The word “plant” has many meanings

One goal of this book is to highlight the aspects of molecular biology that are unique to plants, and that represent mechanisms that cannot be understood simply by studying animals, yeast or bacteria. We therefore need to spend some time discussing what we mean by the word “plant”, which, perhaps surprisingly, does not have a simple or universally accepted definition.

When most people think of a plant, they generally immediately come up with an image of a tomato plant, or a petunia, or corn. A scientist might think of Arabidopsis thaliana, the tiny weed that has been domesticated by molecular biologists. All these are examples of flowering plants (angiosperms), which are the dominant forms of land plants on Earth today. The flowering plants represent a large group that originated in the early Cretaceous (∼140 million years ago, although the exact date is subject to much current debate); the group has subsequently diversified to produce most trees, shrubs, and herbs. The flowering plants include more than 300 000 species; only a few thousand are cultivated, and surprisingly, only a few of these – fewer than twenty – produce the vast majority of the food for all of humanity.

The term “plant” is often used to mean “land plant”, a much larger group that includes the flowering plants, but also the gymnosperms, ferns, lycophytes, mosses, hornworts and liverworts. This large group is monophyletic, a term that refers to all being descendants of a common ancestor, and is often called the Embryophytes because all members produce embryos retained on the parent plant. A phylogeny of the Embryophyta is presented in Figure 1, which is assembled on the basis of the main characteristics that define the major groups of plants. Clades (or groups) within the land plants include the seed plants (flowering plants plus gymnosperms, distinguished by how they bear their seeds) and other vascular plants [ferns (pteridophytes) and lycophytes], in which the diploid sporophyte forms on the independent gametophyte, and dispersal occurs via spores. In contrast, the non-vascular plants (hornworts and liverworts) are distinguished not only by the absence of phloem and xylem vessels, but by having a dominant gametophytic (haploid) stage of life and only a short lived sporophytic (diploid) stage.

Another possible definition of “plant” is the group known as the Streptophytes, which includes the land plants plus their immediate relatives, Chara and Coleochaete (both formerly considered green algae). The Streptophytes all share a peculiar method of cell division, the phragmoplast, and a unique structure of proteins to make cellulose (the sugar polymer that is the primary component of plant cell walls), the cellulose rosettes.

A third definition of “plant” corresponds to organisms that have chloroplasts and make chlorophyll a and b. These are known as the Viridiplantae (Latin for green plants). This group includes the Streptophytes (i.e., land plants plus Coleochaete and Chara) plus all the green algae. The latter group includes the well-studied single cell organism Chlamydomonas.

Finally, a fourth (and uncommon) definition of “plant” includes all organisms with chloroplasts that are the result of a primary endosymbiosis, that is organisms that acquired their chloroplasts by directly aquiring a cyanobacterium (see Chapter 5). Members of this group are Viridiplantae, the red algae (Rhodophyta) and the glaucophytes. Some data suggest that the primary endosymbiosis occurred only once, in the common ancestor of the Viridiplantae, red algae and glaucophytes. Evidence is accumulating to suggest that indeed Viridiplantae, red algae and glaucophytes are all part of a monophyletic group, which is sometimes called the Archaeplastida. However, each primary endosymbiotic event could be independent, with the capture of a cyanobacterium occurring independently several times. In either case, origin of plastids from cyanobacteria has been extremely rare in the history of life.

The plastid bearing organisms diverged from other eukaryote lineages, including animals plus fungi, at least 1 billion years ago (Knoll, 2003). Given this enormously long period of evolution, it is remarkable that there are any similarities at all in the cellular apparatus between animals (i.e., you), fungi (i.e., yeast), and any plants. There are many similarities of course, but we suggest here that they need to be demonstrated, not assumed. In other words, the fact that the transcriptional machinery is similar between animals and yeast, does not necessarily mean that it will also be similar in plants. In addition, the term similarity does not mean identity. Processes in common could have arisen because of convergent forces, and really the metric for similarity has become conservation in the DNA encoding these functions.

