1999/06/01 by Richard B. Meagher, Elizabeth C. McKinney, Muthugapatti K. Kandasamy · 143 citations
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · #Plant Reproductive Biology #Plant Molecular Biology Research #Plant Surface Properties and Treatments #Biology #Gene family #Actin #Gene #Dynamics (music) #Buffer (optical fiber) #Cell biology #Genetics #Computational biology #Evolutionary biology #Gene expression #Computer science
paper · pdf · doi:10.1105/tpc.11.6.995
published in The Plant Cell 11(6), 995-1005 (Oxford University Press)
openalex publication_date 1999/06/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
Most plant and animal genes are members of gene families that are differentially expressed and may encode diverse protein isovariants. With the recent explosion of information in plant genomics, researchers have become acutely aware that the gene families in plants are at least as diverse as their animal counterparts (McGrath et al., 1993; Newman et al., 1994; Henikoff et al., 1997; McKinney and Meagher, 1998). Among plant cytoskeletal gene families in Arabidopsis, there are at least 10 actins, nine α-tubulins, six β-tubulins, six profilins, and dozens of myosins. These and a few other examples of families of plant isoenzymes, signal transduction proteins, and regulatory proteins are listed in Table 1. The general view is that such family members are both selected out and preserved in evolution because they express varying levels of proteins in different temporal and spatial patterns (Meagher, 1995; Meagher et al., 1999). However, the expression of many of these gene family members overlaps considerably. This coexpression of protein isovariants in the same cells is expected to result in more dynamic behavior of these proteins, a process that we refer to as isovariant dynamics. We define isovariant dynamics as the temporal and biochemical expansion of a biological system's responses as a result of the simultaneous expression and interaction of multiple isovariants of a protein. For isovariant dynamics to be operational in a cell, the coexpressed isovariants must be functionally distinct in at least one activity (e.g., binding a substrate or cofactor and/or interactions with other proteins). Because two or more members of each of the families of plant isovariants listed in Table 1appear to be coexpressed in some cells, each has the potential to participate in protein–protein interactions that lead to isovariant dynamics. It has been suggested that more highly networked biochemical systems are inherently more robust (Barkai and Leibler, 1997). If isovariant dynamics do indeed lead to more robust and highly buffered responses of cells, then they should be beneficial to the parent organisms and thus an important factor in the selection and/or preservation of the gene families encoding isovariants. By using a case study of the plant actin family to illustrate our points, we propose that the coexpression of multiple actin isovariants in the same cell results in isovariant dynamics that allow for more complex cytoskeletal responses. Because dynamic processes are those in which energy, force, or motion are continuously changing, the cytoskeleton is an excellent system for studying isovariant dynamics. The cytoskeleton is constantly controlling cell structure and intercellular movement at the expense of chemical bond energy. However, enzymes and regulatory proteins (Table 1) also convert chemical bond energy in dynamic biochemical processes that can be expanded by the expression of multiple isovariants. By illustrating the properties of isovariant dynamics for actin, we hope to stimulate discussion and research on this complex problem for other families of isovariants. The plant actin cytoskeleton is central to many different subcellular processes that could be affected by interactions of actin isovariants. Figure 1shows the complex network of actin filaments and bundles that reach into nearly every part of the cytoplasm of an Arabidopsis cell grown in suspension culture. The nucleus is positioned in the cell within a basket of actin filaments that is connected to the cortical cytoskeleton by strands of actin filaments and bundles. The different cellular processes in which actin plays demonstrated or proposed roles include establishing cell polarity, division plane determination (by positioning the preprophase band), preprogramming of development and cell wall deposition, cell elongation, tip growth (e.g., of pollen tubes, root Examples of Plant Gene Families Encoding Coexpressed Protein Isovariants Examples of Plant Gene Families Encoding Coexpressed Protein Isovariants The dynamic activity of the actin network is a major factor contributing to the viscoelastic properties of cells (Ingber, 1993; Ingber et al., 1994). That is, cells spring back into shape when