Annual Review of Plant Biology - Volume 52, 2001

Recent advances in the cell, developmental, and molecular biology of alkaloid biosynthesis have heightened our appreciation for the complexity and importance of plant secondary pathways. Several biosynthetic genes involved in the formation of tropane, benzylisoquinoline, and terpenoid indole alkaloids have now been isolated. The early events of signal perception, the pathways of signal transduction, and the function of gene promoters have been studied in relation to the regulation of alkaloid metabolism. Enzymes involved in alkaloid biosynthesis are associated with diverse subcellular compartments including the cytosol, vacuole, tonoplast membrane, endoplasmic reticulum, chloroplast stroma, thylakoid membranes, and perhaps unique “biosynthetic” or transport vesicles. Localization studies have shown that sequential alkaloid biosynthetic enzymes can also occur in distinct cell types, suggesting the intercellular transport of pathway intermediates. Isolated genes have also been used to genetically alter the accumulation of specific alkaloids and other plant secondary metabolites. Metabolic modifications include increased indole alkaloid levels, altered tropane alkaloid accumulation, elevated serotonin synthesis, reduced indole glucosinolate production, redirected shikimate metabolism, and increased cell wall–bound tyramine formation. This review discusses the biochemistry, cell biology, molecular regulation, and metabolic engineering of alkaloid biosynthesis in plants.

Gibberellins are hormones that control growth and a wide variety of other plant developmental processes. In recent years, significant progress has been made on the biochemistry of gibberellin biosynthesis and on the mechanisms by which gibberellin levels are regulated in plants. There have also been major advances in the understanding of gibberellin signaling, with several key genes being cloned. This review discusses our current understanding of gibberellin signaling, as seen from the perspective of molecular genetic analysis, and relates these observations to previous biochemical studies. In particular, we highlight an important conclusion of recent years: that GAI/RGA and orthologs play major roles in gibberellin signaling in diverse plant species, and that gibberellin probably stimulates growth by derepression of GAI/RGA.

Cytokinins are structurally diverse and biologically versatile. The chemistry and physiology of cytokinin have been studied extensively, but the regulation of cytokinin biosynthesis, metabolism, and signal transduction is still largely undefined. Recent advances in cloning metabolic genes and identifying putative receptors portend more rapid progress based on molecular techniques. This review centers on cytokinin metabolism with connecting discussions on biosynthesis and signal transduction. Important findings are summarized with emphasis on metabolic enzymes and genes. Based on the information generated to date, implications and future research directions are presented.

The metabolism of one-carbon (C1) units is essential to plants, and plant C1 metabolism has novel features not found in other organisms—plus some enigmas. Despite its centrality, uniqueness, and mystery, plant C1 biochemistry has historically been quite poorly explored, in part because its enzymes and intermediates tend to be labile and low in abundance. Fortunately, the integration of molecular and genetic approaches with biochemical ones is now driving rapid advances in knowledge of plant C1 enzymes and genes. An overview of these advances is presented. There has also been progress in measuring C1 metabolite fluxes and pool sizes, although this remains challenging and there are relatively few data. In the future, combining reverse genetics with flux and pool size determinations should lead to quantitative understanding of how plant C1 pathways function. This is a prerequisite for their rational engineering.

Circadian rhythms, endogenous rhythms with periods of approximately 24 h, are widespread in nature. Although plants have provided many examples of rhythmic outputs and our understanding of photoreceptors of circadian input pathways is well advanced, studies with plants have lagged in the identification of components of the central circadian oscillator. Nonetheless, genetic and molecular biological studies, primarily in Arabidopsis, have begun to identify the components of plant circadian systems at an accelerating pace. There also is accumulating evidence that plants and other organisms house multiple circadian clocks both in different tissues and, quite probably, within individual cells, providing unanticipated complexity in circadian systems.

Organisms acclimate to a continually fluctuating nutrient environment. Acclimation involves responses specific for the limiting nutrient as well as responses that are more general and occur when an organism experiences different stress conditions. Specific responses enable organisms to efficiently scavenge the limiting nutrient and may involve the induction of high-affinity transport systems and the synthesis of hydrolytic enzymes that facilitate the release of the nutrient from extracellular organic molecules or from internal reserves. General responses include changes in cell division rates and global alterations in metabolic activities. In photosynthetic organisms there must be precise regulation of photosynthetic activity since when severe nutrient limitation prevents continued cell growth, excitation of photosynthetic pigments could result in the formation of reactive oxygen species, which can severely damage structural and functional features of the cell. This review focuses on ways that photosynthetic eukaryotes assimilate the macronutrients nitrogen, sulfur, and phosphorus, and the mechanisms that govern assimilatory activities. Also discussed are molecular responses to macronutrient limitation and the elicitation of those responses through integration of environmental and cellular cues.

Phospholipases are a diverse series of enzymes that hydrolyze phospholipids. Multiple forms of phospholipases D, C, and A have been characterized in plants. These enzymes are involved in a broad range of functions in cellular regulation, lipid metabolism, and membrane remodeling. In recent years, increasing attention has been paid to the many roles of phospholipases in signal transduction. This review highlights recent developments in the understanding of biochemical, molecular biological, and functional aspects of various phospholipases in plants.