In the past, the term “plant” was sometimes applied to all photosynthetic organisms. However, such a broad use of the term is now rejected. Many organisms that are able to undergo photosynthesis have gained that ability by acquiring a red alga along with its plastid. In other words, the plastid is a symbiont in the red alga and the red alga is the symbiont in another (previously non-photosynthetic) organism. Such symbioses are known as secondary endosymbioses to distinguish them from the primary endosymbioses of the Archaeplastida. In organisms with a secondary endosymbiont, the structure of the membranes around the symbiont shows that it was once a separate organism that was picked up by its host. Organisms with secondary endosymbioses include the Stramenopiles, the group that includes the brown algae (e.g., Fucus, a common seaweed) and golden brown algae (which occur mostly in freshwater), the dinoflagellates, and the kinetoplastids (e.g., Euglena, trypanosomes, and the apicomplexans, which include the organisms that cause malaria). Each of these groups is as different from plants as animals are, and as different from animals as plants are. In these organisms in particular one might expect to find novel genes, proteins and cellular mechanisms. If the term “plant” were applied to all photosynthetic organisms, the ones with the secondary endosymbioses are so diverse and so totally unrelated (other than all being eukaryotes) that the term would be effectively meaningless.

In summary, the term plant is used to apply to many sets of organisms, the smallest of which is the land plants and the largest is all photosynthetic organisms. Most commonly, however, “plant” refers either to the entire green plant lineage (Viridiplantae), or to the land plants. In common parlance its use is even more restricted to refer informally to flowering plants. In this textbook we will use the term to refer to land plants. Most of the data we present come from flowering plants, so in most cases, the reader can assume that we are extrapolating, generally without evidence, from the flowering plants to the gymnosperms, ferns, lycophytes, mosses, liverworts and hornworts. If we have data from species outside the land plants, we will cite that explicitly.

The basic structure of a plant is deceptively simple

The processes described in this book can in theory occur in any cell in the plant. However, some familiarity with basic plant morphology is assumed. Plant growth occurs from dedicated sets of stem cells, known as meristems. These are active throughout the life of the plant, so that development is continuous and modular. This is quite different from the situation in animals, in which the entire organism develops in a coordinated fashion and then ceases development entirely at maturity. If a human were to grow like a plant, the fingers, toes and the top of the head might keep growing throughout the life of the human.

Meristems are organized during embryonic development. In the seed plants these initially consist of two clusters of cells, the shoot apical meristem and the root apical meristem, at opposite ends of the plant. These are the basis of the bipolar embryo, which is only found in the seed plants. Meristems in non-seed bearing vascular plants (ferns, lycophytes) consist of only a few cells, and the root apical meristem in particular develops late and on one side of the embryonic axis.

A flowering plant has an obvious above ground component, the shoot, and a below-ground component, generally the root (Figure 2). The apical meristem of the shoot produces leaves on its flanks. In the axil of each leaf, another meristem forms, the axillary meristem; this meristem is often dormant for a while but may grow out to form a branch. The root apical meristem forms the primary root. Lateral roots are not formed from the apical meristem, but rather are formed from meristems that arise de novo just outside the vascular tissue. In most eudicots, the primary root persists and forms a prominent below ground structure (think of a carrot or a dandelion root), whereas in most monocots, the primary root only lives for a few months and is replaced by roots forming from the very base of the shoot, near ground level (think of onion or grass roots). The vascular tissue connects all parts of the plant, transporting water, nutrients and some hormones up from the roots into the leaves and meristems of the shoot. At the same time carbohydrates and other hormones are transported both up and down from the leaves.

The basic tissues of the plant are obvious in cross sections of a leaf and a root (Figure 2). Unlike animals, which have an elaborate set of tissue types, plants have only three basic sorts of tissue – the epidermis, which covers all parts of the plant, the vascular tissue, and ground tissue, which includes everything else. The epidermis of a leaf is generally made up of flat translucent cells and is covered with a waxy layer, cuticle which prevents drying. Within the epidermis are specialized holes known as stomata (literally “mouths”) that permit entry of CO₂ for photosynthesis and escape of O₂, the by-product of photosynthesis. The stomata also permit the escape of water vapor. As water escapes, it creates a gradient of water pressure that pulls water up through the vascular system from the roots and hydrates all the cells in the plant. If water is limited, however, the stomata close and prevent drying of the tissues. Stomatal opening and closing is caused by changes in the turgor pressure of the guard cells, which sit on either side of the opening. In addition, the leaf epidermis can also have hairs (also known as trichomes) and glands. Depending on the plant species, they can be unicellular (as in Arabidopsis) or multicellular (e.g., the glands that accumulate peppermintoil in Mentha piperita).

The epidermis of a root includes some cells that will develop long projections known as root hairs. Root hairs are thin-walled, and are central to the uptake of water and nutrients from the soil. In addition, they are the site of interaction with soil bacteria, such as Rhizobia, which interact and form symbioses with some species of plants. Cells that will form root hairs alternate with non-root-hair cells. The pattern of root-hair and non-root-hair cells varies between species but is quite stereotyped in the model plant Arabidopsis where the controls of patterning have been studied extensively. As the root pushes through the soil and grows in diameter, the epidermis is sloughed off and replaced by cells from inner layers of the root. Because of this process, root hairs are only present right behind the root apical meristem and are lost in older roots.