deformed suddenly, although they can be deformed by force applied over an extended period of time. Viscoelastic properties are partially explained by the fact that whereas most actin filaments have half-lives of ~1 min (Theriot and Mitchison, 1991), most cross-links between filaments last <1 sec (Wachsstock et al., 1994). How information about the intensity or quality of mechanical stress is conveyed to signaling pathways is not understood, but most likely it starts by the interaction of the actin or tubulin cytoskeleton with signal molecules. It seems reasonable to propose that the property of viscoelasticity contributes to the dynamic response of plant cells to different physical stresses in their environment (Braam and Davis, 1990). After the cytoskeleton is deformed from external mechanical stress, cues about the quality and quantity of force must be transmitted to cell information pathway(s), as proposed in Figure 2. It is likely that the cytoskeleton plays direct roles in mechanosensation processes (Wang et al., 1993; Bargmann, 1994), such as the touch response of leaves (Xu et al., 1996), the grasping of support by gyrating tendrils (Engelberth et al., 1995), or the avoidance of hard objects in the soil by roots (Okada and Shimura, 1990). Actin Forms Complex Arrays of Filaments and Bundles Interacting with Nearly Every Part of the Cell. Actin filament arrays (green) in an Arabidopsis interphase suspension culture cell (Keith et al., 1991) are stained with a general plant actin monoclonal antibody, MAbGPa, that reacts with all isovariants of plant actin (Kandasamy et al., 1999). The nucleus, stained with 4′,6-diamidino-2-phenylindole, is shown in red. CF, cortical filaments; N, nucleus; NB, nuclear basket. That the actin cytoskeleton responds dynamically to information from signal transduction pathways is better documented (Figure 2; Zigmond, 1996; Yamada and Geiger, 1997). For example, external stimuli activate different members of the Rho GTPase family (e.g., Rho, Rac, and Cdc42) that in turn signal distinct changes in the cytoskeleton (Tapon and Hall, 1997). In animal cells, these changes translate into defined changes in cell morphology and movement, such as the expression of membrane receptors and focal adhesion complexes linked to the cytoskeleton and stress fibers, the assembly of actin filaments just below the cell membrane that produce lamellipodia and ruffles, and the protrusion of filapodia (Hall, 1998). To produce these three different morphologies, each GTPase activity results in the expression of distinct adhesion complexes linking the cytoplasm to the cell membrane. Similarly, in pollen tubes, localization of a Rho GTPase dubbed Rop1Ps suggests that this “molecular switch” might be involved in generative cell movement and tip growth (Lin et al., 1996). Moreover, microinjected anti-Rop1Ps antibodies inhibit pollen tube elongation but not cytoplasmic streaming (Lin and Yang, 1997). In accordance with the model elaborated in animal systems, this experiment helps to associate one plant signal transduction pathway with at least one cellular function. Other plant-specific signal transduction pathways with links to the actin cytoskeleton are now being elucidated. For example, the phytohormone abscisic acid acts near the onset of a complex pathway that is triggered by physical environmental stresses, including temperature, humidity, and osmotic shock. Abscisic acid stimulates marked changes in the cell architecture and subsequent development (Pennisi, 1997; Wu et al., 1997). Thus, the actin cytoskeleton might have roles to play in signaling stress at the beginning of cell communication pathways (i.e., through mechanosensation) and/or in elaborating a developmental response at the end of these pathways. The breadth of possible activities and responses of the plant cytoskeleton is increased by the coexpression of multiple actin isovariants. Plant actins comprise 376 to 377 amino acid residues. They share most of these residues with actins in other kingdoms, typically showing 83 to 88% identity with actins from green algae and most other protists, fungi, and animals. This high degree of conservation is thought to be a direct result of the fact that nearly every surface of actin is involved in protein–protein interactions (Sheterline and Sparrow, 1994; Furukawa and Fechheimer, 1997; Puius et al., 1998). Higher plants and animals contain relatively ancient families of actin proteins, the phylogenies of which can be traced to the origin of vascular plants and vertebrate animals, respectively (Meagher and Williamson, 1994; Meagher, 1995). There is ~94 to 95% amino acid sequence identity within each of these ancient families. The actin gene family in Arabidopsis represents an excellent model system for understanding actin functions in plants. There are only 10 actin genes