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The gene CAP1 is a highly conserved plant-specific gene that encode an arabinokinase-like protein which is critical for pollen development in both monocotyledonous and dicotyledonous plants.

Annotated Information


The gene is composed of 28 exons and encodes a protein of 996 amino acids. It's a member of the galactokinase, homo-Ser kinase, mevalonate kinase, and phosphomevalonate kinase (GHMP) superfamily. The N-terminal half of CAP1 contains a glycosyltransferase family 1 domain (30–338 amino acids), while the C-terminal half contains both a Gal-binding (GB) signature (496–540 amino acids) and a GHMP N-terminal (GHMP-N) domain (638–704 amino acids)[1]. The GHMP-N domain is involved in ATP binding[2][3].The protein CAP1 shows high indentity to l-arabinokinase from Arabidopsis, a kinase which catalyzes the conversion of l-arabinose to l-arabinose 1-phosphate. This indicates that CAP1 is a arabinokinase-like protein and might have the same function with l-arabinokinase.

Genetic analysis indicates that the cap1 mutation has no effect on female reproduction or vegetative growth. But The cap1 heterozygous plant produces equal numbers of normal and collapsed pollen grains, and the collapsed pollen grains lack almost all cytoplasmic materials, nuclei, and intine cell walls and are unable to germinate. Based on the alignment information that CAP1 is a arabinokinase-like protein, cap1 mutant's pollen grain phenotype might be caused by the toxic accumulation of l-arabinose or by the inhibition of cell wall metabolism due to the lack of UDP-l-arabinose derived from l-arabinose 1-phosphate[1].

Genomic structure of the CAP1 locus and pollen phenotypes of allelic mutant lines.jpg Genomic structure of the CAP1 locus and pollen phenotypes of allelic mutant lines (2).jpg

Fig1. Genomic structure of the CAP1 locus and pollen phenotypes of allelic mutant lines[1].

Wild type vs. Mutant

In wild-type plants, almost all pollen grains are uniformly round in shape and contains normal levels of starch. However, in the mutant, 50% pollen grains are abnormal and are smaller in size (approximately 30 µm in diameter) than wild-type pollen grains (40 µm), and many of them are collapsed. The majority of the collapsed grains contain no starch, only in a few cases that a limited number of starch granules are observed. In the individual wild-type pollen grains, two identical sperm cell nuclei and one vegetative nucleus are clearly visible. In the mutant, however, none of the collapsed pollen grains contain nuclei, while the pollen grains with normal levels of starch contain normal nuclei.

The viable pollen grains from wild-type plants are stained purple by Alexander’s stain, while the aborted pollen grains from mutant plants are blue.

No cell wall fluorescence is detectable from collapsed pollen grains stained with calcofluor white solution, whereas all normal pollen grains emit blue-white fluorescence.

To summarize, mutant pollen grains lost almost all cytoplasm and comprised only exine, so they are empty pollen grains[1].

Phenotype and germinability of pollen grains affected by a cap1 mutation.jpg Phenotype and germinability of pollen grains affected by a cap1 mutation 2.jpg

Fig2. Phenotype and germinability of pollen grains affected by a cap1 mutation[1].


Analyzing by RT-PCR, a very weak signal is detectable in meiotic-stage spikelets (stages 7 and 8) and in microspore stage anthers (stages 9 and 10), and no signal is detected in leaf blades, roots, lemmas/paleas, or flowering-stage pistils, nor in tricellular pollen stage anthers (stages 12 and 13), while a prominent signal is detected in anthers at the bicellular pollen stage (stage 11).

By in situ hybridization, no signal is detected in the anther of microspore (stage 10), bicellular pollen (stage 11), and tricellular pollen (stage 13) stages using a digoxigenin (DIG)-labeled CAP1 sense probe as a control. By contrast, the hybridization signals by a DIG-labeled CAP1 antisense probe are present not only in developing pollen, but also in tapetum and endothecium (anther wall).

In summary, CAP1 is preferentially expressed in anthers during pollen development. The developmental stage, when increased CAP1 expression is observed, coincided with the timing of morphological and biochemical alterations in cap1 mutants, suggesting that CAP1 is closely associated with bicellular-stage pollen at stage 11[1].

Gene expression pattern of CAP1..jpg Gene expression pattern of CAP1. (2).jpg

Fig3. Gene expression pattern of CAP1[1].


A closely related protein Os06g0702500 is found in the rice genome which encodes a protein with 79% identity to CAP1 and is termed OsARA1.

Similar proteins could be found in many higher plants, including Gramineae and Arabidopsis (between 90% and 71% identity), the fern Selaginella moellendorffii (67%), and the moss Physcomitrella patens (63%).

In Gramineae, there are at least two similar proteins in a genome that are divided into two phylogenetically distinct clades, the CAP1 clade (with about 90% identity to CAP1) and the OsARA1 clade (about 80% identity).

Similaraly, the Arabidopsis genome also contains two genes similar to CAP1; AtARA1 (At4g16130) has 75% identity to CAP1 and encods an arabinokinase[4][5][6], and AtARA2, has 71% identity.

In bacteria or animal genomes, no highly homologous proteins could be found, which indicates that CAP1 is a highly conserved plant-specific gene[1].

Phylogenetic tree of CAP1 and related proteins in plants.jpg

Fig4. Phylogenetic tree of CAP1 and related proteins in plants[1].

Labs working on this gene

1. Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010–0195, Japan (K.U., F.Y., H.W.)

2. Department of Genetics, The University of Melbourne, Parkville, Australia, 3052.

3. Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, CNRS-ERS 569, F-91405, Orsay, Cedex, France.


  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Ueda K, Yoshimura F, Miyao A, Hirochika H, Nonomura K, Wabiko H. Collapsed abnormal pollen1 gene encoding the Arabinokinase-like protein is involved in pollen development in rice. Plant Physiol. 2013 Jun;162(2):858-71.
  2. Tsay YH, Robinson GW. (1991) Cloning and characterization of ERG8, an essential gene of Saccharomyces cerevisiae that encodes phosphomevalonate kinase. Mol Cell Biol 11: 620–631.
  3. Lee M, Leustek T. (1999) Identification of the gene encoding homoserine kinase from Arabidopsis thaliana and characterization of the recombinant enzyme derived from the gene. Arch Biochem Biophys 372: 135–142.
  4. Dolezal O, Cobbett CS. (1991) Arabinose kinase-deficient mutant of Arabidopsis thaliana. Plant Physiol 96: 1255–1260.
  5. Gy I, Aubourg S, Sherson S, Cobbett CS, Cheron A, Kreis M, Lecharny A. (1998) Analysis of a 14-kb fragment containing a putative cell wall gene and a candidate for the ARA1, arabinose kinase, gene from chromosome IV of Arabidopsis thaliana. Gene 209: 201–210.
  6. Sherson S, Gy I, Medd J, Schmidt R, Dean C, Kreis M, Lecharny A, Cobbett C. (1999) The arabinose kinase, ARA1, gene of Arabidopsis is a novel member of the galactose kinase gene family. Plant Mol Biol 39: 1003–1012.

Structured Information