Vascular tissue is arranged in bundles of conducting cells that extend throughout the plant. The water conducting tissue is xylem, which consists mostly of cells that are dead at maturity; in the vascular bundle of a leaf, the xylem is generally on the top (adaxial) side. Because the water is pulled up the plant following a pressure gradient from the roots to the shoots, the xylem cell walls must be strong enough to withstand the tension on the water column and hence are generally lignified at maturity. The carbohydrate transport tissue is phloem; phloem cells are alive at maturity and in a leaf are generally found on the bottom (abaxial) side of the vascular bundle. Unlike water, which is pulled up the plant under tension, the phloem sap is pushed around the plant under pressure. Because many molecules are dissolved in phloem sap, it generally is hyperosmotic to the surrounding tissues and takes up water.

The cells inside the epidermis and outside the vascular tissue are part of the ground tissue. Depending on the organ and the stage of development, these cells may vary considerably throughout the plant. An example is shown in Figure 2 in the cross section of the leaf, where the ground tissue is known as mesophyll. (The word mesophyll is simply Greek for “middle of the leaf”; meso = middle and phyll = leaf.) In many angiosperm leaves, the upper mesophyll cells form long, closely packed rectangles; because of their appearance in cross section they are known as the palisade layer. The lower mesophyll cells, in contrast, are less tightly packed and more isodiametric and are known as the spongy mesophyll. The cells of the spongy mesophyll cease cell division before those of the palisade, and are pulled apart as the leaf expands, creating air spaces between them.

In the root, the vascular tissue forms a solid cylinder in the center. It is surrounded by a ring of cells, the endodermis, which regulates the flow of water into and out of the vasculature. In most roots, water can enter through the cytoplasm of cells such as root hairs, or can enter the gaps between the cells. It then flows through or around the cells in the cortex. The pathway through cells is known as the symplastic pathway, whereas the pathway around cells is known as the apoplastic pathway. When the water reaches the endodermis, however, the water (and any ions or other substances) must go through the cells, that is, it is forced into a symplastic pathway. The endodermal cells are held in a tight ring by a layer of suberin, the Casparian strip, which prevents water or anything else from going around the cells; in other words, the Casparian strip blocks the apoplastic pathway. By controlling transporters and the osmotic force inside the cells, the endodermis thus controls which substances move in and out.

Individual plant cells have many of the same structures as other eukaryotic cells (Figure 2). Like all living cells (including Bacteria and Archaea), the plant cell is surrounded by a plasma membrane, uses DNA as its genetic material, and synthesizes proteins with ribosomes. Like all other Eukarya, the plant cell has a nucleus with a nuclear membrane that is contiguous with the endoplasmic reticulum, and has mitochondria, peroxisomes, and Golgi apparatus. The endoplasmic reticulum may be smooth or rough depending on whether ribosomes are attached to it. The cytoskeleton is made up of microfilaments (formed by the protein actin), intermediate filaments, and microtubules (formed by the protein tubulin).

Other structures are not shared with animals, although they may occur in other eukaryotes. Unlike most animals (e.g., any mammal), the plant cell is enclosed in a wall made up of cellulose. The wall often is penetrated by specialized tunnels known as plasmodesmata; the plasma membrane is continuous through these tunnels and the diameter of the plasmodesmata is tightly regulated by proteins that reside in the membrane. The plant cell contains chloroplasts, symbiotic bacteria that are the site of photosynthesis. Also many plant cells have a prominent vacuole surrounded by an independent membrane known as a tonoplast. In mesophyll cells the vacuole often fills up so much of the center of the cell that the cytoplasm and organelles are pressed to the edges against the plasma membrane. Compared with such cells, the vacuole drawn in Figure 2 is abnormally small.

This very brief introduction to plant structure and plant evolutionary history should provide a foundation for the rest of this book. In the chapters that follow, we will provide a view of biology focusing on aspects that characterize the many species of land plants. You have probably already read biology textbooks that focus on humans as a representative mammal, but recall that there are only about 5000 species of mammals, and among them humans have strikingly low genetic diversity. In contrast there may be almost 70–100 times as many species of land plants, although exact numbers are unknown. Plants dominate our environment, provide food, clothing and shelter, and create the air we breathe. Without land plants, there would be no land animals and certainly no humans. Plants thus support all of life on land; here we present their genes, genomes, and genetics.

Reference

1. Knoll, A.H. (2003) Life on a Young Planet: The First Three Billion Years, Princeton University Press.