in Arabidopsis, all of which have been cloned, sequenced, and characterized in detail (McDowell et al., 1996b). The actin genes are all relatively small (i.e., <3 kb) and are individually dispersed in the genome (McKinney and Meagher, 1998). At least eight of the actin genes appear to be functional and are strongly expressed at some time and place during plant development (An et al., 1996a, 1996b; Huang et al., 1996a, 1997; McDowell et al., 1996a). Among the eight encoded functional actin proteins, there are a relatively large number of nonconservative amino acid substitutions (Meagher, 1991; McDowell et al., 1996b). For example, there are seven charged residue interchanges (e.g., His43→Thr43) and two changes between an α amino acid and proline (e.g., Lys272→Pro272), the latter of which are likely to alter the peptide backbone. All of these changes map to the surface of the eight Arabidopsis actin proteins. In addition, there are several nonconservative interchanges (e.g., Met201→Ser201) affecting amino acids with hydrophobic side chains (Hightower and Meagher, 1986; McDowell et al., 1996b). As a result of this sequence diversity, five to six distinct actin isovariants can be resolved from many plant species by using two-dimensional electrophoretic separations of polypeptides (McLean et al., 1990). The isoelectric points of the plant actins vary over a relatively wide range of 0.7 pH units (Meagher and McLean, 1990). G-Actin Monomers and F-Actin Filaments Interact with Profilin and Many Other Actin Binding Proteins. Proteins from multiple signal transduction cascades direct change in cytoarchitecture by acting directly on actin. The actin cytoskeleton may itself be involved in signaling mechanical stress to the rest of the organism through the same or other proteins. Numerous actin binding proteins interact with actin monomers, filaments, and bundles to effect these changes. The dynamics of these interactions should be greatly expanded by the expression of multiple actin isovariants in most plant cells. Pointed (−) and barbed (+) ends of an F-actin filament are indicated. ABA, abscisic acid; Ca (II), calcium ions; PIP2, phosphatidylinositol diphosphate;?, unknown pathway; *, ADP and ADP-bound actin monomers. By contrast, there are no analogous nonconservative changes among the six vertebrate actin proteins, even though the muscle and cytoplasmic actins have not shared a common ancestor for an estimated 500 million years. Moreover, the isoelectric points within animal actin families vary over only 0.3 pH units, and as a result, no more than three isovariants can be resolved by standard isoelectric focusing (see Meagher and McLean, 1990). Even the few conservative charged residue interchanges (e.g., Glu2→Asp2) that do occur among the first few N-terminal residues of vertebrate actins can lead to different physical properties for the isovariants (Garrels and Gibson, 1976). Despite their relative similarity, vertebrate nonmuscle actins bind profilin and thymosin in preference over muscle actins (Larsson and Lindberg, 1988; Oshima et al., 1989; Weber et al., 1992). In addition, vertebrate nonmuscle actins polymerize less readily but are ADP ribosylated far more efficiently by Botulinum chlostridium C2 toxin than are muscle actins, and smooth muscle actins are more readily heat denatured than are other muscle isoforms (Rubenstein, 1990). Thus, even minor changes in the amino acid sequence of an actin can alter protein function. The six Drosophila actins also can be subdivided into cytoplasmic and muscle-specific classes (Fyrberg et al., 1981, 1983), but these classes are thought to have evolved independently of the analogous two classes in vertebrates. There is only one full charged-residue interchange among all six Drosophila Even expression of cytoplasmic actin of muscle actin in Drosophila muscle to Moreover, a gene with the interchange from in the muscle to in the two cytoplasmic for the muscle actin gene a (Fyrberg et al., 1998). most acid changes from the muscle actin sequence no multiple residues to those of isovariant muscle function. It should be that these functional are even though there is less in the Drosophila actin family than in plant actin These that the highly plant actin isovariants must vary in their physical chemical and must interact differentially with some actin binding proteins of levels and the expression of actin to the in plants has been on the eight functional Arabidopsis actin genes (An et al., 1996a, 1996b; Huang et al., 1996a, 1997; McDowell et al., 1996a). on their distinct temporal and spatial expression the eight functional Arabidopsis actin genes can be into and classes (McDowell et al., 1996b; Meagher et al., 1999). There are two and the expression of which in nearly all the expression of which is in and is to most There are three the expression