Meta-Biol

• Pathways

There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-glutamine cycle.

The SLC1 gene family includes five high-affinity glutamate transporters encoded by SLC1, 2, 3, 6 and 7. These transporters can mediate transport of L-Glutamate (L-Glu), L-Aspartate (L-Asp) and D-Aspartate (D-Asp) with cotransport of 3 Na+ ions and H+ and antiport of a K+ ion. This mechanism allows glutamate into cells against a concentration gradient. This is a crucial factor in the protection of neurons against glutamate excitotoxicity (the excitation of nerve cells to their death) in the CNS (Zhou & Danbolt 2014).

SLC1A1 encodes an excitatory amino-acid carrier 1 (EAAC1, also called EAAT3) and is abundant particularly in brain but also in kidney, liver, muscle, ovary, testis and in retinoblastoma cell lines. In the kidney, SLC1A1 is present at apical membranes of proximal tubes where it serves as a major route of glutamate and aspartate reuptake from urine. Defects in SLC1A1 are the cause of dicarboxylic aminoaciduria (DCBXA; MIM:222730), an autosomal recessive glutamate-aspartate transport defect in the kidney and intestine (Bailey et al. 2011). Mutations that can cause DCBXA are R445W and I395del (Bailey et al. 2011).

A defect in SLC1A1 is also implicated in schizophrenia 18 (SCZD18; MIM:615232). Schizophrenia (SCZD; MIM:181500) is a complex, multifactorial psychotic disorder characterised by disturbances in the form and content of thought, in mood, in sense of self and relationship to the external world and in behaviour. It ranks amongst the world's top 10 causes of long-term disability. At the neuropathological level, SCZD appears to be characterised by synaptic deficits, alterations in glutamate and dopamine neurotransmission and hypofrontality (a state of decreased cerebral blood flow (CBF) in the prefrontal cortex of the brain). Variations in the SLC1A1 gene can confer susceptibility to SCZD18 (Harris et al. 2013). In the remote Pacific island of Palau, the risk of SCZD is 2-3 times the worldwide rate. In a 5-generation Palauan family, an 84kb deletion was carried by psychosis patients and proposed to increase the disease risk more than 18-fold for family members (Myles-Worsley et al. 2013).

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.