The endosperm develops from the central cell of the megagametophyte after introduction of the second male gamete into the diploid central cell. Of the three forms of endosperm in angiosperms, the nuclear type is prevalent in economically important species, including the cereals. Landmarks in nuclear endosperm development are the coenocytic, cellularization, differentiation, and maturation stages. The differentiated endosperm contains four major cell types: starchy endosperm, aleurone, transfer cells, and the cells of the embryo surrounding region. Recent research has demonstrated that the first two phases of endosperm occur via mechanisms that are conserved among all groups of angiosperms, involving directed nuclear migration during the coenocytic stage and anticlinal cell wall deposition by cytoplasmic phragmoplasts formed in interzones between radial microtubular systems emanating from nuclear membranes. Complete cellularization of the endosperm coenocyte is achieved through centripetal growth of cell files, extending to the center of the endosperm cavity. Key points in cell cycle control and control of the MT (microtubular) cytoskeletal apparatus central to endosperm development are discussed. Specification of cell fates in the cereal endosperm appears to occur via positional signaling; cells in peripheral positions, except over the main vascular tissues, assume aleurone cell fate. Cells over the main vascular tissue become transfer cells and all interior cells become starchy endosperm cells. Studies in maize have implicated Crinkly4, a protein receptor kinase-like molecule, in aleurone cell fate specification.

Nitrogenase is the complex metalloenzyme responsible for biological dinitrogen reduction. This reaction represents the single largest contributor to the reductive portion of the global nitrogen cycle. Recent developments in understanding the mechanism of the Mo-based nitrogenase are reviewed. Topics include how nucleotide binding and hydrolysis are coupled to electron transfer and substrate reduction, how electrons are accumulated and transferred within the MoFe-protein, and how substrates bind and are reduced at the active site metal cluster.

The majority of terrestrial plants, including many important crops such as rice, wheat, soybean, and potato, are classified as C3 plants that assimilate atmospheric CO2 directly through the C3 photosynthetic pathway. C4 plants such as maize and sugarcane evolved from C3 plants, acquiring the C4 photosynthetic pathway to achieve high photosynthetic performance and high water- and nitrogen-use efficiencies. The recent application of recombinant DNA technology has made considerable progress in the molecular engineering of C4 photosynthesis over the past several years. It has deepened our understanding of the mechanism of C4 photosynthesis and provided valuable information as to the evolution of the C4 photosynthetic genes. It also has enabled us to express enzymes involved in the C4 pathway at high levels and in desired locations in the leaves of C3 plants for engineering of primary carbon metabolism.

Plastid division is essential for the maintenance of plastid populations in cells undergoing division and for the accumulation of large chloroplast numbers in photosynthetic tissues. Although the mechanisms mediating plastid division are poorly understood, ultrastructural studies imply this process is accomplished by a dynamic macromolecular machine organized into ring structures at the plastid midpoint. A key component of the engine that powers this machine is the motor-like protein FtsZ, a cytoskeletal GTPase of endosymbiotic origin that forms a ring at the plastid division site, similar to the function of its prokaryotic relatives in bacterial cytokinesis. This review considers the phylogenetic distribution and structural properties of two recently identified plant FtsZ protein families in the context of their distinct roles in plastid division and describes current evidence regarding factors that govern their placement at the division site. Because of their evolutionary and mechanistic relationship, the process of bacterial cell division provides a valuable, though incomplete, paradigm for understanding plastid division in plants.

In many plants lipids represent up to 80% of dry weight of storage tissues. In seeds, lipids accumulate as triacylglycerols (TAGs), which are formed by an extension of the membrane-lipid biosynthetic pathway common to all plant tissues. In contrast to the conserved fatty acid (FA) composition of membrane lipids, the observed divergence in seed oil acyl chains among different species is very high. The acyl groups of seed TAGs can vary in their chain length (from 8 to 24) as well as in their degree of unsaturation. In addition to methylene-interrupted double bonds, many seeds contain TAGs that have unusual functional groups in their FAs, such as hydroxyl, oxirane, or acetylene groups. All of the major steps in the biosynthetic pathway to TAG are now known and sequence information for genes encoding most of the enzymes involved is available. Here we present the current knowledge of the metabolic mechanisms involved in the divergence from the membrane-lipid biosynthetic pathway during storage lipid formation.

The unicellular green alga Chlamydomonas offers a simple life cycle, easy isolation of mutants, and a growing array of tools and techniques for molecular genetic studies. Among the principal areas of current investigation using this model system are flagellar structure and function, genetics of basal bodies (centrioles), chloroplast biogenesis, photosynthesis, light perception, cell-cell recognition, and cell cycle control. A genome project has begun with compilation of expressed sequence tag data and gene expression studies and will lead to a complete genome sequence. Resources available to the research community include wild-type and mutant strains, plasmid constructs for transformation studies, and a comprehensive on-line database.