of which is in and and which are expressed in and and which are expressed during pollen the among actin classes and defined by expression patterns with those on actin sequence (McDowell et al., 1996b). If each of actin expressed in only one cell or of other actins, there be no for isovariant dynamics to play a in the plant actin In two or more actin are strongly expressed in most and For example, in a and are expressed in the and to be expressed in the of the including and filaments, whereas and to be expressed in and are strongly expressed in pollen development and during pollen tube All eight of the actin genes appear to be expressed at reasonable levels in vascular The expression of multiple actin isovariants in the same cells in the dynamic behavior of the The of this is likely to be distinct of actin isovariant dynamics that into play for example, the of actin into F-actin and during the interaction of actin with (Figure These two of isovariant dynamics and their possible on the cytoskeleton are two actin and are expressed in the same cell, there is the potential to or with of the two isovariants. We the of actin to just one end of an actin filament (i.e., the or which ends with an or an In this there are to and for example, and represents the of to an If then be even when are relatively as are only when The degree of on and the However, because be for example, have a to then this property of isovariant dynamics have a on cell morphology and is a that first to the effect of amino acid substitutions among ancient classes of coexpressed animal tubulin isovariants and and 1998). In this of isovariant in from highly of isovariants are less than those from or less of isovariants to in the of among isovariants. The protein sequence among plant tubulin isovariants to result in of for plant tubulin than for the animal et al., 1997). and F-actin bind to other proteins affecting changes in cell architecture (Figure 2; and 1993; Puius et al., 1998). We the of isovariant dynamics on the of actin by profilin into Profilin is a major that is in high in most cells (i.e., in most animal Profilin is involved in the of actin into on of actin from complexes to the barbed ends of actin filaments, and binding to that profilin binding to actin. We on just the first of these the binding of actin into pollen development in Arabidopsis, at least three actin are coexpressed et al., 1996; Huang et al., 1996b). The expression can be as is the of the complex into actin isovariant and profilin isovariant The interaction of only one actin with one et al., is relatively There be a distinct and for the and of the The more complex with the coexpression of the and each has a different and for the of the and All three actins in pollen for and all three are in the actin If these three interactions each have different and then these be an important factor in the plant The of the actin cytoskeleton to to that and and to or actin be greatly expanded with the with a actin For example, more through a interaction with then filaments could also more The of this could be growth of filaments at the tip of the pollen tube at the expense of other more The plant profilin family in Arabidopsis to be as large and diverse as the Arabidopsis actin family et al., 1996; Huang et al., 1996b). on these and the on pollen et al., it is likely that there be multiple profilin isovariants also expressed in Arabidopsis Moreover, recent results pollen et al., and on Arabidopsis and Meagher, that different profilin isovariants vary over a to range in their (i.e., for actin and Thus, isovariant dynamics are a part of plant cytoskeletal the coexpression of profilin isovariants to actin isovariant dynamics. that all the other actin binding proteins for and as as proteins may be encoded by gene families in the potential for isovariant dynamics in the plant actin cytoskeleton is this diverse cytoskeletal system has evolved not only to direct plant cell developmental processes but also to to a wide of environmental changes. and have a model in which the highly networked structure of such a complex system this the simultaneous expression of actin and profilin isovariants result in this cytoskeletal system being relatively to in biochemical of the and in less for of each protein. In other networked systems are better buffered changes from temporal in gene expression or among changes in the actin network are about by a number of These include or actin to the cell or filaments, with and other movement proteins, or ends and (i.e., to at filament and and filaments (Figure These processes are about by the interaction of distinct actin with diverse and 1993; Puius et al., 1998). Among dozens of possible examples of these the spatial of actin filament links to the membrane is to cell architecture and development and 1996; Yamada and Geiger, 1997). of