since the discovery of the fragile x mental retardation 1 ( fmr1 ) gene in 1991 , our knowledge of the molecular mechanisms underlying fragile x syndrome ( fxs ) has increased tremendously . the disorder is caused by dynamic mutation of a single trinucleotide sequence , cgg , on the x chromosome . in patients , cgg repeat expansion and subsequent methylation silences the fmr1 gene , preventing transcription of the fragile x mental retardation protein ( fmrp ) . fmrp is an rna binding protein involved in mrna transport and stability and also in local protein translation . the protein is estimated to interact with 4% of all brain mrnas and with an unknown number of proteins in the mammalian brain . absence of fmrp leads to perturbation of the normal cellular function of many mrnas and proteins . the resulting fragile x phenotype is characterized by intellectual disability , specific physical abnormalities , behavioral problems and epileptic seizures . elucidating the pathophysiology of fxs is therefore not only important for the identification of potential therapeutic targets , but could also provide further insights into the general mechanisms of cognition and behavior . various techniques have been used to determine the mrna targets of fmrp , including co - immunoprecipitation followed by microarray analysis , antibody - positioned rna amplification ( apra ) and , most recently , high - throughput sequencing of rnas isolated by crosslinking immunoprecipitation ( hits - clip ) . each study identified a large number of mrna targets , encoding proteins involved in synaptic signaling pathways , such as glutamate and -aminobutyric acid ( gaba ) , in addition to proteins involved in many other intracellular pathways . proteomic analysis of murine hippocampal synapses revealed abnormalities due to loss of translational regulation of fmrp . altered expression profiles were found predominantly for proteins in specific functional groups , such as synaptic structure and cytoskeleton organization , neurotransmission and metabolism . a recent study by davidovic and colleagues , published in genome research , provides a new dimension to fragile x research by analyzing the brain metabolome of fmr1-deficient mice . by combining metabonomics data with results from previously published studies and with the knowledge of signaling and metabolic pathways gathered from databases , this work significantly increases our insight into the aberrant signaling pathways in fxs . metabonomics measures the dynamic multiparametric metabolic response of living systems to pathological stimuli or genetic modification . the collection of all metabolites ( the intermediate and end products of cellular processes ) in a biological sample is represented by the metabolome , which can reflect the ultimate response of biological systems to genetic or environmental changes . metabonomics is a rapidly developing field with many potential applications in cancer and neurodegenerative disease diagnostics , monitoring of disease progression , evaluation of drug toxicity and development of therapeutics . traditionally , genomics and proteomics approaches have been used to study the effect of genetic disorders . however , finding the relationship between altered gene or protein expression and the biological consequences is not always straightforward , especially given that the effect of a single genetic variation is often not limited to one biochemical pathway . metabonomics can help to identify the metabolites of seemingly unrelated biochemical pathways , and therefore might reveal potential new sites for therapeutic intervention . the metabolites can be detected by approaches based on mass spectrometry or nuclear magnetic resonance ( nmr ) spectroscopy . in their study , davidovic et al . used solid state nmr , specifically h magic - angle - spinning nmr ( h hr - mas nmr ) spectroscopy . this method has the advantage of being able to analyze small amounts of intact tissues , unlike other methods , which require metabolites to be in solution . the technique can thus be used even if further analysis of the tissue sample is required . the outcome of the metabonomic analysis showed 25 metabolites with altered concentrations in the fragile x brain ( figure 1 ) . these 25 metabolites could be grouped into a small number of affected pathways , involved in one of four categories : neurotransmission , osmoregulation , energy metabolism and oxidative stress response . some alterations are in line with reported anomalies in fxs , including abnormalities in the glutamatergic and the gabaergic pathways . for instance , a reduced amount of gaba in the cortex and cerebellum is compatible with earlier reports of a compromised gabaergic system in the disorder . increased glutamatergic signaling is another hallmark of the disorder . it can be hypothesized that the reduced amount of free glutamate observed by davidovic et al .   is a protective reaction of the organism to the overstimulation of the group there have been isolated reports that the cholinergic system , a second inhibitory system in brain , is also involved in the disorder , mainly on the basis of results from fly studies . the davidovic et al . study   clearly shows that several components in the cholinergic pathway are compromised in the mouse model . this adds further evidence to the hypothesis that fxs is a consequence of the disturbance of the delicate balance between excitatory and inhibitory signaling in the brain . the metabolites found to be downregulated ( down - arrows in the left columns ) or upregulated ( up - arrows in the right columns ) in fmr1 knockout mice compared with wild - type mice are shown for each brain region . co , cortex ; st , striatum ; ce , cerebellum ; hi , hippocampus . to integrate the abnormal metabolite concentrations with the data available from previous studies , the authors   developed a novel integrated metabolome and interactome mapping ( imim ) approach . this systems biology approach was considered necessary because fmrp does not interact directly with the metabolites themselves and therefore can not directly influence their concentrations . all the 25 metabolites were linked to fmrp in the network by , on average , just over three intermediate proteins . the distance within the network represents the mechanistic link between fmrp and each metabolite . within the interaction network , only 12 mrnas and one protein are linked directly to fmrp . of these , some are known interactors , including the paralogous protein fxr2p and mrnas encoding subunits of the gabaa receptor . interestingly , a key interactor is the amyloid beta precursor protein ( app ) mrna , which is implicated in alzheimer 's disease . a previous study indicated that fmrp binds app mrna , but it is striking that app is predicted to be in the center of the metabolite network , implying a pivotal role . rhoa is a member of the rho gtpase family , and different members of this gene family have opposite roles in neurite outgrowth and retraction . although it was known that the rho gtpase rac1 , which promotes neural spine formation , was involved in the disorder , this study supports the involvement of the rhoa signaling pathway , which induces spine retraction . in line with this , expression of larg , encoding a protein that activates rhoa , was reported to be compromised in fxs in an earlier study . these findings emphasize the involvement of rho gtpases in the neuro - anatomical pathophysiology of fxs , more specifically in the aberrant spine morphology associated with the disease . this story   adds another layer of understanding to the complex phenotype of fxs and it contains both good and bad news for the design of drugs to treat the disorder . although it confirms a key role of inhibitory and excitatory pathways , the abnormalities in these and other affected systems seem to be specific to particular brain regions and thus may require much more sophisticated drug treatments than currently anticipated . in addition , the abnormalities were detected in very young animals and an effect of brain development on the disturbances of metabolite concentrations can not be excluded . the study from davidovic and colleagues   highlights many similarities between the metabolome of fxs and that of other neurological disorders . examples include the neurodevelopmental disorder rett syndrome and the neurodegenerative disorders batten disease and huntington 's disease , which have been analyzed by other groups using metabonomics . alterations in the balance between the excitatory ( glutamate ) and inhibitory ( gaba ) neurotransmitters , osmoregulation ( myo - inositol ) , lipid metabolism ( choline ) and energy metabolism ( creatine ) were the most commonly observed metabolic changes across all these diseases . thus , collectively these findings contribute to our understanding of the mechanisms underlying neurological disorders in general . app : amyloid beta precursor protein ; fmr1 : fragile x mental retardation 1 gene ; fmrp : fragile x mental retardation protein ; fxs : fragile x syndrome ; gaba : -aminobutyric acid ; larg : leukemia - associated rho guanine nucleotide exchange factor ; nmr : nuclear magnetic resonance ; rhoa : ras homology protein a. we are supported by the agency for innovation by science and technology in flanders ( iwt ) and the belgian national fund for scientific research - flanders ( fwo ) .