Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

Taly, Jean-François; Magis, Cedrik; Bussotti, Giovanni; Chang, Jia‐Ming; Tommaso, Paolo Di; Erb, Ionas; Espinosa-Carrasco, José; Kemena, Carsten; Notredame, Cédric

doi:10.1038/nprot.2011.393

Cited by 88 publications

(72 citation statements)

References 38 publications

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“…4 A-C). As RNA secondary structure alignment programs are developed and optimized (31,32), it will be interesting to use the R4 stem-loop structure to search for similar structures in other mRNAs and to then determine whether these mRNAs are synaptically localized.…”

Section: Discussionmentioning

confidence: 99%

Identification of a cis-acting element that localizes mRNA to synapses

Meer

Wang²,

Sangmok³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Messenger RNA (mRNA) localization and regulated translation can spatially restrict gene expression to each of the thousands of synaptic compartments formed by a single neuron. Although cisacting RNA elements have been shown to direct localization of mRNAs from the soma into neuronal processes, less is known about signals that target transcripts specifically to synapses. In Aplysia sensory-motor neuronal cultures, synapse formation rapidly redistributes the mRNA encoding the peptide neurotransmitter sensorin from neuritic shafts into synapses. We find that the export of sensorin mRNA from soma to neurite and the localization to synapse are controlled by distinct signals. The 3′ UTR is sufficient for export into distal neurites, whereas the 5′ UTR is required for concentration of reporter mRNA at synapses. We have identified a 66-nt element in the 5′ UTR of sensorin that is necessary and sufficient for synaptic mRNA localization. Mutational and chemical probing analyses are consistent with a role for secondary structure in this process.M essenger RNA (mRNA) localization and regulated translation provide a means of spatially restricting gene expression within distinct subcellular compartments. In the brain, local protein synthesis is critical to the development and experience-driven refinement of neural circuits, playing roles in axon guidance, synaptogenesis, and synaptic plasticity (1, 2). A large but select population of transcripts localizes to axons and dendrites (3-8), indicating that local translation subserves diverse cell biological functions. Where studied, the localization of mRNAs to axons or dendrites has been shown to depend on cisacting localization elements (LEs) usually found in the 3′ UTR, although occasionally present in the coding sequence or 5′ UTR (1, 2, 9). These cis-acting mRNA LEs recruit specific transacting RNA binding proteins, and the resulting messenger ribonucleoproteins are packaged into RNA transport granules that interact with molecular motors to be delivered to their final subcellular destination (10-12).In situ hybridization studies in neurons indicate that localized mRNAs in neurons are targeted to distinct subcellular compartments and domains within neuronal processes. For example, MAP2 mRNA concentrates within proximal dendrites, whereas calcium-calmodulin dependent protein kinase IIα (CaMKIIα) mRNA extends to distal dendrites (13). mRNA localization also seems to be dynamically regulated during development and with activity. In mature neurons, β-actin mRNA localizes to dendrites, and its concentration to distal dendrites is stimulated by depolarization (14). Stimuli that activate NMDA or neurotrophic receptor tyrosine kinase 2 (TrkB) receptors drive specific BDNF mRNA isoforms into distal dendrites of hippocampal neurons (15). High-frequency stimulation of perforant path projections to the dentate gyrus has been shown to direct localization of the mRNA encoding the immediate-early gene Arc selectively and specifically to activated dendritic lamina (16) and to drive localizati...

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Section: Discussionmentioning

confidence: 99%

Identification of a cis-acting element that localizes mRNA to synapses

Meer

Wang²,

Sangmok³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Two echinocandin-sensitive isolates, C115 and C117, were used as controls. The sequences were aligned (36,37) to the homologous FKS1 region from an irrelevant C. kefyr (ATCC 4922) strain and to C. albicans (SC5314). The amino acid changes in C113 and C116 are shaded in gray.…”

Section: Discussionmentioning

confidence: 99%

Target Enzyme Mutations Confer Differential Echinocandin Susceptibilities in Candida kefyr

Staab

Neofytos

Rhee

et al. 2014

Antimicrob Agents Chemother

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cCandida kefyr is an increasingly reported pathogen in patients with hematologic malignancies. We studied a series of bloodstream isolates that exhibited reduced echinocandin susceptibilities (RES). Clinical and surveillance isolates were tested for susceptibilities to all three echinocandins, and those isolates displaying RES to one or more echinocandins were selected for molecular and biochemical studies. The isolates were analyzed for genetic similarities, and a subset was analyzed for mutations in the echinocandin target gene FKS1 and glucan synthase echinocandin sensitivities using biochemical methods. The molecular typing did not indicate strong genetic relatedness among the isolates except for a series of strains recovered from a single patient. Two unrelated isolates with RES had previously uncharacterized FKS1 mutations: R647G and deletion of amino acid 641 (F641⌬). Biochemical analysis of the semipurified R647G glucan synthase generated differential echinocandin sensitivity (resistance to micafungin only), while the deletion of F641 resulted in a glucan synthase highly insensitive to all three echinocandins. The consecutive isolates from a single patient with RES all harbored the common S645P mutation, which conferred resistance to all three echinocandins. The MIC values paralleled the glucan synthase inhibition kinetic data, although the S645P isolates displayed relatively higher susceptibility to caspofungin (2 g/ml) than the other two echinocandins (>8 g/ml). These findings highlight novel and common FKS1 mutations in C. kefyr isolates. The observation of differential susceptibilities to echinocandins may provide important mechanistic insights for echinocandin antifungals.

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“…Prior to homology searches, we carried out good-practice checks such as detecting the presence of coiled coils, low-complexity sequences, transmembrane segments and signal peptides, as described by Ferron et al (2006), using ANNIE (Ooi et al, 2009). We used Psi-Coffee (Di Tommaso et al, 2011;Taly et al, 2011) for multiple sequence alignments. All alignments are presented using Jalview (Waterhouse et al, 2009) with the CLUSTAL_X colouring scheme (Procter et al, 2010).…”

Section: Methodsmentioning

confidence: 99%

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

Chen

Karlin

et al. 2013

Journal of General Virology

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Emaravirus is a recently described genus of negative-strand RNA plant viruses. Emaravirus P4 protein localizes to plasmodesmata, suggesting that it could be a viral movement protein (MP). In the current study, we showed that the P4 protein of raspberry leaf blotch emaravirus (RLBV) rescued the cell-to-cell movement of a defective potato virus X (PVX) that had a deletion mutation in the triple gene block 1 movement-associated protein. This demonstrated that RLBV P4 is a functional MP. Sequence analyses revealed that P4 is a distant member of the 30K superfamily of MPs. All MPs of this family contain two highly conserved regions predicted to form b-strands, namely b1 and b2. We explored by alanine mutagenesis the role of two residues of P4 (Ile106 and Asp127) located in each of these strands. We also made the equivalent substitutions in the 29K MP of tobacco rattle virus, another member of the 30K superfamily. All substitutions abolished the ability to complement PVX movement, except for the I106A substitution in the b1 region of P4. This region has been shown to mediate membrane association of 30K MPs; our results show that it is possible to make non-conservative substitutions of a well-conserved aliphatic residue within b1 without preventing the membrane association or movement function of P4.

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Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

Cited by 88 publications

References 38 publications

Identification of a cis-acting element that localizes mRNA to synapses

Identification of a cis-acting element that localizes mRNA to synapses

Target Enzyme Mutations Confer Differential Echinocandin Susceptibilities in Candida kefyr

Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily

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