The Arabidopsis cytoskeletal genome

Abstract

In the past decade the first Arabidopsis genes encoding cytoskeletal proteins were identified. A few dozen genes in the actin and tubulin cytoskeletal systems have been characterized thoroughly, including gene families encoding actins, profilins, actin depolymerizing factors, α-tubulins, and β-tubulins. Conventional molecular genetics have shown these family members to be differentially expressed at the temporal and spatial levels with an ancient split separating those genes expressed in vegetative tissues from those expressed in reproductive tissues. A few members of other cytoskeletal gene families have also been partially characterized, including an actin-related protein, annexins, fimbrins, kinesins, myosins, and villins. In the year 2001 the Arabidopsis genome sequence was completed. Based on sequence homology with well-characterized animal, fungal, and protist sequences, we find candidate cytoskeletal genes in the Arabidopsis database: more than 150 actin-binding proteins (ABPs), including monomer binding, capping, cross-linking, attachment, and motor proteins; more than 200 microtubule-associated proteins (MAPs); and, surprisingly, 10 to 40 potential intermediate filament (IF) proteins. Most of these sequences are uncharacterized and were not identified as related to cytoskeletal proteins. Several Arabidopsis ABPs, MAPs, and IF proteins are represented by individual genes and most were represented as as small gene families. However, several classes of cytoskeletal genes including myosin, eEF1α, CLIP, tea1, and kinesin are part of large gene families with 20 to 70 potential gene members each. This treasure trove of data provides an unprecedented opportunity to make rapid advances in understanding the complex plant cytoskeletal proteome. However, the functional analysis of these proposed cytoskeletal proteins and their mutants will require detailed analysis at the cell biological, molecular genetic, and biochemical levels. New approaches will be needed to move more efficiently and rapidly from this mass of DNA sequence to functional studies on cytoskeletal proteins.

Keywords: actin-binding proteins; intermediate filaments; kinesin; microfilaments; microtubule-binding proteins; myosin; plant proteome; tubulin.

Figure 1.

Domain structures of the animal and protist villin- and gelsolin-related actin-binding proteins used as query sequences. Most members of this superfamily including severin, fragmin gelsolin, villin, and protovillin share a common actin-binding domain (AB; oval drawn in blue). Members of this family also share protein repeat units (yellow ovals) with three repeats in severin and fragmin and to groups of these three repeats for a total of six repeats in gelsolin, villin, and protovilin. Dematin is related through its common actin-binding domain with villin (AB; rectangle drawn in blue). The approximate molecular weights of example proteins in kilo Daltons (kDa) are shown on the left.

Figure 2.

Domain structures of the animal β-barrel actin-binding proteins used as query sequences. Coronin, scruin, and kelch all contain β-barrels repeats (βB, drawn in blue), or kelch repeats. The portions of these repeats that bind actin are not well defined, but their approximate positions are indicated in the structure of scruin (AB). CB is a calmodulin-binding domain. The βB repeat in coronin is also known as the widely distributed WD40 repeat found in G-β proteins that do not bind actin. The approximate molecular weights of example proteins in kilo Daltons (kDa) are shown on the left.

Figure 3.

Domain structures of several animal and protist calponin-related actin crosslinking and anchoring proteins used as query sequences. The domain structures of several crosslinking and anchoring proteins are summarized in this diagram. Subdomains are labeled with the following abbreviations: BS, β-sheet repeats also called filamin repeats; CC, α-helical coiled coil domain; CH, actin-binding calponin homology domain of ∼100 a.a. shared by all members of this family drawn in blue; EF, EF hand calcium binding domain; HR, helical repeat common to spectrin also called spectrin repeats; WW, two adjacent tryptophan residues conserved in dystrophins. The N-terminal region of each protein is marked with the letter N. In the cases where the proteins function as dimers or heterodimers (α-actinin, spectrin, ABP120, and filamin), the N- to C-terminal orientation may be flipped to show the second molecule. Calponin is not a crosslinking or anchoring protein, but is included in this figure for comparison to the numerous proteins containing a calponin homology (CH) domain. The approximate molecular weights of single example polypeptide chains in kilo Daltons (kDa) are shown on the left.