Very large amounts of isoprene are emitted from vegetation, especially from mosses, ferns, and trees. This hydrocarbon flux to the atmosphere, roughly equal to the flux of methane, has a large effect on the oxidizing potential of the atmosphere. Isoprene emission results from de novo synthesis by the deoxyxylulose phosphate/methyl erythritol 4-phosphate pathway in plastids. Dimethylallyl pyrophosphate made by this pathway is converted to isoprene by isoprene synthase. Isoprene synthase activity in plants has a high pH optimum and requirement for Mg²⁺ that is consistent with its location inside chloroplasts. Isoprene emission costs the plant significant amounts of carbon, ATP, and reducing power. Researchers hypothesize that plants benefit from isoprene emission because it helps photosynthesis recover from short high-temperature episodes. The evolution of isoprene emission may have been important in allowing plants to survive the rapid temperature changes that can occur in air because of the very low heat capacity of isoprene relative to water.

The structure of the familiar antioxidant L-ascorbic acid (vitamin C) was described in 1933 yet remarkably, its biosynthesis in plants remained elusive until only recently. It became clear from radioisotopic labeling studies in the 1950s that plant ascorbic acid biosynthesis does not proceed in toto via a route similar to that in mammals. The description in 1996 of an Arabidopsis thaliana mutant deficient in ascorbic acid prompted renewed research effort in this area, and subsequently in 1998 a new pathway was discovered that is backed by strong biochemical and molecular genetic evidence. This pathway proceeds through the intermediates GDP-D-mannose, L-galactose, and L-galactono-1,4-lactone. Much research has focused on the properties of the terminal enzyme responsible for conversion of the aldonolactone to ascorbate, and on related enzymes in both mammals and fungi. Two of the plant biosynthetic genes have been studied at the molecular level and additional ascorbate-deficient A. thaliana mutants may hold the key to other proteins involved in plant ascorbate metabolism. An analysis of the biosynthesis of ascorbate and its analogues in algae and fungi as well as the study of alternative proposed pathways should broaden our understanding of ascorbate metabolism in plants. With a biosynthetic pathway in hand, research on areas such as the control of ascorbate biosynthesis and the physiological roles of ascorbate should progress rapidly.

Regulation of the contents and volume of vacuoles in plant cells depends on the coordinated activities of transporters and channels located in the tonoplast (vacuolar membrane). The three major components of the tonoplast are two proton pumps, the vacuolar H⁺-ATPase (V-ATPase) and H⁺-pyrophosphatase (V-PPase), and aquaporins. The tertiary structure of the V-ATPase complex and properties of its subunits have been characterized by biochemical and genetic techniques. These studies and a comparison with the F-type ATPase have enabled estimation of the dynamics of V-ATPase activity during catalysis. V-PPase, a simple proton pump, has been identified and cloned from various plant species and other organisms, such as algae and phototrophic bacteria, and functional motifs of the enzyme have been determined. Aquaporin, serving as the water channel, is the most abundant protein in the tonoplast in most plants. A common molecular architecture of aquaporins in mammals and plants has been determined by two-dimensional crystallographic analysis. Furthermore, recent molecular biological studies have revealed several other types of tonoplast transporters, such as the Ca²⁺-ATPase, Ca²⁺/H⁺ antiporter and Na⁺/H⁺ antiporter. Many other transporters and channels in the tonoplast remain to be identified; their activities have already been detected. This review presents an overview of the field and discusses recent findings on the tonoplast protein components that have been identified and their physiological consequences.

Analytical methods for probing plant metabolism are taking on new significance in the era of functional genomics and metabolic engineering. Among the available methods, nuclear magnetic resonance (NMR) spectroscopy is a technique that can provide insights into the integration and regulation of plant metabolism through a combination of in vivo and in vitro measurements. Thus NMR can be used to identify, quantify, and localize metabolites, to define the intracellular environment, and to explore pathways and their operation. We review these applications and their significance from a metabolic perspective. Topics of current interest include applications of NMR to metabolic flux analysis, metabolite profiling, and metabolite imaging. These and other areas are discussed in relation to NMR investigations of intermediary carbon and nitrogen metabolism. We conclude that metabolic NMR has a continuing role to play in the development of a quantitative understanding of plant metabolism and in the characterization of metabolic phenotypes.

The rhizosphere is the zone of soil immediately surrounding plant roots that is modified by root activity. In this critical zone, plants perceive and respond to their environment. As a consequence of normal growth and development, a large range of organic and inorganic substances are exchanged between the root and soil, which inevitably leads to changes in the biochemical and physical properties of the rhizosphere. Plants also modify their rhizosphere in response to certain environmental signals and stresses. Organic anions are commonly detected in this region, and their exudation from plant roots has now been associated with nutrient deficiencies and inorganic ion stresses. This review summarizes recent developments in the understanding of the function, mechanism, and regulation of organic anion exudation from roots. The benefits that plants derive from the presence of organic anions in the rhizosphere are described and the potential for biotechnology to increase organic anion exudation is highlighted.