Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models

Fariselli, Piero; Molinini, Daniele; Casadio, Rita; Krogh, Anders

doi:10.1007/978-3-540-71233-6_23

Cited by 17 publications

(10 citation statements)

References 15 publications

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“…The nucleotide and amino acid alignments were performed by C lustal W (Larkin et al ., ) and Espript 3.0 (Robert and Gouet, ). The CC secondary structures of the Sw‐5 proteins were predicted by http://gpcr.biocomp.unibo.it/cgi/predictors/cc/pred_cchmm.cgi (Hochreiter et al ., ). The NB‐ARC and LRR domains were predicted by SMART (Letunic et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Cell death triggering and effector recognition by Sw‐5 SD‐CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus

Oliveira

Koolhaas

Boiteux

et al. 2016

Molecular Plant Pathology

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Summary Only a limited number of dominant resistance genes acting against plant viruses have been cloned, and further functional studies of these have been almost entirely limited to the resistance genes Rx against Potato virus X (PVX) and N against Tobacco mosaic virus (TMV). Recently, the cell‐to‐cell movement protein (NS M ) of Tomato spotted wilt virus (TSWV) has been identified as the avirulence determinant (Avr) of Sw‐5b‐mediated resistance, a dominant resistance gene which belongs to the class of SD‐CC‐NB‐LRR (Solanaceae domain‐coiled coil‐nucleotide‐binding‐leucine‐rich repeat, SD‐CNL) resistance genes. On transient expression of the NS M protein in tomato and transgenic Nicotiana benthamiana harbouring the Sw‐5b gene, a hypersensitive cell death response (HR) is triggered. Here, it is shown that high accumulation of the Sw‐5b protein in N. benthamiana leaves, achieved by co‐expression of the Sw‐5b protein with RNA silencing suppressors (RSSs), leads to auto‐activity in the absence of NS M . In a similar approach, Sw‐5a, the highest conserved paralogue of Sw‐5b from Solanum peruvianum , also triggered HR by auto‐activation, whereas the highest conserved orthologue from susceptible S. lycopersicum , named Sw‐5a S , did not. However, neither of the last two homologues was able to trigger an NS M ‐dependent HR. Truncated and mutated versions of these Sw‐5 proteins revealed that the NB‐ARC [nucleotide‐binding adaptor shared by Apaf‐1 (from humans), R proteins and CED‐4 (from nematodes)] domain is sufficient for the triggering of HR and seems to be suppressed by the SD‐CC domain. Furthermore, a single mutation was sufficient to restore auto‐activity within the NB‐ARC domain of Sw‐5a S . When the latter domain was fused to the Sw‐5b LRR domain, NS M ‐dependent HR triggering was regained, but not in the presence of its own Sw‐5a S LRR domain. Expression analysis in planta revealed a nucleocytoplasmic localization pattern of Sw‐5b, in which the SD‐CC domain seems to be required for nuclear translocation. Although the Sw‐5 N‐terminal CC domain, in contrast with Rx , contains an additional SD, most findings from this study support a conserved role of domains within NB‐LRR (NLR) proteins against plant viruses.

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Section: Methodsmentioning

confidence: 97%

Cell death triggering and effector recognition by Sw‐5 SD‐CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus

Oliveira

Koolhaas

Boiteux

et al. 2016

Molecular Plant Pathology

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“…The extent of the coiled-coil domain was predicted as residues 4–134 (green) by CCHMM [58] and MARCOILS [59], the NB-ARC domain to be residues 150 to 494 (blue) by Pfam [51,52] (predicted domain spanning residues 165–441 in bold), and the LRR domain from 718–888 (dark orange) by LRR Finder [54] and LRRsearch [55]. Light orange indicates a putative LRR region.…”

Section: Resultsmentioning

confidence: 99%

Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor

2019

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Plant NLRs are modular immune receptors that trigger rapid cell death in response to attempted infection by pathogens. A highly conserved n ucleotide- b inding domain shared with A PAF-1, various R -proteins and C ED-4 (NB-ARC domain) is proposed to act as a molecular switch, cycling between ADP (repressed) and ATP (active) bound forms. Studies of plant NLR NB-ARC domains have revealed functional similarities to mammalian homologues, and provided insight into potential mechanisms of regulation. However, further advances have been limited by difficulties in obtaining sufficient yields of protein suitable for structural and biochemical techniques. From protein expression screens in Escherichia coli and Sf9 insect cells, we defined suitable conditions to produce the NB-ARC domain from the tomato NLR NRC1. Biophysical analyses of this domain showed it is a folded, soluble protein. Structural studies revealed the NRC1 NB-ARC domain had co-purified with ADP, and confirmed predicted structural similarities between plant NLR NB-ARC domains and their mammalian homologues.

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“…We did not include the tools SOSUIcoil 27 and RFcoil 28 , because these are not accessible anymore. The tools CCHMM 29 and CCHMM-PROF 30 were also excluded, because these can only be accessed via a web interface, which is not applicable for a systematic evaluation. Furthermore, a short test for prediction performance using the globular and coiled-coil free myosin motor domain resulted in many predicted coiled-coil regions, which are obviously not correct (Supplementary Figure 1).…”

Section: Prediction Of Coiled-coils In Protein Structures and Their Smentioning

confidence: 99%

Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data

Simm

Hatje

Waack

et al. 2019

Preprint

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Coiled-coil regions were among the first protein motifs described structurally and theoretically. The beauty and simplicity of the motif gives hope to detecting coiled-coil regions with reasonable accuracy and precision in any protein sequence. Here, we reevaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Base (PDB), down to each amino acid and its secondary structure. Apart from the thirtyfold difference in number of predicted coiled-coils the tools strongly vary in their predictions, across structures and within structures. The evaluation of the false discovery rate and Matthews correlation coefficient, a widely used performance metric for imbalanced data sets, suggests that the tested tools have only limited applicability for large data sets. Coiled-coil predictions strongly impact the functional characterization of proteins, are used for functional genome annotation, and should therefore be supported and validated by additional information.

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Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models

Cited by 17 publications

References 15 publications

Cell death triggering and effector recognition by Sw‐5 SD‐CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus

Cell death triggering and effector recognition by Sw‐5 SD‐CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus

Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor

Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data

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