Role of leucine-rich repeat proteins in the development and function of neural circuits

RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures

MOTIVATION

Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view, finding solenoids may be complicated by the presence of insertions or multiple domains. To the best of our knowledge, no automated methods are available to characterize solenoid repeats from structure.

RESULTS

Here we introduce RAPHAEL, a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified. RAPHAEL periodicities have a Spearman correlation coefficient of 0.877 against the manually established ones. A baseline algorithm for insertion detection in identified solenoids has a Q(2) value of 79.8%, suggesting room for further improvement. RAPHAEL finds 1931 highly confident repeat structures not previously annotated as solenoids in the Protein Data Bank records.

Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non-small cell lung carcinoma from Chinese patients

Lung cancer has become the top killer among malignant tumors in China and is significantly associated with somatic genetic alterations. We performed exome sequencing of 14 non-small cell lung carcinomas (NSCLCs) with matched adjacent normal lung tissues extracted from Chinese patients. In addition to the lung cancer-related genes (TP53, EGFR, KRAS, PIK3CA, and ROS1), this study revealed "novel" genes not previously implicated in NSCLC. Especially, matrix-remodeling associated 5 was the second most frequently mutated gene in NSCLC (first is TP53). Subsequent Sanger sequencing of matrix-remodeling associated 5 in an additional sample set consisting of 52 paired tumor-normal DNA samples revealed that 15% of Chinese NSCLCs contained somatic mutations in matrix-remodeling associated 5. These findings, together with the results from pathway analysis, strongly indicate that altered extracellular matrix-remodeling may be involved in the etiology of NSCLC.

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa

Plant microRNAs have a vital role in various abiotic stress responses by regulating gene expression. Heat stress is one of the most severe abiotic stresses, and affects plant growth and development, even leading to death. To identify heat-responsive miRNAs at the genome-wide level in Populus, Solexa sequencing was employed to sequence two libraries from Populus tomentosa, treated and untreated by heat stress. Sequence analysis identified 134 conserved miRNAs belonging to 30 miRNA families, and 16 novel miRNAs belonging to 14 families. Among these miRNAs, 52 miRNAs from 15 families were responsive to heat stress and most of them were down-regulated. qRT-PCR analysis confirmed that the conserved and novel miRNAs were expressed in P. tomentosa, and revealed similar expression trends to the Solexa sequencing results obtained under heat stress. One hundred and nine targets of the novel miRNAs were predicted. This study opens up a new avenue for understanding the regulatory mechanisms of miRNAs involvement in the heat stress response of trees.

Generation of neuromuscular specificity in Drosophila: novel mechanisms revealed by new technologies

The Drosophila larval neuromuscular system is one of the best-characterized model systems for axon targeting. In each abdominal hemisegment, only 36 identified motor neurons form synaptic connections with just 30 target muscles in a highly specific and stereotypic manner. Studies in the 1990s identified several cell-surface and secreted proteins that are expressed in specific muscles and contribute to target specificity. Emerging evidence suggests that target selection is determined not only by attraction to the target cells but also by exclusion from non-target cells. Proteins with leucine-rich repeats (LRR proteins) appear to be a major molecular family of proteins responsible for the targeting. While the demonstrated roles of the target-derived cues point to active recognition by presynaptic motor neurons, postsynaptic muscles also reach out and recognize specific motor neurons by sending out cellular protrusions called myopodia. Simultaneous live imaging of myopodia and growth cones has revealed that local and mutual recognition at the tip of myopodia is critical for selective synapse formation. A large number of candidate target cues have been identified on a single muscle, suggesting that target specificity is determined by the partially redundant and combinatorial function of multiple cues. Analyses of the seemingly simple neuromuscular system in Drosophila have revealed an unexpected complexity in the mechanisms of axon targeting.

FLRT proteins are endogenous latrophilin ligands and regulate excitatory synapse development

Latrophilins (LPHNs) are a small family of G protein-coupled receptors known to mediate the massive synaptic exocytosis caused by the black widow spider venom α-latrotoxin, but their endogenous ligands and function remain unclear. Mutations in LPHN3 are strongly associated with attention deficit hyperactivity disorder, suggesting a role for latrophilins in human cognitive function. Using affinity chromatography and mass spectrometry, we identify the FLRT family of leucine-rich repeat transmembrane proteins as endogenous postsynaptic ligands for latrophilins. We demonstrate that the FLRT3 and LPHN3 ectodomains interact with high affinity in trans and that interference with this interaction using soluble recombinant LPHN3, LPHN3 shRNA, or FLRT3 shRNA reduces excitatory synapse density in cultured neurons. In addition, reducing FLRT3 levels with shRNA in vivo decreases afferent input strength and dendritic spine number in dentate granule cells. These observations indicate that LPHN3 and its ligand FLRT3 play an important role in glutamatergic synapse development.

Sonic hedgehog, BOC, and synaptic development: new players for an old game

In this issue of Neuron, Harwell et al. (2012) identify a new role for the secreted molecule Shh and its receptor Boc in synapse formation. These results add an unexpected new player to the expanding list of extracellular cues regulating the spatial specificity of synapse formation.

Teneurins instruct synaptic partner matching in an olfactory map

Neurons are interconnected with extraordinary precision to assemble a functional nervous system. Compared to axon guidance, far less is understood about how individual pre- and post-synaptic partners are matched. To ensure the proper relay of olfactory information in flies, axons of ~50 classes of olfactory receptor neurons (ORNs) form one-to-one connections with dendrites of ~50 classes of projection neurons (PNs). Using genetic screens, we identified two evolutionarily conserved EGF-repeat transmembrane Teneurins, Ten-m and Ten-a, as synaptic partner matching molecules between PN dendrites and ORN axons. Ten-m and Ten-a are highly expressed in select PN-ORN matching pairs. Teneurin loss- and gain-of-function cause specific mismatching of select ORNs and PNs. Finally, Teneurins promote homophilic interactions in vitro, and Ten-m co-expression in non-partner PNs and ORNs promotes their ectopic connections in vivo. We propose that Teneurins instruct matching specificity between synaptic partners through homophilic attraction.