High-performance signal peptide prediction based on sequence alignment techniques

Frank, Karl H.; Sippl, Manfred J.

doi:10.1093/bioinformatics/btn422

Cited by 121 publications

(71 citation statements)

References 10 publications

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“…Many ER-resident proteins have specific retention and retrieval signals that prevent them from leaving the ER [41]. Sequence analysis of human CLEC61A (via SignalBlast [42], SignalP [43] and PSORT [44]) did not reveal a classical retention motif. Clearly, further clarification in the context of ER localization will be necessary to reveal the biological functions of this unusual human C-type lectinlike receptor as well as the potential mechanisms in which it is it is involved.…”

Section: Discussionmentioning

confidence: 99%

Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus

Zouk

d’Hennezel

et al. 2014

Clinical and Experimental Immunology

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SummaryThe type 1 diabetes-associated 16p13 locus contains the CLEC16A gene. Its preferential immune cell expression suggests involvement in autoimmunity. Given its elevated expression in dendritic and B cells -known professional antigen-presenting cells (APCs) -we hypothesize that C-type lectin domain family 16 member A (CLEC16A) may be involved in T cell co-stimulation and consequent activation and proliferation. We also sought to identify CLEC16A's subcellular localization. The effect of the CLEC16A knock-down (KD) on B cell co-stimulation and activation of T cells was tested in human lymphoblastoid cell lines (LCLs) by co-culture with CD4 + T cells. T cell activation and proliferation were determined by flow-cytometric analysis of CD69 and CD25 expression and carboxyfluorescein succinimidyl ester (CFSE) dilution, respectively. CLEC16A subcellular localization in K562 cells was examined by immunofluorescence. We show that the CLEC16A KD did not affect the tested indices of lymphoblastoid cell line (LCL) APC capacity. Additionally, the percentage of activated T cells following LCL co-culture was not affected significantly by the CLEC16A KD. T cells co-cultured with KD or control LCLs also exhibited similar cell division profiles. CLEC16A co-localized with an endoplasmic reticulum (ER) marker, suggesting that it may be an ER protein. In conclusion, CLEC16A may not be involved in T cell co-stimulation. Additional studies on CLEC16A, accounting for its ER localization, are needed to uncover its biological role.

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Section: Discussionmentioning

confidence: 99%

Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus

Zouk

d’Hennezel

et al. 2014

Clinical and Experimental Immunology

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“…Prediction of signal peptide of maize Dmc1 was performed by SignalP 3.0 Server -prediction using neural networks (NN) and hidden Markov models (HMM) trained on eukaryote (Bendtsen et al, 2004). Another program that was used for homology search was signal blast (Frank and Sippl, 2008). …”

Section: Comparative and Functional Structure Of Maize Dmc1 Proteinmentioning

confidence: 99%

Genome wide cloning of maize meiotic recombinase Dmc1 and its functional structure through molecular phylogeny

Etedali

Kohnehrouz²,

Valizadeh³

et al. 2011

Genet. Mol. Res.

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ABSTRACT. The development of meiotic division and associated genetic recombination paved the way for evolutionary changes. However, the secondary and tertiary structure and functional domains of many of the proteins involved in genetic recombination have not been studied in detail. We used the human Dmc1 gene product along with secondary and tertiary domain structures of Escherichia coli RecA protein to help determine the molecular structure and function of maize Dmc1, which is required for synaptonemal complex formation and cell cycle progression. The maize recombinase Dmc1 gene was cloned and characterized, using rice Dmc1 cDNA as an orthologue. The deduced amino acid sequence was used for Cloning of maize meiotic recombinase Dmc1 and its structure elaborating its 3-D structure, and functional analysis was made with the CDD software, showing significant identity of the Dmc1 gene product in Zea mays with that of Homo sapiens. Based on these results, the domains and motives of WalkerA and WalkerB as ATP binding sites, a multimer site (BRC) interface, the putative ssDNA binding L1 and L2 loops, the putative dsDNA binding helix-hairpinhelix, a polymerization motif, the subunit rotation motif, and a small N-terminal domain were proposed for maize recombinase Dmc1.

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“…medicagohapmap.org/downloads_genome/Mt3.5/Mt3.5v3_annotation_files.tar.gz), by using the SignalP program (Bendtsen et al, 2004;Frank and Sippl, 2008). Putative SPs were compared with MtENOD8's SP using EMBOSS:_Needle (Rice et al, 2000).…”

Section: Sp Analysismentioning

confidence: 99%

Multiple Domains in MtENOD8 Protein Including the Signal Peptide Target It to The Symbiosome

et al. 2012

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Symbiotic nitrogen fixation occurs in nodules, specialized organs on the roots of legumes. Within nodules, host plant cells are infected with rhizobia that are encapsulated by a plant-derived membrane forming a novel organelle, the symbiosome. In Medicago truncatula, the symbiosome consists of the symbiosome membrane, a single rhizobium, and the soluble space between them, called the symbiosome space. The symbiosome space is enriched with plant-derived proteins, including the M. truncatula EARLY NODULIN8 (MtENOD8) protein. Here, we present evidence from green fluorescent protein (GFP) fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP). When ectopically expressed in nonnodulated root tissue, the MtENOD8 SP delivers GFP to the vacuole. During the course of nodulation, there is a nodule-specific redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates and subsequently to symbiosomes, with redirection of MtENOD8-SP-GFP from the vacuole to punctate intermediates preceding intracellular rhizobial infection. Experiments with M. truncatula mutants having defects in rhizobial infection and symbiosome development demonstrated that the MtNIP/LATD gene is required for redirection of the MtENOD8-SP-GFP from the vacuoles to punctate intermediates in nodules. Our evidence shows that MtENOD8 has evolved redundant targeting sequences for symbiosome targeting and that intracellular localization of ectopically expressed MtENOD8-SP-GFP is useful as a marker for monitoring the extent of development in mutant nodules.

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High-performance signal peptide prediction based on sequence alignment techniques

Abstract: Signal-BLAST is available online at http://sigpep.services.came.sbg.ac.at/signalblast.html.

Cited by 121 publications

References 10 publications

Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus

Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus

Genome wide cloning of maize meiotic recombinase Dmc1 and its functional structure through molecular phylogeny

Multiple Domains in MtENOD8 Protein Including the Signal Peptide Target It to The Symbiosome

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