea cycle disorder argininosuccinic aciduria

Pandey

Balmer

et al. 2015

J of Inher Metab Disea

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Molecular Genetics of Argininosuccinic Aciduria

Trevisson

Doimo

Salviati

2014

Encyclopedia of Life Sciences

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Argininosuccinic aciduria is an autosomal recessive disorder of the urea cycle caused by mutations in argininosuccinate lyase ( ASL ). Two main clinical phenotypes are reported: an acute neonatal form characterised by severe hyperammonaemia and coma, and a subacute, late‐onset form which may present with relatively milder neurological symptoms. More than 120 ASL mutations have been reported so far: the majority are missense, but virtually all types of point mutations are found. Large rearrangements are rare and standard genomic deoxyribonucleic acid (DNA) analysis has a high diagnostic yield. Genotype–phenotype correlations have been difficult to establish as standard biochemical techniques are not sufficiently sensitive to measure residual activity, and other factors such as intragenic complementation, overexpression of nonfunctional ASL transcripts and environmental factors may modulate the phenotype. Clinical manifestations result from the block in the urea cycle and also from impairment of nitric oxide biosynthesis, and the therapy is aimed at restoring these two functions. Key Concepts: Argininosuccinic aciduria is caused by deficiency of argininosuccinate lyase (ASL). ASL is a component of the urea cycle and is essential for detoxification of ammonia, and for the synthesis of arginine and nitric oxide (NO). Two clinical forms of argininosuccinic aciduria exist: an acute, potentially lethal, neonatal onset disease and a milder, late‐onset form. More than 120 ASL mutations have been described but the exact genotype/phenotype correlations are still not completely clear. Other factors (genetic and environmental) may influence the clinical phenotype. Treatment is based on protein restriction, arginine, nitrogen scavengers and NO donors.

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Identification of compound–protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds

et al. 2016

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Compound-protein interactions play important roles in every cell via the recognition and regulation of specific functional proteins. The correct identification of compound-protein interactions can lead to a good comprehension of this complicated system and provide useful input for the investigation of various attributes of compounds and proteins. In this study, we attempted to understand this system by extracting properties from both proteins and compounds, in which proteins were represented by gene ontology and KEGG pathway enrichment scores and compounds were represented by molecular fragments. Advanced feature selection methods, including minimum redundancy maximum relevance, incremental feature selection, and the basic machine learning algorithm random forest, were used to analyze these properties and extract core factors for the determination of actual compound-protein interactions. Compound-protein interactions reported in The Binding Databases were used as positive samples. To improve the reliability of the results, the analytic procedure was executed five times using different negative samples. Simultaneously, five optimal prediction methods based on a random forest and yielding maximum MCCs of approximately 77.55 % were constructed and may be useful tools for the prediction of compound-protein interactions. This work provides new clues to understanding the system of compound-protein interactions by analyzing extracted core features. Our results indicate that compound-protein interactions are related to biological processes involving immune, developmental and hormone-associated pathways.

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Understanding the Role of Argininosuccinate Lyase Transcript Variants in the Clinical and Biochemical Variability of the Urea Cycle Disorder Argininosuccinic Aciduria

Cited by 10 publications

References 50 publications

Unstable argininosuccinate lyase in variant forms of the urea cycle disorder argininosuccinic aciduria

Unstable argininosuccinate lyase in variant forms of the urea cycle disorder argininosuccinic aciduria

Molecular Genetics of Argininosuccinic Aciduria

Identification of compound–protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds

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