dynamic actin behavior is actin filaments can in one part of a cell by the of monomers, they are or being in part of the This can even occur on the different ends of the same actin filament The streaming of cytoplasm actin bundles and is thought to be to and between of plant cells of these and many other processes may be by isovariant dynamics. If isovariant dynamics are of to the of the plant then it is that they might be to over time. By this selection the of genes or proteins, acting as at the of isovariant dynamics in plants. The coexpression of isovariants may have in the temporal and biochemical expansion and of the properties of these biochemical systems, which in turn may have a to the plants the isovariants. This can be partially with the expression of isovariants in a number of cell in and as for Drosophila actin isovariants (Fyrberg et al., 1998). For the we can for of the isovariant This that the actin gene family members may have been selected for expression in but that their coexpression in other represents from the to genes (Meagher, 1995). the is not there are several this seems to for the Arabidopsis have to the distinct protein of each of the five of actin. for this from the conservation of three of actin protein (i.e., and and and and the of each from three (McDowell et al., 1996b). in three different Arabidopsis actin genes (e.g., and as that are from plant et al., 1998). but to these two (i.e., the selection of isovariant dynamics is by the plant gene family encoding the small of In this ancient and gene family members gene and only organisms with protein sequence among the protein family members (Meagher et al., isovariant dynamics be among small proteins, and we must that they are Many other families with coexpressed and isovariants have been in as shown by the examples in Table 1. The and of many of these gene families appear to be in plants than in animals and should lead to more complex behavior of plant systems et al., 1997). The of isovariant dynamics may be different for families of enzymes and regulatory proteins than they are for cytoskeletal proteins. The in among and regulatory protein isovariants could alter substrate substrate protein–protein response to and positioning of the protein within the the biological is not from two isovariants of have properties relative to and 1986; and 1989; and et al., 1997). dynamics in regulatory protein families could their binding to or for other or signaling For example, of the two proteins, and can bind the sequence Arabidopsis but each protein et al., 1996). In one of the potential for dynamic interactions among coexpressed protein family Arabidopsis isovariants bind and activate binding of nuclear proteins In the isovariant the binding of two to three more efficiently than or et al., 1996). the of isovariant dynamics to cellular and functions is complex and the of a wide of and In it must be demonstrated that isovariants are not and that in protein sequence and not gene are for the effect being For example, can genes encoding two isovariants to ancient gene that have been preserved among species et al., or they are genes (Meagher et al., can be to the amino acid residue is likely to have an on protein (Meagher and McLean, McDowell et al., 1996b). can isovariants are functionally by et al., this by that selection acts on a et al., 1998). The degree of of a with a different isovariant should be one of the most to the biological of an isovariant dynamics (Fyrberg et al., 1998). In highly networked systems the the central proteins have multiple it not be to those most affected by the coexpression of isovariants. biological properties of isovariants can be more by of and Meagher, because has only a actin into cells has to be a for protein functions and among isovariants et al., 1997; et al., 1997; et al., 1998). chemical applied in can those that vary in a protein (e.g., and for substrate or and for or Many of these complex have been for animal and actins et al., and et al., 1994; et al., 1994; et al., 1996). antibodies be to different subcellular localization of coexpressed isovariants et al., and in of within cells could be to protein localization is to or protein et al., 1994; et al., 1995; et al., 1996). all the with of and isovariant can define those protein most likely to participate in these interactions et al., 1998). This information can then be to and physical The that multiple isovariants for actin and plays in the cytoskeleton and in cytoskeletal dynamics a to the study of plant However, understanding the dynamic interactions of protein isovariants coexpressed in the same cells be an To the of isovariant dynamics for actin or other protein we to these systems at the cell and We for with the and Furukawa for their into cytoskeletal and and for This research and and are by the of and from the of