Meta-Biol

• Pathways

Neutral and basic amino acid transport protein rBAT (SLC3A1) and b(0,+)-type amino acid transporter 1 (SLC7A9) are linked by a disulfide bridge to form system b(0,+)-like activity in the high affinity transport of neutral and dibasic amino acids and cystine. The SLC7A9:SLC3A1 heterodimer mediates the electrogenic exchange of extracellular amino acids such as L-arginine (L-Arg) and L-lysine (L-lys) and cystine (CySS-, the oxidised form of L-cysteine) for intracellular neutral amino acids such as L-leucine (L-Leu). These solute carriers are mainly expressed in the kidney and small intestine where they remove dibasic amino acids and cystine from the renal tubular and intestinal lumen respectively (Schweikhard & Ziegler 2012). Defects in SLC3A1 (or SLC7A9) can cause cystinuria (CSNU; MIM:220100), an autosomal recessive disorder characterised by impaired epithelial cell transport of cystine and dibasic amino acids in the proximal renal tubule and GI tract. The build-up and low solubility of cystine causes the formation of calculi in the urinary tract, resulting in obstructive uropathy, pyelonephritis and in severe cases, renal failure (Palacin et al. 2001, Mattoo & Goldfarb 2008, Fotiadis et al. 2013, Saravakos et al. 2014). Cystinuria is subcategorized as type A (mutations on SLC3A1) and type B (mutations on SLC7A9).

Proteins with transporting functions can be roughly classified into 3 categories: ATP hydrolysis-coupled pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of substrates across the membrane against their electrochemical gradient. Channels in their open state can transfer substrates (ions or water) down their electrochemical gradient at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate either against or with their concentration gradient at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process. Diseases caused by defects in these transporter proteins are detailed in this section. Disorders associated with ABC transporters and SLC transporters are annotated here (Dean 2005).

Biological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular viewpoint, human disease pathways have three mechanistic causes: the inclusion of microbially-expressed proteins, altered functions of human proteins, or changed expression levels of otherwise functionally normal human proteins.

The first group encompasses the infectious diseases such as influenza, tuberculosis and HIV infection. The second group involves human proteins modified either by a mutation or by an abnormal post-translational event that produces an aberrant protein with a novel function. Examples include somatic mutations of EGFR and FGFR (epidermal and fibroblast growth factor receptor) genes, which encode constitutively active receptors that signal even in the absence of their ligands, or the somatic mutation of IDH1 (isocitrate dehydrogenase 1) that leads to an enzyme active on 2-oxoglutarate rather than isocitrate, or the abnormal protein aggregations of amyloidosis which lead to diseases such as Alzheimer's.

Infectious diseases are represented in Reactome as microbial-human protein interactions and the consequent events. The existence of variant proteins and their association with disease-specific biological processes is represented by inclusion of the modified protein in a new or variant reaction, an extension to the 'normal' pathway. Diseases which result from proteins performing their normal functions but at abnormal rates can also be captured, though less directly. Many mutant alleles encode proteins that retain their normal functions but have abnormal stabilities or catalytic efficiencies, leading to normal reactions that proceed to abnormal extents. The phenotypes of such diseases can be revealed when pathway annotations are combined with expression or rate data from other sources.

Depending on the biological pathway/process immediately affected by disease-causing gene variants, non-infectious diseases in Reactome are organized into diseases of signal transduction by growth factore receptors and second messengers, diseases of mitotic cell cycle, diseases of cellular response to stress, diseases of programmed cell death, diseases of DNA repair, disorders of transmembrane transporters, diseases of metabolism, diseases of immune system, diseases of neuronal system, disorders of developmental biology, disorders of extracellular matrix organization, and diseases of hemostatis.