Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database

Abstract

Increasing evidence demonstrates the importance of long coiled-coil proteins for the spatial organization of cellular processes. Although several protein classes with long coiled-coil domains have been studied in animals and yeast, our knowledge about plant long coiled-coil proteins is very limited. The repeat nature of the coiled-coil sequence motif often prevents the simple identification of homologs of animal coiled-coil proteins by generic sequence similarity searches. As a consequence, counterparts of many animal proteins with long coiled-coil domains, like lamins, golgins, or microtubule organization center components, have not been identified yet in plants. Here, all Arabidopsis proteins predicted to contain long stretches of coiled-coil domains were identified by applying the algorithm MultiCoil to a genome-wide screen. A searchable protein database, ARABI-COIL (http://www.coiled-coil.org/arabidopsis), was established that integrates information on number, size, and position of predicted coiled-coil domains with subcellular localization signals, transmembrane domains, and available functional annotations. ARABI-COIL serves as a tool to sort and browse Arabidopsis long coiled-coil proteins to facilitate the identification and selection of candidate proteins of potential interest for specific research areas. Using the database, candidate proteins were identified for Arabidopsis membrane-bound, nuclear, and organellar long coiled-coil proteins.

Figure 1.

Comparison of different algorithms for coiled-coil domain prediction. At3g16000 (AtMFP1, GenBank accession no. BAB02666; Harder et al., 2000; Jeong et al., 2003) is shown as an example. A to C, Probability scores plotted against the length of the protein in amino acids (aa) and bar diagram generated from plots. The dashed lines mark the cutoff score of 0.5. Coiled-coil domains are shown in gray in the bar diagram. A, COILS; B, PAIRCOIL; C, MultiCoil. D, Bar diagram generated after processing of MultiCoil data through ExtractProp (“Materials and Methods”) to eliminate short gaps in coiled-coil domain predictions. E, Comparison of domain predictions by MultiCoil using the same score and length cutoff parameters for human and Arabidopsis structural maintenance of chromosomes 2 proteins. HsSMC2, NP_006435; AtSMC2, NP_190330; AtTTN3, NP_201047.

Figure 2.

Putative functions of proteins in ARABI-COIL based on annotations. TFs, Transcription factors; DNA RMR, DNA recombination, modification, and repair.

Figure 3.

Putative membrane proteins with high coiled-coil coverage. Proteins are of at least 500 amino acids in length and at least 25% coiled-coil coverage, sorted from top to bottom by decreasing percentage of coiled-coil coverage. Bar diagrams show the coiled-coil domain structure as represented in the ARABI-COIL database; gray boxes, coiled-coil domains; black boxes, transmembrane domains according to ARAMEMNON. Proteins belonging to gene families are boxed together. a, Proteins are characterized by published data (see Table V for comparison).

Figure 4.

Summary of subcellular targeting predictions of proteins in ARABI-COIL. The mean values of all prediction programs used (see Table VI) were computed and localization predictions with a mean value above a probability cutoff score of 0.5 were counted as positive for that location. Proteins with mean values above cutoff for two or more compartments of the cell were labeled “unclear.”

Figure 5.

Putative nuclear proteins with high coiled-coil coverage. Proteins are of at least 500 amino acids in length and at least 25% coiled-coil coverage, sorted from top to bottom by decreasing percentage of coiled-coil coverage. Bar diagrams, Coiled-coil domain structure as represented in the ARABI-COIL database; gray boxes, coiled-coil domains; black boxes, transmembrane domains according to ARAMEMNON. Proteins belonging to gene families are boxed together. a, Proteins are characterized by published data (see Table V for comparison).

Figure 6.

Proteins with high coiled-coil coverage and putative N-terminal targeting signals. Proteins are of at least 500 amino acids in length and at least 25% coiled-coil coverage, sorted from top to bottom by decreasing percentage of coiled-coil coverage. Bar diagrams, Coiled-coil domain structure as represented in the ARABI-COIL database; gray boxes, coiled-coil domains; black boxes, transmembrane domains according to ARAMEMNON. Proteins belonging to gene families are boxed together. a, Proteins are characterized by published data (see Table V for comparison). cTP, Chloroplast targeting peptide; mTP, mitochondrial targeting peptide; SP, signal peptide for secretory pathway.

Figure 7.

Putative cytosolic proteins with high coiled-coil coverage. Proteins are of at least 500 amino acids in length and at least 25% coiled-coil coverage, sorted from top to bottom by decreasing percentage of coiled-coil coverage. Bar diagrams, Coiled-coil domain structure as represented in the ARABI-COIL database; gray boxes, coiled-coil domains. Proteins belonging to gene families are boxed together. a, Proteins are characterized by published data (see Table V for comparison).